Starting phenix.real_space_refine on Tue May 14 02:10:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v84_43021/05_2024/8v84_43021_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v84_43021/05_2024/8v84_43021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v84_43021/05_2024/8v84_43021.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v84_43021/05_2024/8v84_43021.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v84_43021/05_2024/8v84_43021_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v84_43021/05_2024/8v84_43021_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2180 5.49 5 Mg 1 5.21 5 S 217 5.16 5 C 68312 2.51 5 N 21929 2.21 5 O 28603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "3 TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 121244 Number of models: 1 Model: "" Number of chains: 53 Chain: "1" Number of atoms: 42190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1970, 42190 Classifications: {'RNA': 1970} Modifications used: {'rna2p_pur': 191, 'rna2p_pyr': 121, 'rna3p_pur': 919, 'rna3p_pyr': 738} Link IDs: {'rna2p': 312, 'rna3p': 1657} Chain breaks: 19 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "2" Number of atoms: 3189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3189 Classifications: {'RNA': 150} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 13, 'rna3p_pur': 61, 'rna3p_pyr': 61} Link IDs: {'rna2p': 27, 'rna3p': 122} Chain breaks: 2 Chain: "3" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2884 Classifications: {'peptide': 355} Link IDs: {'PTRANS': 15, 'TRANS': 339} Chain breaks: 3 Chain: "6" Number of atoms: 1227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1227 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 13, 'rna3p_pur': 19, 'rna3p_pyr': 17} Link IDs: {'rna2p': 21, 'rna3p': 36} Chain breaks: 3 Chain: "7" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 87 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "8" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1203 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 1, 'TRANS': 141} Chain breaks: 1 Chain: "A" Number of atoms: 2080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2080 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 240} Chain breaks: 1 Chain: "B" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2626 Classifications: {'peptide': 331} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 319} Chain breaks: 1 Chain: "C" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2611 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 326} Chain: "D" Number of atoms: 3377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3377 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 21, 'TRANS': 401} Chain breaks: 2 Chain: "E" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1205 Classifications: {'peptide': 151} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 143} Chain breaks: 1 Chain: "F" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1936 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 11, 'TRANS': 229} Chain: "G" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1272 Classifications: {'peptide': 164} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 155} Chain: "H" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1510 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "I" Number of atoms: 3126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3126 Classifications: {'peptide': 394} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 381} Chain breaks: 1 Chain: "J" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1271 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain: "K" Number of atoms: 2135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2135 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 10, 'TRANS': 254} Chain breaks: 2 Chain: "L" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 884 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 104} Chain: "M" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1041 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "N" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1513 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain breaks: 1 Chain: "O" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1386 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 166} Chain breaks: 1 Chain: "P" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1062 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 5, 'TRANS': 131} Chain breaks: 1 Chain: "Q" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1110 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 7, 'TRANS': 136} Chain: "R" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1578 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 6, 'TRANS': 183} Chain: "S" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1432 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 7, 'TRANS': 162} Chain: "T" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 625 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'TRANS': 78} Chain: "V" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 903 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "W" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1870 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain: "Y" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 984 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "Z" Number of atoms: 2020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2020 Classifications: {'peptide': 253} Link IDs: {'PCIS': 4, 'PTRANS': 9, 'TRANS': 239} Chain breaks: 2 Chain: "a" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1668 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 200} Chain: "b" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3429 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 21, 'TRANS': 401} Chain breaks: 2 Chain: "e" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1010 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "f" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "h" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "i" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 665 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "j" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Link IDs: {'PCIS': 1, 'TRANS': 70} Chain: "l" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1394 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "m" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1759 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 23, 'TRANS': 187} Chain breaks: 2 Chain: "n" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2760 Classifications: {'peptide': 337} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 317} Chain breaks: 3 Chain: "o" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1107 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "q" Number of atoms: 2799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2799 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 341} Chain: "r" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1615 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 8, 'TRANS': 191} Chain breaks: 4 Chain: "t" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1973 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 9, 'TRANS': 239} Chain breaks: 1 Chain: "u" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 944 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "v" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1242 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 1 Chain: "w" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2058 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain breaks: 1 Chain: "x" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2362 Classifications: {'peptide': 279} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 266} Chain breaks: 1 Chain: "y" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1701 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 98965 SG CYS j 19 110.199 143.410 169.867 1.00 25.28 S ATOM 98990 SG CYS j 22 113.417 141.530 168.987 1.00 23.67 S ATOM 99090 SG CYS j 34 110.106 140.302 167.708 1.00 23.08 S ATOM 99108 SG CYS j 37 110.968 140.009 171.422 1.00 15.85 S ATOM A0A00 SG CYS u 6 119.506 164.141 60.089 1.00 17.76 S ATOM A0A5W SG CYS u 32 122.580 163.847 62.075 1.00 31.23 S ATOM A0A6S SG CYS u 36 119.891 165.243 63.627 1.00 16.67 S Time building chain proxies: 41.93, per 1000 atoms: 0.35 Number of scatterers: 121244 At special positions: 0 Unit cell: (246.24, 228.96, 311.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 217 16.00 P 2180 15.00 Mg 1 11.99 O 28603 8.00 N 21929 7.00 C 68312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 38.84 Conformation dependent library (CDL) restraints added in 9.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN j 100 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 19 " pdb=" ZN u 201 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 32 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 36 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 6 " Number of angles added : 6 18238 Ramachandran restraints generated. 9119 Oldfield, 0 Emsley, 9119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17594 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 342 helices and 92 sheets defined 48.2% alpha, 14.9% beta 655 base pairs and 1104 stacking pairs defined. Time for finding SS restraints: 62.36 Creating SS restraints... Processing helix chain '3' and resid 363 through 374 Processing helix chain '3' and resid 382 through 393 Processing helix chain '3' and resid 441 through 456 removed outlier: 3.890A pdb=" N VAL 3 445 " --> pdb=" O THR 3 441 " (cutoff:3.500A) Processing helix chain '3' and resid 467 through 481 Processing helix chain '3' and resid 489 through 496 removed outlier: 4.490A pdb=" N GLY 3 495 " --> pdb=" O VAL 3 491 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL 3 496 " --> pdb=" O ALA 3 492 " (cutoff:3.500A) Processing helix chain '3' and resid 512 through 525 removed outlier: 4.250A pdb=" N ARG 3 522 " --> pdb=" O HIS 3 518 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N THR 3 523 " --> pdb=" O ARG 3 519 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA 3 524 " --> pdb=" O VAL 3 520 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG 3 525 " --> pdb=" O GLY 3 521 " (cutoff:3.500A) Processing helix chain '3' and resid 537 through 552 Proline residue: 3 542 - end of helix Processing helix chain '3' and resid 557 through 571 removed outlier: 3.584A pdb=" N ARG 3 571 " --> pdb=" O VAL 3 567 " (cutoff:3.500A) Processing helix chain '3' and resid 599 through 618 removed outlier: 4.806A pdb=" N PHE 3 618 " --> pdb=" O MET 3 614 " (cutoff:3.500A) Processing helix chain '3' and resid 619 through 638 Processing helix chain '3' and resid 642 through 656 Processing helix chain '3' and resid 669 through 682 removed outlier: 3.922A pdb=" N ASN 3 681 " --> pdb=" O ALA 3 677 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ARG 3 682 " --> pdb=" O LYS 3 678 " (cutoff:3.500A) Processing helix chain '3' and resid 687 through 692 Processing helix chain '3' and resid 698 through 729 Proline residue: 3 712 - end of helix Processing helix chain '7' and resid 105 through 115 Processing helix chain '8' and resid 296 through 314 removed outlier: 4.171A pdb=" N LYS 8 314 " --> pdb=" O LYS 8 310 " (cutoff:3.500A) Processing helix chain '8' and resid 315 through 337 Processing helix chain '8' and resid 343 through 397 removed outlier: 4.556A pdb=" N GLY 8 395 " --> pdb=" O LYS 8 391 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS 8 396 " --> pdb=" O ASP 8 392 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LYS 8 397 " --> pdb=" O ASN 8 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 57 Proline residue: A 57 - end of helix Processing helix chain 'A' and resid 71 through 82 removed outlier: 4.496A pdb=" N ASN A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU A 76 " --> pdb=" O GLN A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 146 removed outlier: 4.894A pdb=" N GLU A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER A 145 " --> pdb=" O GLN A 141 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 140 through 146' Processing helix chain 'A' and resid 147 through 160 Processing helix chain 'A' and resid 244 through 278 removed outlier: 3.546A pdb=" N ARG A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'B' and resid 111 through 120 removed outlier: 3.868A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N LYS B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 140 Processing helix chain 'B' and resid 141 through 154 Processing helix chain 'B' and resid 165 through 170 removed outlier: 4.191A pdb=" N THR B 169 " --> pdb=" O GLN B 165 " (cutoff:3.500A) Proline residue: B 170 - end of helix No H-bonds generated for 'chain 'B' and resid 165 through 170' Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.717A pdb=" N VAL B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'C' and resid 23 through 28 removed outlier: 4.466A pdb=" N SER C 27 " --> pdb=" O PRO C 23 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 23 through 28' Processing helix chain 'C' and resid 31 through 46 removed outlier: 4.119A pdb=" N LYS C 44 " --> pdb=" O THR C 40 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASN C 45 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LYS C 46 " --> pdb=" O VAL C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 131 removed outlier: 3.879A pdb=" N ALA C 130 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 139 Processing helix chain 'C' and resid 153 through 159 removed outlier: 4.835A pdb=" N GLU C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER C 158 " --> pdb=" O THR C 154 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 153 through 159' Processing helix chain 'C' and resid 161 through 173 Processing helix chain 'C' and resid 174 through 185 removed outlier: 3.814A pdb=" N LYS C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 removed outlier: 3.944A pdb=" N ARG C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASN C 196 " --> pdb=" O GLY C 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 191 through 196' Processing helix chain 'C' and resid 214 through 221 removed outlier: 4.584A pdb=" N ASN C 221 " --> pdb=" O LYS C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 240 Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 251 through 262 removed outlier: 4.514A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 292 removed outlier: 3.947A pdb=" N SER C 292 " --> pdb=" O ARG C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 299 removed outlier: 3.932A pdb=" N ALA C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 328 Processing helix chain 'C' and resid 329 through 338 removed outlier: 4.607A pdb=" N VAL C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 48 removed outlier: 3.861A pdb=" N LEU D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LYS D 48 " --> pdb=" O PHE D 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 43 through 48' Processing helix chain 'D' and resid 50 through 61 Processing helix chain 'D' and resid 66 through 79 Proline residue: D 74 - end of helix Processing helix chain 'D' and resid 91 through 108 Proline residue: D 99 - end of helix Processing helix chain 'D' and resid 123 through 139 Processing helix chain 'D' and resid 153 through 164 Processing helix chain 'D' and resid 171 through 181 Processing helix chain 'D' and resid 197 through 205 Processing helix chain 'D' and resid 206 through 218 Proline residue: D 218 - end of helix Processing helix chain 'D' and resid 232 through 243 Processing helix chain 'D' and resid 272 through 288 removed outlier: 3.535A pdb=" N ARG D 276 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N PHE D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LEU D 278 " --> pdb=" O ASP D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 313 Processing helix chain 'D' and resid 324 through 339 removed outlier: 5.385A pdb=" N GLU D 339 " --> pdb=" O PHE D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 352 removed outlier: 5.704A pdb=" N GLY D 352 " --> pdb=" O VAL D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'D' and resid 398 through 409 removed outlier: 4.910A pdb=" N LEU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ARG D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR D 404 " --> pdb=" O GLY D 400 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER D 408 " --> pdb=" O TYR D 404 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS D 409 " --> pdb=" O LEU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 436 Processing helix chain 'D' and resid 437 through 457 Processing helix chain 'D' and resid 464 through 469 removed outlier: 5.330A pdb=" N ASP D 469 " --> pdb=" O ILE D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 478 Processing helix chain 'E' and resid 80 through 85 removed outlier: 3.996A pdb=" N VAL E 84 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ILE E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 80 through 85' Processing helix chain 'E' and resid 102 through 107 Processing helix chain 'E' and resid 131 through 150 removed outlier: 3.927A pdb=" N ALA E 147 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 162 removed outlier: 5.079A pdb=" N SER E 162 " --> pdb=" O TYR E 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 73 Processing helix chain 'F' and resid 96 through 107 Processing helix chain 'F' and resid 120 through 131 removed outlier: 3.684A pdb=" N GLU F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 151 Processing helix chain 'F' and resid 165 through 173 removed outlier: 3.799A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN F 172 " --> pdb=" O ILE F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 191 removed outlier: 4.038A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 203 removed outlier: 4.977A pdb=" N TRP F 203 " --> pdb=" O ASN F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 244 removed outlier: 4.489A pdb=" N LYS F 238 " --> pdb=" O GLU F 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 80 removed outlier: 4.868A pdb=" N PHE G 78 " --> pdb=" O THR G 74 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLN G 79 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N TYR G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 98 removed outlier: 3.800A pdb=" N LYS G 96 " --> pdb=" O LYS G 92 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 119 Processing helix chain 'G' and resid 135 through 146 Processing helix chain 'G' and resid 165 through 174 Processing helix chain 'G' and resid 182 through 191 removed outlier: 3.732A pdb=" N LEU G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL G 190 " --> pdb=" O LEU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 227 removed outlier: 4.694A pdb=" N ALA G 209 " --> pdb=" O ALA G 205 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ALA G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP G 224 " --> pdb=" O ALA G 220 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS G 225 " --> pdb=" O ASN G 221 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP G 227 " --> pdb=" O ALA G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 233 removed outlier: 6.694A pdb=" N TRP G 233 " --> pdb=" O VAL G 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 84 removed outlier: 3.950A pdb=" N ALA H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU H 68 " --> pdb=" O HIS H 64 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG H 69 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 166 removed outlier: 4.095A pdb=" N CYS H 165 " --> pdb=" O LEU H 161 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ARG H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 176 removed outlier: 4.864A pdb=" N LEU H 176 " --> pdb=" O ILE H 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 131 removed outlier: 4.382A pdb=" N LEU I 123 " --> pdb=" O ASP I 119 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER I 128 " --> pdb=" O GLU I 124 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LYS I 129 " --> pdb=" O SER I 125 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER I 130 " --> pdb=" O LEU I 126 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N VAL I 131 " --> pdb=" O SER I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 327 through 332 removed outlier: 4.530A pdb=" N LEU I 331 " --> pdb=" O THR I 327 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN I 332 " --> pdb=" O PHE I 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 327 through 332' Processing helix chain 'J' and resid 197 through 209 Processing helix chain 'J' and resid 211 through 216 removed outlier: 4.249A pdb=" N HIS J 215 " --> pdb=" O PRO J 211 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N SER J 216 " --> pdb=" O TRP J 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 211 through 216' Processing helix chain 'J' and resid 228 through 234 removed outlier: 5.284A pdb=" N LYS J 234 " --> pdb=" O ASP J 230 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 265 Processing helix chain 'J' and resid 281 through 315 removed outlier: 4.222A pdb=" N LYS J 287 " --> pdb=" O GLU J 283 " (cutoff:3.500A) Processing helix chain 'J' and resid 316 through 346 Processing helix chain 'K' and resid 33 through 50 removed outlier: 4.359A pdb=" N LYS K 50 " --> pdb=" O LYS K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 76 removed outlier: 4.536A pdb=" N LYS K 76 " --> pdb=" O GLU K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 117 Proline residue: K 109 - end of helix removed outlier: 4.443A pdb=" N THR K 116 " --> pdb=" O GLU K 112 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA K 117 " --> pdb=" O ALA K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 133 removed outlier: 4.600A pdb=" N LYS K 133 " --> pdb=" O ASP K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 145 Processing helix chain 'K' and resid 156 through 163 Processing helix chain 'K' and resid 166 through 177 removed outlier: 3.921A pdb=" N GLN K 176 " --> pdb=" O ALA K 172 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N PHE K 177 " --> pdb=" O PHE K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 194 removed outlier: 4.753A pdb=" N THR K 188 " --> pdb=" O ASP K 184 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N SER K 189 " --> pdb=" O SER K 185 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU K 190 " --> pdb=" O ILE K 186 " (cutoff:3.500A) Proline residue: K 191 - end of helix Processing helix chain 'K' and resid 195 through 201 removed outlier: 4.196A pdb=" N TYR K 199 " --> pdb=" O GLY K 195 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS K 201 " --> pdb=" O LYS K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 218 through 232 Processing helix chain 'K' and resid 250 through 255 removed outlier: 4.207A pdb=" N LEU K 254 " --> pdb=" O ASN K 250 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ARG K 255 " --> pdb=" O LEU K 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 250 through 255' Processing helix chain 'K' and resid 256 through 274 Processing helix chain 'K' and resid 294 through 300 removed outlier: 5.025A pdb=" N LEU K 298 " --> pdb=" O ASN K 294 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLU K 300 " --> pdb=" O ASP K 296 " (cutoff:3.500A) Processing helix chain 'K' and resid 327 through 336 Processing helix chain 'L' and resid 27 through 47 Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 86 through 94 removed outlier: 3.540A pdb=" N THR L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 123 Processing helix chain 'M' and resid 59 through 64 removed outlier: 4.274A pdb=" N VAL M 63 " --> pdb=" O ASN M 59 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N VAL M 64 " --> pdb=" O LEU M 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 59 through 64' Processing helix chain 'M' and resid 77 through 89 Processing helix chain 'M' and resid 90 through 98 removed outlier: 5.367A pdb=" N SER M 98 " --> pdb=" O TRP M 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 112 Processing helix chain 'M' and resid 113 through 137 removed outlier: 4.352A pdb=" N LYS M 137 " --> pdb=" O LYS M 133 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 14 removed outlier: 4.058A pdb=" N LYS N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LYS N 14 " --> pdb=" O LEU N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 34 removed outlier: 3.890A pdb=" N GLN N 32 " --> pdb=" O TRP N 28 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS N 33 " --> pdb=" O GLU N 29 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ASN N 34 " --> pdb=" O TYR N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 Processing helix chain 'N' and resid 97 through 111 removed outlier: 3.644A pdb=" N ALA N 111 " --> pdb=" O GLY N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 145 Processing helix chain 'N' and resid 148 through 153 removed outlier: 4.636A pdb=" N CYS N 152 " --> pdb=" O TYR N 148 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP N 153 " --> pdb=" O ASN N 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 148 through 153' Processing helix chain 'N' and resid 158 through 163 Processing helix chain 'N' and resid 165 through 173 Processing helix chain 'N' and resid 177 through 182 removed outlier: 4.584A pdb=" N ASN N 182 " --> pdb=" O HIS N 178 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 196 removed outlier: 3.625A pdb=" N THR N 190 " --> pdb=" O GLY N 186 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N TRP N 191 " --> pdb=" O ARG N 187 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLN N 194 " --> pdb=" O THR N 190 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR N 196 " --> pdb=" O LYS N 192 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 30 Processing helix chain 'O' and resid 46 through 61 removed outlier: 4.647A pdb=" N ALA O 61 " --> pdb=" O PHE O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 89 removed outlier: 3.811A pdb=" N MET O 87 " --> pdb=" O ALA O 83 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL O 88 " --> pdb=" O LEU O 84 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N SER O 89 " --> pdb=" O ARG O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 102 removed outlier: 3.566A pdb=" N ARG O 101 " --> pdb=" O ALA O 97 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU O 102 " --> pdb=" O ALA O 98 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 116 removed outlier: 7.970A pdb=" N LYS O 114 " --> pdb=" O PRO O 110 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS O 115 " --> pdb=" O PRO O 111 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LYS O 116 " --> pdb=" O TYR O 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 110 through 116' Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 137 through 146 Processing helix chain 'O' and resid 151 through 183 removed outlier: 3.529A pdb=" N LYS O 170 " --> pdb=" O GLU O 166 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 15 removed outlier: 4.403A pdb=" N SER P 14 " --> pdb=" O ASN P 10 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ALA P 15 " --> pdb=" O PRO P 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 10 through 15' Processing helix chain 'P' and resid 25 through 37 removed outlier: 3.773A pdb=" N ILE P 36 " --> pdb=" O THR P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 54 Processing helix chain 'P' and resid 70 through 77 removed outlier: 4.676A pdb=" N LYS P 74 " --> pdb=" O THR P 70 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLU P 75 " --> pdb=" O ALA P 71 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N PHE P 76 " --> pdb=" O GLN P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 106 Processing helix chain 'Q' and resid 23 through 40 Processing helix chain 'Q' and resid 42 through 54 removed outlier: 3.977A pdb=" N LYS Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU Q 54 " --> pdb=" O LYS Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 60 Proline residue: Q 60 - end of helix Processing helix chain 'Q' and resid 63 through 73 removed outlier: 3.841A pdb=" N LYS Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLN Q 73 " --> pdb=" O ARG Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 80 removed outlier: 4.663A pdb=" N LYS Q 79 " --> pdb=" O GLY Q 75 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N THR Q 80 " --> pdb=" O ALA Q 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 75 through 80' Processing helix chain 'Q' and resid 107 through 118 removed outlier: 3.524A pdb=" N GLY Q 118 " --> pdb=" O ILE Q 114 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 131 Processing helix chain 'R' and resid 2 through 12 Processing helix chain 'R' and resid 43 through 48 removed outlier: 4.867A pdb=" N SER R 48 " --> pdb=" O PRO R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 71 removed outlier: 4.046A pdb=" N ALA R 70 " --> pdb=" O THR R 66 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N HIS R 71 " --> pdb=" O PRO R 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 66 through 71' Processing helix chain 'R' and resid 85 through 98 Processing helix chain 'R' and resid 101 through 129 removed outlier: 5.186A pdb=" N GLU R 129 " --> pdb=" O LEU R 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 173 removed outlier: 4.833A pdb=" N LYS R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE R 158 " --> pdb=" O VAL R 154 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N GLU R 159 " --> pdb=" O ALA R 155 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LYS R 160 " --> pdb=" O ALA R 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 191 Processing helix chain 'S' and resid 33 through 49 Processing helix chain 'S' and resid 52 through 57 removed outlier: 4.858A pdb=" N GLU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 114 Processing helix chain 'S' and resid 117 through 122 removed outlier: 3.891A pdb=" N ILE S 121 " --> pdb=" O ARG S 117 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N HIS S 122 " --> pdb=" O PHE S 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 117 through 122' Processing helix chain 'S' and resid 137 through 145 removed outlier: 5.136A pdb=" N PHE S 143 " --> pdb=" O TYR S 139 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU S 144 " --> pdb=" O VAL S 140 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR S 145 " --> pdb=" O LYS S 141 " (cutoff:3.500A) Processing helix chain 'T' and resid 172 through 215 removed outlier: 3.964A pdb=" N ALA T 185 " --> pdb=" O GLU T 181 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU T 186 " --> pdb=" O LYS T 182 " (cutoff:3.500A) Processing helix chain 'T' and resid 221 through 250 Processing helix chain 'V' and resid 119 through 127 Proline residue: V 127 - end of helix Processing helix chain 'V' and resid 128 through 133 Processing helix chain 'W' and resid 19 through 37 removed outlier: 3.807A pdb=" N LYS W 23 " --> pdb=" O GLY W 19 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASP W 35 " --> pdb=" O ARG W 31 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 61 removed outlier: 3.702A pdb=" N TRP W 60 " --> pdb=" O ILE W 56 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA W 61 " --> pdb=" O ARG W 57 " (cutoff:3.500A) Processing helix chain 'W' and resid 69 through 78 Processing helix chain 'W' and resid 88 through 96 removed outlier: 4.595A pdb=" N LEU W 92 " --> pdb=" O ASN W 88 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU W 95 " --> pdb=" O GLN W 91 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS W 96 " --> pdb=" O LEU W 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 108 through 119 Processing helix chain 'W' and resid 150 through 155 removed outlier: 5.106A pdb=" N VAL W 155 " --> pdb=" O ALA W 151 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 168 removed outlier: 4.221A pdb=" N GLU W 162 " --> pdb=" O ILE W 158 " (cutoff:3.500A) Proline residue: W 163 - end of helix Processing helix chain 'W' and resid 196 through 207 Processing helix chain 'Y' and resid 11 through 22 Processing helix chain 'Y' and resid 23 through 32 removed outlier: 3.776A pdb=" N VAL Y 29 " --> pdb=" O SER Y 25 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER Y 32 " --> pdb=" O ARG Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 44 Processing helix chain 'Y' and resid 100 through 105 removed outlier: 3.836A pdb=" N LEU Y 104 " --> pdb=" O HIS Y 100 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N VAL Y 105 " --> pdb=" O PRO Y 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 100 through 105' Processing helix chain 'Y' and resid 112 through 123 Processing helix chain 'Z' and resid 16 through 23 Proline residue: Z 23 - end of helix Processing helix chain 'Z' and resid 31 through 37 Processing helix chain 'Z' and resid 38 through 52 removed outlier: 4.104A pdb=" N GLN Z 42 " --> pdb=" O HIS Z 38 " (cutoff:3.500A) Processing helix chain 'Z' and resid 66 through 78 Proline residue: Z 76 - end of helix Processing helix chain 'Z' and resid 116 through 125 removed outlier: 5.066A pdb=" N LYS Z 125 " --> pdb=" O LYS Z 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 138 removed outlier: 4.213A pdb=" N ASN Z 137 " --> pdb=" O ASP Z 133 " (cutoff:3.500A) Proline residue: Z 138 - end of helix Processing helix chain 'Z' and resid 155 through 174 removed outlier: 4.182A pdb=" N PHE Z 173 " --> pdb=" O PHE Z 169 " (cutoff:3.500A) Proline residue: Z 174 - end of helix Processing helix chain 'Z' and resid 182 through 187 removed outlier: 3.778A pdb=" N ILE Z 186 " --> pdb=" O SER Z 182 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LYS Z 187 " --> pdb=" O LEU Z 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 182 through 187' Processing helix chain 'a' and resid 8 through 22 Processing helix chain 'a' and resid 70 through 81 Processing helix chain 'a' and resid 86 through 92 removed outlier: 4.399A pdb=" N LYS a 92 " --> pdb=" O ASP a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 96 through 107 Processing helix chain 'a' and resid 117 through 125 Proline residue: a 121 - end of helix Processing helix chain 'a' and resid 126 through 132 Processing helix chain 'a' and resid 143 through 154 removed outlier: 3.854A pdb=" N THR a 154 " --> pdb=" O ASP a 150 " (cutoff:3.500A) Processing helix chain 'a' and resid 175 through 195 removed outlier: 4.964A pdb=" N LYS a 195 " --> pdb=" O VAL a 191 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 29 Processing helix chain 'b' and resid 38 through 66 removed outlier: 3.787A pdb=" N ILE b 64 " --> pdb=" O LYS b 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 86 Processing helix chain 'b' and resid 87 through 120 removed outlier: 4.121A pdb=" N LYS b 117 " --> pdb=" O VAL b 113 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N PHE b 118 " --> pdb=" O ARG b 114 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY b 119 " --> pdb=" O LEU b 115 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN b 120 " --> pdb=" O LEU b 116 " (cutoff:3.500A) Processing helix chain 'b' and resid 121 through 144 removed outlier: 3.687A pdb=" N LYS b 142 " --> pdb=" O THR b 138 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU b 143 " --> pdb=" O ILE b 139 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG b 144 " --> pdb=" O VAL b 140 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 161 removed outlier: 4.391A pdb=" N ARG b 159 " --> pdb=" O GLN b 155 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU b 160 " --> pdb=" O HIS b 156 " (cutoff:3.500A) Proline residue: b 161 - end of helix Processing helix chain 'b' and resid 179 through 188 Processing helix chain 'b' and resid 233 through 245 removed outlier: 3.550A pdb=" N GLN b 238 " --> pdb=" O ASN b 234 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER b 239 " --> pdb=" O ILE b 235 " (cutoff:3.500A) Processing helix chain 'b' and resid 263 through 279 Proline residue: b 276 - end of helix removed outlier: 4.232A pdb=" N ALA b 279 " --> pdb=" O LYS b 275 " (cutoff:3.500A) Processing helix chain 'b' and resid 305 through 312 removed outlier: 4.472A pdb=" N VAL b 309 " --> pdb=" O LEU b 305 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS b 310 " --> pdb=" O LEU b 306 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU b 311 " --> pdb=" O GLU b 307 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL b 312 " --> pdb=" O SER b 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 305 through 312' Processing helix chain 'b' and resid 324 through 341 Processing helix chain 'b' and resid 379 through 385 removed outlier: 3.605A pdb=" N LEU b 385 " --> pdb=" O SER b 381 " (cutoff:3.500A) Processing helix chain 'b' and resid 398 through 407 Processing helix chain 'b' and resid 415 through 420 removed outlier: 4.588A pdb=" N LYS b 419 " --> pdb=" O ASN b 415 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR b 420 " --> pdb=" O LEU b 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 415 through 420' Processing helix chain 'b' and resid 424 through 431 removed outlier: 4.329A pdb=" N ASN b 429 " --> pdb=" O ASP b 425 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ASP b 430 " --> pdb=" O GLU b 426 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE b 431 " --> pdb=" O TRP b 427 " (cutoff:3.500A) Processing helix chain 'b' and resid 440 through 445 removed outlier: 3.758A pdb=" N PHE b 444 " --> pdb=" O ASN b 440 " (cutoff:3.500A) Processing helix chain 'b' and resid 448 through 467 removed outlier: 4.568A pdb=" N LYS b 452 " --> pdb=" O GLU b 448 " (cutoff:3.500A) Processing helix chain 'e' and resid 21 through 26 removed outlier: 4.828A pdb=" N HIS e 26 " --> pdb=" O SER e 22 " (cutoff:3.500A) Processing helix chain 'e' and resid 40 through 45 Processing helix chain 'e' and resid 78 through 86 removed outlier: 3.867A pdb=" N THR e 84 " --> pdb=" O LYS e 80 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU e 85 " --> pdb=" O ASP e 81 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR e 86 " --> pdb=" O LEU e 82 " (cutoff:3.500A) Processing helix chain 'e' and resid 101 through 116 removed outlier: 3.992A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 45 removed outlier: 4.423A pdb=" N PHE f 43 " --> pdb=" O GLN f 39 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR f 44 " --> pdb=" O ASP f 40 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU f 45 " --> pdb=" O ALA f 41 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 13 removed outlier: 3.939A pdb=" N THR h 11 " --> pdb=" O TYR h 7 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS h 12 " --> pdb=" O GLU h 8 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N SER h 13 " --> pdb=" O LEU h 9 " (cutoff:3.500A) Processing helix chain 'h' and resid 14 through 36 removed outlier: 4.153A pdb=" N LEU h 36 " --> pdb=" O LYS h 32 " (cutoff:3.500A) Processing helix chain 'h' and resid 42 through 71 removed outlier: 3.885A pdb=" N THR h 46 " --> pdb=" O PRO h 42 " (cutoff:3.500A) Processing helix chain 'h' and resid 77 through 82 removed outlier: 5.477A pdb=" N ALA h 82 " --> pdb=" O LYS h 78 " (cutoff:3.500A) Processing helix chain 'h' and resid 85 through 91 Processing helix chain 'h' and resid 93 through 99 Processing helix chain 'h' and resid 101 through 112 Proline residue: h 112 - end of helix Processing helix chain 'i' and resid 27 through 32 removed outlier: 4.352A pdb=" N GLY i 31 " --> pdb=" O SER i 27 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ALA i 32 " --> pdb=" O TYR i 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 27 through 32' Processing helix chain 'i' and resid 34 through 49 removed outlier: 3.848A pdb=" N GLY i 49 " --> pdb=" O ARG i 45 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 64 Processing helix chain 'i' and resid 65 through 78 Processing helix chain 'i' and resid 79 through 99 Processing helix chain 'j' and resid 50 through 58 Processing helix chain 'j' and resid 66 through 77 removed outlier: 4.134A pdb=" N VAL j 70 " --> pdb=" O TYR j 66 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER j 71 " --> pdb=" O LEU j 67 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ARG j 72 " --> pdb=" O LYS j 68 " (cutoff:3.500A) Processing helix chain 'l' and resid 5 through 20 removed outlier: 3.810A pdb=" N TYR l 19 " --> pdb=" O LYS l 15 " (cutoff:3.500A) Processing helix chain 'l' and resid 22 through 30 removed outlier: 4.245A pdb=" N PHE l 26 " --> pdb=" O ARG l 22 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU l 27 " --> pdb=" O ASN l 23 " (cutoff:3.500A) Processing helix chain 'l' and resid 48 through 59 removed outlier: 4.328A pdb=" N SER l 57 " --> pdb=" O LYS l 53 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL l 58 " --> pdb=" O LEU l 54 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ALA l 59 " --> pdb=" O ALA l 55 " (cutoff:3.500A) Processing helix chain 'l' and resid 82 through 93 removed outlier: 4.161A pdb=" N LEU l 86 " --> pdb=" O HIS l 82 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N THR l 87 " --> pdb=" O ILE l 83 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL l 88 " --> pdb=" O THR l 84 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS l 91 " --> pdb=" O THR l 87 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N HIS l 92 " --> pdb=" O VAL l 88 " (cutoff:3.500A) Processing helix chain 'l' and resid 100 through 110 removed outlier: 3.879A pdb=" N MET l 105 " --> pdb=" O PRO l 101 " (cutoff:3.500A) Proline residue: l 106 - end of helix Processing helix chain 'l' and resid 114 through 119 removed outlier: 4.893A pdb=" N GLY l 119 " --> pdb=" O LYS l 115 " (cutoff:3.500A) Processing helix chain 'l' and resid 149 through 157 removed outlier: 5.262A pdb=" N GLN l 157 " --> pdb=" O SER l 153 " (cutoff:3.500A) Processing helix chain 'l' and resid 169 through 176 removed outlier: 4.494A pdb=" N LEU l 173 " --> pdb=" O ILE l 169 " (cutoff:3.500A) Processing helix chain 'm' and resid 161 through 167 removed outlier: 4.635A pdb=" N TYR m 165 " --> pdb=" O PRO m 161 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLU m 167 " --> pdb=" O SER m 163 " (cutoff:3.500A) Processing helix chain 'm' and resid 262 through 268 removed outlier: 4.281A pdb=" N PHE m 266 " --> pdb=" O PRO m 262 " (cutoff:3.500A) Proline residue: m 268 - end of helix Processing helix chain 'm' and resid 269 through 286 Processing helix chain 'm' and resid 290 through 305 Processing helix chain 'm' and resid 347 through 357 Processing helix chain 'm' and resid 373 through 378 removed outlier: 3.748A pdb=" N VAL m 377 " --> pdb=" O ALA m 373 " (cutoff:3.500A) Proline residue: m 378 - end of helix No H-bonds generated for 'chain 'm' and resid 373 through 378' Processing helix chain 'm' and resid 382 through 396 Processing helix chain 'n' and resid 17 through 26 Processing helix chain 'n' and resid 28 through 40 Processing helix chain 'n' and resid 64 through 75 Proline residue: n 75 - end of helix Processing helix chain 'n' and resid 76 through 97 Processing helix chain 'n' and resid 98 through 109 removed outlier: 4.285A pdb=" N ARG n 109 " --> pdb=" O LEU n 105 " (cutoff:3.500A) Processing helix chain 'n' and resid 114 through 123 Proline residue: n 123 - end of helix Processing helix chain 'n' and resid 124 through 146 removed outlier: 4.858A pdb=" N ASP n 133 " --> pdb=" O ILE n 129 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASP n 134 " --> pdb=" O ARG n 130 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA n 135 " --> pdb=" O ASP n 131 " (cutoff:3.500A) Proline residue: n 146 - end of helix Processing helix chain 'n' and resid 152 through 174 Processing helix chain 'n' and resid 214 through 241 removed outlier: 4.328A pdb=" N MET n 218 " --> pdb=" O ASP n 214 " (cutoff:3.500A) Processing helix chain 'n' and resid 249 through 256 Processing helix chain 'n' and resid 258 through 263 removed outlier: 4.585A pdb=" N TYR n 262 " --> pdb=" O GLY n 258 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ILE n 263 " --> pdb=" O LEU n 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 258 through 263' Processing helix chain 'n' and resid 354 through 359 removed outlier: 6.347A pdb=" N SER n 358 " --> pdb=" O SER n 354 " (cutoff:3.500A) Processing helix chain 'n' and resid 372 through 384 Processing helix chain 'n' and resid 389 through 395 removed outlier: 4.026A pdb=" N MET n 393 " --> pdb=" O SER n 389 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASP n 394 " --> pdb=" O GLU n 390 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLN n 395 " --> pdb=" O ALA n 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 389 through 395' Processing helix chain 'n' and resid 428 through 439 removed outlier: 4.099A pdb=" N ILE n 432 " --> pdb=" O GLN n 428 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE n 433 " --> pdb=" O PRO n 429 " (cutoff:3.500A) Processing helix chain 'o' and resid 103 through 115 removed outlier: 4.381A pdb=" N GLN o 113 " --> pdb=" O LYS o 109 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE o 114 " --> pdb=" O TYR o 110 " (cutoff:3.500A) Processing helix chain 'o' and resid 141 through 153 Processing helix chain 'o' and resid 192 through 215 Processing helix chain 'q' and resid 196 through 214 Processing helix chain 'q' and resid 223 through 239 removed outlier: 3.793A pdb=" N TYR q 227 " --> pdb=" O SER q 223 " (cutoff:3.500A) Processing helix chain 'q' and resid 242 through 253 Processing helix chain 'q' and resid 254 through 268 removed outlier: 5.113A pdb=" N ALA q 268 " --> pdb=" O ALA q 264 " (cutoff:3.500A) Processing helix chain 'q' and resid 281 through 293 Processing helix chain 'q' and resid 319 through 325 removed outlier: 3.540A pdb=" N LEU q 323 " --> pdb=" O THR q 319 " (cutoff:3.500A) Processing helix chain 'q' and resid 331 through 342 removed outlier: 3.738A pdb=" N LEU q 336 " --> pdb=" O ALA q 332 " (cutoff:3.500A) Proline residue: q 337 - end of helix Processing helix chain 'q' and resid 357 through 368 Processing helix chain 'q' and resid 379 through 394 Processing helix chain 'q' and resid 404 through 412 Proline residue: q 409 - end of helix Processing helix chain 'q' and resid 429 through 434 Processing helix chain 'q' and resid 435 through 440 Processing helix chain 'q' and resid 441 through 463 Proline residue: q 449 - end of helix Processing helix chain 'q' and resid 481 through 497 removed outlier: 4.669A pdb=" N VAL q 488 " --> pdb=" O GLU q 484 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ILE q 489 " --> pdb=" O ASP q 485 " (cutoff:3.500A) Proline residue: q 497 - end of helix Processing helix chain 'q' and resid 532 through 537 removed outlier: 3.555A pdb=" N TYR q 536 " --> pdb=" O TYR q 532 " (cutoff:3.500A) Processing helix chain 'q' and resid 522 through 529 removed outlier: 3.714A pdb=" N LYS q 526 " --> pdb=" O PRO q 523 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG q 529 " --> pdb=" O LYS q 526 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 14 Processing helix chain 'r' and resid 20 through 38 removed outlier: 4.422A pdb=" N SER r 32 " --> pdb=" O GLU r 28 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 44 through 73 Processing helix chain 'r' and resid 98 through 118 Processing helix chain 'r' and resid 129 through 134 removed outlier: 5.211A pdb=" N PHE r 134 " --> pdb=" O GLU r 130 " (cutoff:3.500A) Processing helix chain 'r' and resid 206 through 213 Processing helix chain 'r' and resid 248 through 253 removed outlier: 4.354A pdb=" N GLY r 253 " --> pdb=" O PRO r 249 " (cutoff:3.500A) Processing helix chain 't' and resid 57 through 88 Processing helix chain 't' and resid 156 through 167 Processing helix chain 't' and resid 180 through 191 Proline residue: t 185 - end of helix Processing helix chain 't' and resid 200 through 211 Processing helix chain 't' and resid 231 through 240 removed outlier: 3.757A pdb=" N VAL t 235 " --> pdb=" O ASP t 231 " (cutoff:3.500A) Processing helix chain 't' and resid 246 through 257 Processing helix chain 't' and resid 260 through 269 removed outlier: 5.040A pdb=" N GLN t 269 " --> pdb=" O ASN t 265 " (cutoff:3.500A) Processing helix chain 't' and resid 281 through 299 Processing helix chain 't' and resid 313 through 322 Processing helix chain 'u' and resid 33 through 43 removed outlier: 3.859A pdb=" N ARG u 43 " --> pdb=" O ALA u 39 " (cutoff:3.500A) Processing helix chain 'u' and resid 45 through 50 removed outlier: 4.086A pdb=" N LEU u 49 " --> pdb=" O ASN u 45 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LYS u 50 " --> pdb=" O PRO u 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 45 through 50' Processing helix chain 'u' and resid 52 through 60 Processing helix chain 'u' and resid 66 through 73 removed outlier: 3.991A pdb=" N THR u 70 " --> pdb=" O ASP u 66 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N PHE u 71 " --> pdb=" O SER u 67 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ALA u 72 " --> pdb=" O THR u 68 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLN u 73 " --> pdb=" O LEU u 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 66 through 73' Processing helix chain 'u' and resid 82 through 112 removed outlier: 3.729A pdb=" N ALA u 94 " --> pdb=" O LEU u 90 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG u 95 " --> pdb=" O LYS u 91 " (cutoff:3.500A) Processing helix chain 'v' and resid 3 through 13 removed outlier: 5.409A pdb=" N SER v 13 " --> pdb=" O MET v 9 " (cutoff:3.500A) Processing helix chain 'v' and resid 21 through 28 removed outlier: 4.696A pdb=" N ILE v 28 " --> pdb=" O LYS v 24 " (cutoff:3.500A) Processing helix chain 'v' and resid 33 through 40 Processing helix chain 'v' and resid 45 through 54 Processing helix chain 'v' and resid 156 through 168 Processing helix chain 'v' and resid 178 through 192 Processing helix chain 'v' and resid 195 through 202 Processing helix chain 'v' and resid 211 through 227 removed outlier: 4.112A pdb=" N GLY v 227 " --> pdb=" O LYS v 223 " (cutoff:3.500A) Processing helix chain 'w' and resid 1 through 12 Processing helix chain 'w' and resid 14 through 29 removed outlier: 3.695A pdb=" N LYS w 27 " --> pdb=" O GLU w 23 " (cutoff:3.500A) Processing helix chain 'w' and resid 31 through 38 removed outlier: 3.934A pdb=" N ASN w 37 " --> pdb=" O GLN w 33 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LYS w 38 " --> pdb=" O PHE w 34 " (cutoff:3.500A) Processing helix chain 'w' and resid 39 through 56 Processing helix chain 'w' and resid 58 through 76 removed outlier: 4.393A pdb=" N HIS w 73 " --> pdb=" O LEU w 69 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLY w 74 " --> pdb=" O GLY w 70 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU w 75 " --> pdb=" O GLU w 71 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N TYR w 76 " --> pdb=" O LEU w 72 " (cutoff:3.500A) Processing helix chain 'w' and resid 89 through 110 Processing helix chain 'w' and resid 114 through 140 removed outlier: 5.140A pdb=" N ASP w 119 " --> pdb=" O ARG w 115 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LYS w 120 " --> pdb=" O TYR w 116 " (cutoff:3.500A) Processing helix chain 'w' and resid 142 through 152 Processing helix chain 'w' and resid 166 through 186 Proline residue: w 170 - end of helix removed outlier: 5.451A pdb=" N LEU w 178 " --> pdb=" O VAL w 174 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ASP w 179 " --> pdb=" O ASP w 175 " (cutoff:3.500A) Processing helix chain 'w' and resid 197 through 213 removed outlier: 3.838A pdb=" N LYS w 211 " --> pdb=" O GLU w 207 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR w 212 " --> pdb=" O SER w 208 " (cutoff:3.500A) Proline residue: w 213 - end of helix Processing helix chain 'w' and resid 214 through 228 removed outlier: 3.875A pdb=" N ILE w 220 " --> pdb=" O ASP w 216 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE w 221 " --> pdb=" O VAL w 217 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N TYR w 228 " --> pdb=" O ILE w 224 " (cutoff:3.500A) Processing helix chain 'w' and resid 231 through 241 Processing helix chain 'w' and resid 245 through 252 removed outlier: 4.283A pdb=" N VAL w 249 " --> pdb=" O ASP w 245 " (cutoff:3.500A) Processing helix chain 'w' and resid 78 through 84 removed outlier: 3.671A pdb=" N ASN w 82 " --> pdb=" O PRO w 79 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER w 83 " --> pdb=" O LYS w 80 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR w 84 " --> pdb=" O ASP w 81 " (cutoff:3.500A) Processing helix chain 'x' and resid 11 through 45 Proline residue: x 45 - end of helix Processing helix chain 'x' and resid 46 through 56 removed outlier: 5.004A pdb=" N VAL x 56 " --> pdb=" O LEU x 52 " (cutoff:3.500A) Processing helix chain 'x' and resid 59 through 64 Processing helix chain 'x' and resid 76 through 84 Processing helix chain 'x' and resid 104 through 118 Processing helix chain 'x' and resid 131 through 143 Processing helix chain 'x' and resid 204 through 218 Processing helix chain 'x' and resid 283 through 289 removed outlier: 4.219A pdb=" N ASP x 287 " --> pdb=" O LYS x 283 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS x 288 " --> pdb=" O PRO x 284 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLU x 289 " --> pdb=" O GLU x 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 283 through 289' Processing helix chain 'y' and resid 12 through 17 removed outlier: 4.107A pdb=" N PHE y 16 " --> pdb=" O GLU y 12 " (cutoff:3.500A) Processing helix chain 'y' and resid 32 through 43 Processing helix chain 'y' and resid 58 through 63 removed outlier: 4.078A pdb=" N MET y 62 " --> pdb=" O ILE y 58 " (cutoff:3.500A) Processing helix chain 'y' and resid 77 through 88 Processing helix chain 'y' and resid 103 through 108 Processing helix chain 'y' and resid 122 through 133 Processing helix chain 'y' and resid 147 through 152 Processing helix chain 'y' and resid 166 through 178 Processing helix chain 'y' and resid 192 through 197 removed outlier: 3.595A pdb=" N MET y 197 " --> pdb=" O VAL y 193 " (cutoff:3.500A) Processing helix chain 'y' and resid 211 through 223 Processing sheet with id= 1, first strand: chain '3' and resid 459 through 462 removed outlier: 3.505A pdb=" N VAL 3 487 " --> pdb=" O SER 3 460 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE 3 462 " --> pdb=" O VAL 3 487 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY 3 530 " --> pdb=" O ASN 3 351 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL 3 594 " --> pdb=" O MET 3 354 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '8' and resid 274 through 277 removed outlier: 4.244A pdb=" N ARG 8 275 " --> pdb=" O ARG 8 284 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ARG 8 282 " --> pdb=" O THR 8 277 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 58 through 62 removed outlier: 4.641A pdb=" N SER A 37 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ALA A 91 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ASN A 84 " --> pdb=" O PRO A 104 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 116 through 119 removed outlier: 5.384A pdb=" N ASN A 116 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL A 220 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS A 111 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A 225 " --> pdb=" O LYS A 111 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 135 through 139 removed outlier: 6.526A pdb=" N ASP A 174 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N THR A 190 " --> pdb=" O ILE A 215 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 185 through 189 Processing sheet with id= 7, first strand: chain 'B' and resid 45 through 50 removed outlier: 4.462A pdb=" N ARG B 334 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N VAL B 220 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N HIS B 273 " --> pdb=" O THR B 221 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 53 through 59 Processing sheet with id= 9, first strand: chain 'B' and resid 84 through 87 removed outlier: 6.105A pdb=" N LEU B 161 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'B' and resid 88 through 91 removed outlier: 3.856A pdb=" N THR B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'B' and resid 159 through 164 removed outlier: 4.514A pdb=" N HIS B 177 " --> pdb=" O THR B 164 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'B' and resid 213 through 216 removed outlier: 4.295A pdb=" N GLU B 213 " --> pdb=" O ILE B 282 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'C' and resid 4 through 7 No H-bonds generated for sheet with id= 13 Processing sheet with id= 14, first strand: chain 'C' and resid 75 through 78 removed outlier: 4.359A pdb=" N GLN C 87 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'C' and resid 224 through 230 removed outlier: 5.281A pdb=" N PHE C 247 " --> pdb=" O GLY C 204 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'D' and resid 144 through 148 removed outlier: 3.878A pdb=" N VAL D 82 " --> pdb=" O SER D 224 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'D' and resid 291 through 296 removed outlier: 3.766A pdb=" N ASN D 413 " --> pdb=" O GLN D 266 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL D 270 " --> pdb=" O TYR D 415 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'D' and resid 316 through 319 Processing sheet with id= 19, first strand: chain 'E' and resid 37 through 43 removed outlier: 3.898A pdb=" N THR E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS E 50 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU E 64 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'F' and resid 133 through 138 removed outlier: 7.253A pdb=" N TYR F 133 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER F 113 " --> pdb=" O ARG F 88 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ASN F 112 " --> pdb=" O LEU F 207 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'F' and resid 152 through 155 removed outlier: 6.365A pdb=" N GLY F 152 " --> pdb=" O LEU F 163 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'G' and resid 176 through 181 Processing sheet with id= 23, first strand: chain 'H' and resid 5 through 12 removed outlier: 5.034A pdb=" N GLN H 51 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU H 52 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'H' and resid 17 through 20 removed outlier: 5.740A pdb=" N ARG H 23 " --> pdb=" O LEU H 38 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'H' and resid 100 through 105 removed outlier: 6.149A pdb=" N LYS H 110 " --> pdb=" O VAL H 128 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'H' and resid 132 through 137 removed outlier: 5.713A pdb=" N GLU H 143 " --> pdb=" O SER H 137 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ASP H 142 " --> pdb=" O TYR H 92 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.676A pdb=" N ARG I 2 " --> pdb=" O LEU I 410 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE I 406 " --> pdb=" O SER I 6 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'I' and resid 48 through 53 removed outlier: 6.484A pdb=" N GLU I 57 " --> pdb=" O ILE I 53 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASP I 56 " --> pdb=" O ILE I 72 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL I 66 " --> pdb=" O ARG I 62 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU I 69 " --> pdb=" O THR I 111 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'I' and resid 142 through 145 removed outlier: 5.866A pdb=" N ASN I 153 " --> pdb=" O LYS I 169 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N GLY I 162 " --> pdb=" O LEU I 183 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'I' and resid 190 through 193 removed outlier: 4.974A pdb=" N ILE I 204 " --> pdb=" O TYR I 193 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR I 203 " --> pdb=" O ILE I 219 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU I 216 " --> pdb=" O ILE I 229 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N SER I 225 " --> pdb=" O ASP I 220 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'I' and resid 250 through 254 removed outlier: 4.575A pdb=" N GLN I 269 " --> pdb=" O LEU I 254 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TYR I 268 " --> pdb=" O THR I 284 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N SER I 277 " --> pdb=" O LEU I 296 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA I 292 " --> pdb=" O LYS I 281 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'I' and resid 303 through 307 removed outlier: 4.414A pdb=" N VAL I 342 " --> pdb=" O VAL I 355 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY I 353 " --> pdb=" O LYS I 344 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'I' and resid 366 through 370 removed outlier: 8.084A pdb=" N LYS I 373 " --> pdb=" O ILE I 389 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE I 386 " --> pdb=" O LEU I 395 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS I 393 " --> pdb=" O ASP I 388 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'I' and resid 66 through 69 Processing sheet with id= 35, first strand: chain 'I' and resid 382 through 386 removed outlier: 8.026A pdb=" N ARG I 382 " --> pdb=" O VAL I 400 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'K' and resid 97 through 101 Processing sheet with id= 37, first strand: chain 'K' and resid 122 through 126 Processing sheet with id= 38, first strand: chain 'K' and resid 242 through 249 removed outlier: 5.380A pdb=" N THR K 242 " --> pdb=" O ASN K 84 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU K 78 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE K 279 " --> pdb=" O LEU K 291 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'L' and resid 55 through 59 Processing sheet with id= 40, first strand: chain 'M' and resid 19 through 23 removed outlier: 4.430A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYS M 31 " --> pdb=" O ILE M 23 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'M' and resid 36 through 39 removed outlier: 6.502A pdb=" N LYS M 43 " --> pdb=" O ILE M 39 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'N' and resid 35 through 39 removed outlier: 6.368A pdb=" N VAL N 35 " --> pdb=" O ARG N 65 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLY N 58 " --> pdb=" O ASP N 136 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'N' and resid 117 through 121 removed outlier: 6.761A pdb=" N TYR N 129 " --> pdb=" O VAL N 121 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'O' and resid 6 through 10 Processing sheet with id= 45, first strand: chain 'P' and resid 16 through 20 removed outlier: 7.167A pdb=" N LYS P 111 " --> pdb=" O LYS P 153 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'P' and resid 57 through 60 removed outlier: 5.009A pdb=" N LYS P 80 " --> pdb=" O PHE P 60 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'P' and resid 115 through 122 Processing sheet with id= 48, first strand: chain 'R' and resid 50 through 55 removed outlier: 5.368A pdb=" N LEU R 60 " --> pdb=" O LEU R 82 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'S' and resid 24 through 31 removed outlier: 4.476A pdb=" N GLU S 6 " --> pdb=" O ILE S 64 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'S' and resid 86 through 96 removed outlier: 4.966A pdb=" N ASN S 74 " --> pdb=" O ILE S 129 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'V' and resid 20 through 24 removed outlier: 4.046A pdb=" N ALA V 21 " --> pdb=" O ILE V 36 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'V' and resid 79 through 82 removed outlier: 4.522A pdb=" N ALA V 82 " --> pdb=" O ASP V 97 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASP V 97 " --> pdb=" O ALA V 82 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'W' and resid 63 through 67 removed outlier: 4.776A pdb=" N VAL W 99 " --> pdb=" O LEU W 45 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N ARG W 38 " --> pdb=" O ASN W 223 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA W 219 " --> pdb=" O VAL W 42 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR W 227 " --> pdb=" O ASP W 222 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'W' and resid 120 through 123 removed outlier: 3.713A pdb=" N ARG W 121 " --> pdb=" O PHE W 213 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'W' and resid 173 through 176 Processing sheet with id= 56, first strand: chain 'Y' and resid 72 through 75 Processing sheet with id= 57, first strand: chain 'Y' and resid 86 through 89 removed outlier: 4.385A pdb=" N ALA Y 93 " --> pdb=" O LYS Y 89 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'Z' and resid 24 through 30 removed outlier: 4.421A pdb=" N GLN Z 87 " --> pdb=" O VAL Z 30 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL Z 94 " --> pdb=" O VAL Z 111 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR Z 336 " --> pdb=" O LEU Z 112 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N LEU Z 339 " --> pdb=" O GLY Z 199 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N GLY Z 199 " --> pdb=" O LEU Z 339 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'Z' and resid 264 through 269 removed outlier: 3.843A pdb=" N ALA Z 264 " --> pdb=" O ILE Z 326 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL Z 266 " --> pdb=" O LYS Z 324 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'Z' and resid 105 through 109 removed outlier: 3.637A pdb=" N LYS Z 341 " --> pdb=" O THR Z 108 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'Z' and resid 205 through 210 removed outlier: 6.377A pdb=" N HIS Z 205 " --> pdb=" O LEU Z 331 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'a' and resid 64 through 69 Processing sheet with id= 63, first strand: chain 'a' and resid 163 through 169 removed outlier: 6.266A pdb=" N LEU a 163 " --> pdb=" O LEU a 38 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL a 32 " --> pdb=" O VAL a 169 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'b' and resid 204 through 210 removed outlier: 4.626A pdb=" N ARG b 168 " --> pdb=" O ARG b 215 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N GLY b 174 " --> pdb=" O THR b 221 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N SER b 282 " --> pdb=" O SER b 248 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN b 288 " --> pdb=" O MET b 254 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU b 316 " --> pdb=" O VAL b 283 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'e' and resid 71 through 77 Processing sheet with id= 66, first strand: chain 'f' and resid 10 through 15 removed outlier: 5.885A pdb=" N LYS f 10 " --> pdb=" O GLU f 33 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU f 29 " --> pdb=" O LEU f 14 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ARG f 82 " --> pdb=" O THR f 72 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LYS f 63 " --> pdb=" O ALA f 55 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LYS f 47 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ARG f 48 " --> pdb=" O PHE f 101 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'f' and resid 8 through 14 No H-bonds generated for sheet with id= 67 Processing sheet with id= 68, first strand: chain 'j' and resid 15 through 18 removed outlier: 8.571A pdb=" N SER j 15 " --> pdb=" O HIS j 28 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N HIS j 28 " --> pdb=" O SER j 15 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N THR j 17 " --> pdb=" O SER j 26 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'l' and resid 36 through 39 removed outlier: 7.029A pdb=" N VAL l 44 " --> pdb=" O LEU l 70 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE l 68 " --> pdb=" O TYR l 46 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'l' and resid 95 through 99 removed outlier: 5.057A pdb=" N TYR l 95 " --> pdb=" O GLY l 130 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY l 142 " --> pdb=" O VAL l 133 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'm' and resid 125 through 128 removed outlier: 5.428A pdb=" N SER m 132 " --> pdb=" O TYR m 128 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'm' and resid 170 through 174 removed outlier: 7.922A pdb=" N HIS m 170 " --> pdb=" O ARG m 182 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ARG m 182 " --> pdb=" O HIS m 170 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLY m 172 " --> pdb=" O ILE m 180 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LYS m 178 " --> pdb=" O ASP m 174 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'n' and resid 177 through 182 removed outlier: 3.685A pdb=" N GLY n 185 " --> pdb=" O SER n 182 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'n' and resid 385 through 388 Processing sheet with id= 75, first strand: chain 'o' and resid 118 through 123 removed outlier: 5.212A pdb=" N TYR o 134 " --> pdb=" O ALA o 123 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLY o 91 " --> pdb=" O PHE o 139 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ILE o 92 " --> pdb=" O LEU o 167 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'q' and resid 306 through 309 removed outlier: 3.903A pdb=" N ILE q 271 " --> pdb=" O ILE q 309 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N HIS q 326 " --> pdb=" O ASN q 276 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'q' and resid 398 through 403 removed outlier: 6.376A pdb=" N ASP q 421 " --> pdb=" O MET q 352 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N CYS q 478 " --> pdb=" O ALA q 422 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY q 471 " --> pdb=" O LYS q 548 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS q 545 " --> pdb=" O VAL q 502 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ASN q 498 " --> pdb=" O ILE q 549 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'r' and resid 190 through 195 removed outlier: 3.616A pdb=" N VAL r 191 " --> pdb=" O HIS r 186 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN r 256 " --> pdb=" O THR r 246 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N TYR r 242 " --> pdb=" O LEU r 260 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR r 219 " --> pdb=" O VAL r 245 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 't' and resid 128 through 134 Processing sheet with id= 80, first strand: chain 't' and resid 193 through 198 removed outlier: 5.537A pdb=" N TYR t 193 " --> pdb=" O VAL t 147 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ASN t 172 " --> pdb=" O LEU t 273 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 't' and resid 213 through 217 Processing sheet with id= 82, first strand: chain 'u' and resid 3 through 6 removed outlier: 4.620A pdb=" N SER u 11 " --> pdb=" O CYS u 6 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'u' and resid 18 through 23 removed outlier: 3.801A pdb=" N LYS u 27 " --> pdb=" O ARG u 23 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'x' and resid 120 through 124 removed outlier: 4.696A pdb=" N THR x 99 " --> pdb=" O VAL x 124 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N THR x 145 " --> pdb=" O LEU x 165 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'x' and resid 177 through 180 removed outlier: 4.549A pdb=" N SER x 177 " --> pdb=" O THR x 264 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N THR x 264 " --> pdb=" O SER x 177 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR x 264 " --> pdb=" O SER x 176 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TYR x 172 " --> pdb=" O LYS x 268 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'x' and resid 195 through 200 Processing sheet with id= 87, first strand: chain 'x' and resid 238 through 242 Processing sheet with id= 88, first strand: chain 'y' and resid 1 through 5 Processing sheet with id= 89, first strand: chain 'y' and resid 23 through 27 Processing sheet with id= 90, first strand: chain 'y' and resid 69 through 73 Processing sheet with id= 91, first strand: chain 'y' and resid 114 through 117 Processing sheet with id= 92, first strand: chain 'y' and resid 158 through 162 3539 hydrogen bonds defined for protein. 10509 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1628 hydrogen bonds 2660 hydrogen bond angles 0 basepair planarities 655 basepair parallelities 1104 stacking parallelities Total time for adding SS restraints: 79.24 Time building geometry restraints manager: 42.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 19319 1.33 - 1.45: 43169 1.45 - 1.57: 60940 1.57 - 1.69: 4332 1.69 - 1.81: 361 Bond restraints: 128121 Sorted by residual: bond pdb=" C1' G 1 406 " pdb=" N9 G 1 406 " ideal model delta sigma weight residual 1.465 1.442 0.023 1.50e-02 4.44e+03 2.37e+00 bond pdb=" C1' G 11250 " pdb=" N9 G 11250 " ideal model delta sigma weight residual 1.475 1.454 0.021 1.50e-02 4.44e+03 2.05e+00 bond pdb=" C1' C 13350 " pdb=" N1 C 13350 " ideal model delta sigma weight residual 1.470 1.491 -0.021 1.50e-02 4.44e+03 1.95e+00 bond pdb=" C1' G 11349 " pdb=" N9 G 11349 " ideal model delta sigma weight residual 1.465 1.444 0.021 1.50e-02 4.44e+03 1.95e+00 bond pdb=" N9 G 11349 " pdb=" C4 G 11349 " ideal model delta sigma weight residual 1.375 1.401 -0.026 2.00e-02 2.50e+03 1.66e+00 ... (remaining 128116 not shown) Histogram of bond angle deviations from ideal: 99.76 - 107.08: 14891 107.08 - 114.40: 79195 114.40 - 121.72: 60443 121.72 - 129.04: 26605 129.04 - 136.37: 2267 Bond angle restraints: 183401 Sorted by residual: angle pdb=" O4' G 1 406 " pdb=" C1' G 1 406 " pdb=" N9 G 1 406 " ideal model delta sigma weight residual 108.20 114.94 -6.74 1.50e+00 4.44e-01 2.02e+01 angle pdb=" N VAL G 190 " pdb=" CA VAL G 190 " pdb=" C VAL G 190 " ideal model delta sigma weight residual 113.71 109.69 4.02 9.50e-01 1.11e+00 1.79e+01 angle pdb=" C3' A 11886 " pdb=" O3' A 11886 " pdb=" P A 11887 " ideal model delta sigma weight residual 120.20 125.28 -5.08 1.50e+00 4.44e-01 1.15e+01 angle pdb=" O4' A 11886 " pdb=" C1' A 11886 " pdb=" N9 A 11886 " ideal model delta sigma weight residual 108.20 112.71 -4.51 1.50e+00 4.44e-01 9.03e+00 angle pdb=" CA VAL G 190 " pdb=" C VAL G 190 " pdb=" N ASN G 191 " ideal model delta sigma weight residual 119.87 115.97 3.90 1.34e+00 5.57e-01 8.46e+00 ... (remaining 183396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 75107 35.98 - 71.97: 4991 71.97 - 107.95: 499 107.95 - 143.93: 9 143.93 - 179.92: 25 Dihedral angle restraints: 80631 sinusoidal: 53538 harmonic: 27093 Sorted by residual: dihedral pdb=" O4' U 13306 " pdb=" C1' U 13306 " pdb=" N1 U 13306 " pdb=" C2 U 13306 " ideal model delta sinusoidal sigma weight residual 200.00 21.51 178.49 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 13214 " pdb=" C1' U 13214 " pdb=" N1 U 13214 " pdb=" C2 U 13214 " ideal model delta sinusoidal sigma weight residual 200.00 22.89 177.11 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 1 954 " pdb=" C1' U 1 954 " pdb=" N1 U 1 954 " pdb=" C2 U 1 954 " ideal model delta sinusoidal sigma weight residual 200.00 32.23 167.77 1 1.50e+01 4.44e-03 8.44e+01 ... (remaining 80628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 19442 0.050 - 0.101: 2291 0.101 - 0.151: 515 0.151 - 0.202: 23 0.202 - 0.252: 2 Chirality restraints: 22273 Sorted by residual: chirality pdb=" C1' A 13174 " pdb=" O4' A 13174 " pdb=" C2' A 13174 " pdb=" N9 A 13174 " both_signs ideal model delta sigma weight residual False 2.46 2.21 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C1' A 2 88 " pdb=" O4' A 2 88 " pdb=" C2' A 2 88 " pdb=" N9 A 2 88 " both_signs ideal model delta sigma weight residual False 2.46 2.24 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C1' G 1 406 " pdb=" O4' G 1 406 " pdb=" C2' G 1 406 " pdb=" N9 G 1 406 " both_signs ideal model delta sigma weight residual False 2.44 2.24 0.20 2.00e-01 2.50e+01 9.79e-01 ... (remaining 22270 not shown) Planarity restraints: 15165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 1 406 " -0.076 2.00e-02 2.50e+03 2.89e-02 2.51e+01 pdb=" N9 G 1 406 " 0.032 2.00e-02 2.50e+03 pdb=" C8 G 1 406 " 0.023 2.00e-02 2.50e+03 pdb=" N7 G 1 406 " 0.010 2.00e-02 2.50e+03 pdb=" C5 G 1 406 " 0.013 2.00e-02 2.50e+03 pdb=" C6 G 1 406 " -0.013 2.00e-02 2.50e+03 pdb=" O6 G 1 406 " -0.034 2.00e-02 2.50e+03 pdb=" N1 G 1 406 " -0.011 2.00e-02 2.50e+03 pdb=" C2 G 1 406 " 0.005 2.00e-02 2.50e+03 pdb=" N2 G 1 406 " 0.007 2.00e-02 2.50e+03 pdb=" N3 G 1 406 " 0.021 2.00e-02 2.50e+03 pdb=" C4 G 1 406 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 2 39 " -0.049 2.00e-02 2.50e+03 2.05e-02 1.26e+01 pdb=" N9 G 2 39 " 0.046 2.00e-02 2.50e+03 pdb=" C8 G 2 39 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G 2 39 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G 2 39 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G 2 39 " -0.006 2.00e-02 2.50e+03 pdb=" O6 G 2 39 " -0.016 2.00e-02 2.50e+03 pdb=" N1 G 2 39 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G 2 39 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G 2 39 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G 2 39 " 0.011 2.00e-02 2.50e+03 pdb=" C4 G 2 39 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER e 67 " -0.043 5.00e-02 4.00e+02 6.58e-02 6.92e+00 pdb=" N PRO e 68 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO e 68 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO e 68 " -0.036 5.00e-02 4.00e+02 ... (remaining 15162 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 1714 2.62 - 3.19: 97156 3.19 - 3.76: 209784 3.76 - 4.33: 291359 4.33 - 4.90: 426352 Nonbonded interactions: 1026365 Sorted by model distance: nonbonded pdb=" O3B GDP b 801 " pdb="MG MG b 802 " model vdw 2.053 2.170 nonbonded pdb=" OE1 GLU B 108 " pdb=" ND1 HIS B 109 " model vdw 2.137 2.520 nonbonded pdb=" O2' C 1 675 " pdb=" OP1 U 1 679 " model vdw 2.155 2.440 nonbonded pdb=" O2' C 1 633 " pdb=" O ARG f 21 " model vdw 2.162 2.440 nonbonded pdb=" O2' G 1 591 " pdb=" O ALA E 17 " model vdw 2.179 2.440 ... (remaining 1026360 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 16.080 Check model and map are aligned: 0.600 Set scattering table: 0.700 Process input model: 329.930 Find NCS groups from input model: 3.170 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 363.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 128121 Z= 0.173 Angle : 0.472 12.101 183401 Z= 0.248 Chirality : 0.035 0.252 22273 Planarity : 0.004 0.066 15165 Dihedral : 19.223 179.916 63037 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.30 % Allowed : 3.24 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.09), residues: 9119 helix: 2.38 (0.08), residues: 3826 sheet: 0.50 (0.14), residues: 1397 loop : -0.13 (0.10), residues: 3896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 106 HIS 0.004 0.001 HIS D 440 PHE 0.023 0.001 PHE F 229 TYR 0.021 0.001 TYR C 194 ARG 0.005 0.000 ARG j 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18238 Ramachandran restraints generated. 9119 Oldfield, 0 Emsley, 9119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18238 Ramachandran restraints generated. 9119 Oldfield, 0 Emsley, 9119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1975 residues out of total 8126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1951 time to evaluate : 7.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 729 MET cc_start: 0.0733 (mmm) cc_final: 0.0527 (pp-130) REVERT: 8 298 LYS cc_start: 0.6844 (mtpt) cc_final: 0.6202 (tppp) REVERT: 8 378 GLU cc_start: 0.7715 (tp30) cc_final: 0.7416 (mm-30) REVERT: 8 404 MET cc_start: 0.8054 (mmm) cc_final: 0.7778 (mmp) REVERT: A 50 GLN cc_start: 0.6433 (tp40) cc_final: 0.5917 (mt0) REVERT: A 73 GLN cc_start: 0.7267 (mt0) cc_final: 0.7009 (pt0) REVERT: A 95 GLN cc_start: 0.6138 (mt0) cc_final: 0.5913 (tt0) REVERT: A 160 PHE cc_start: 0.6857 (m-80) cc_final: 0.6619 (m-80) REVERT: A 186 ILE cc_start: 0.6803 (mt) cc_final: 0.6500 (mm) REVERT: B 56 ILE cc_start: 0.7860 (mt) cc_final: 0.7422 (pp) REVERT: B 113 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6739 (mt-10) REVERT: B 354 VAL cc_start: 0.8074 (m) cc_final: 0.7820 (t) REVERT: C 18 ASN cc_start: 0.8230 (m110) cc_final: 0.7583 (t0) REVERT: C 55 LYS cc_start: 0.8087 (mttt) cc_final: 0.7844 (mtmm) REVERT: C 211 GLU cc_start: 0.8220 (tp30) cc_final: 0.7988 (mp0) REVERT: C 265 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7531 (mp0) REVERT: C 304 GLN cc_start: 0.8350 (mt0) cc_final: 0.7808 (mt0) REVERT: C 338 LYS cc_start: 0.7880 (mmtt) cc_final: 0.7419 (mttm) REVERT: D 77 LEU cc_start: 0.5832 (mt) cc_final: 0.5286 (tt) REVERT: D 105 HIS cc_start: 0.5186 (t70) cc_final: 0.4681 (t70) REVERT: D 141 HIS cc_start: 0.5767 (m-70) cc_final: 0.5508 (m-70) REVERT: D 167 MET cc_start: 0.6987 (ttm) cc_final: 0.6502 (ptp) REVERT: D 311 TYR cc_start: 0.7677 (t80) cc_final: 0.7418 (t80) REVERT: D 332 PHE cc_start: 0.6067 (t80) cc_final: 0.5788 (t80) REVERT: D 365 ASP cc_start: 0.5879 (m-30) cc_final: 0.5624 (m-30) REVERT: E 29 LYS cc_start: 0.7882 (ptmm) cc_final: 0.7366 (mttp) REVERT: F 12 GLN cc_start: 0.8305 (tt0) cc_final: 0.8074 (mp10) REVERT: F 24 GLU cc_start: 0.7316 (tt0) cc_final: 0.7085 (mt-10) REVERT: F 25 GLN cc_start: 0.7356 (tt0) cc_final: 0.6830 (mt0) REVERT: F 38 LYS cc_start: 0.8373 (tppp) cc_final: 0.8080 (tttt) REVERT: F 76 TYR cc_start: 0.7700 (t80) cc_final: 0.7447 (t80) REVERT: G 77 GLN cc_start: 0.8739 (pt0) cc_final: 0.8459 (pt0) REVERT: G 89 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7573 (mp0) REVERT: G 96 LYS cc_start: 0.8593 (mtmt) cc_final: 0.8344 (mttp) REVERT: G 100 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7404 (pt0) REVERT: G 111 LYS cc_start: 0.8104 (ttpp) cc_final: 0.7726 (mtmm) REVERT: H 17 THR cc_start: 0.8262 (p) cc_final: 0.7932 (m) REVERT: H 42 ASP cc_start: 0.8520 (m-30) cc_final: 0.8264 (m-30) REVERT: H 59 ASN cc_start: 0.7815 (m-40) cc_final: 0.7564 (t0) REVERT: H 63 LYS cc_start: 0.7936 (ptmm) cc_final: 0.7651 (ttpt) REVERT: H 135 GLU cc_start: 0.7715 (pt0) cc_final: 0.7337 (pt0) REVERT: H 160 ASP cc_start: 0.7571 (m-30) cc_final: 0.7260 (m-30) REVERT: H 161 LEU cc_start: 0.8451 (tp) cc_final: 0.8250 (tp) REVERT: H 163 GLN cc_start: 0.8227 (mt0) cc_final: 0.7753 (mt0) REVERT: H 177 ASP cc_start: 0.7577 (m-30) cc_final: 0.7355 (m-30) REVERT: I 13 ILE cc_start: 0.8358 (mt) cc_final: 0.8145 (pt) REVERT: I 44 LYS cc_start: 0.7190 (pttt) cc_final: 0.6964 (mtmt) REVERT: I 119 ASP cc_start: 0.6641 (t0) cc_final: 0.6264 (OUTLIER) REVERT: I 124 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6912 (tp30) REVERT: I 128 SER cc_start: 0.7158 (m) cc_final: 0.6883 (p) REVERT: I 134 THR cc_start: 0.8097 (p) cc_final: 0.7894 (m) REVERT: I 135 LYS cc_start: 0.7875 (ttpp) cc_final: 0.7530 (ttpm) REVERT: I 174 LYS cc_start: 0.7387 (mttt) cc_final: 0.6859 (mtpp) REVERT: I 218 GLU cc_start: 0.7392 (tt0) cc_final: 0.7144 (tt0) REVERT: I 224 GLN cc_start: 0.7417 (mm-40) cc_final: 0.6931 (mp10) REVERT: I 312 LYS cc_start: 0.8397 (mttt) cc_final: 0.7920 (mptm) REVERT: I 330 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7808 (mp0) REVERT: I 359 ASP cc_start: 0.8133 (t70) cc_final: 0.7825 (t70) REVERT: I 388 ASP cc_start: 0.8098 (t70) cc_final: 0.7788 (t0) REVERT: I 390 LYS cc_start: 0.8568 (tttt) cc_final: 0.8329 (tttm) REVERT: I 414 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6576 (pm20) REVERT: K 69 ASP cc_start: 0.3133 (t0) cc_final: 0.2798 (t0) REVERT: K 108 LYS cc_start: 0.6105 (tppp) cc_final: 0.5570 (mmmm) REVERT: K 111 LYS cc_start: 0.5903 (ttmm) cc_final: 0.5485 (tttp) REVERT: L 23 LYS cc_start: 0.7535 (ptmt) cc_final: 0.7103 (ttpp) REVERT: L 67 ARG cc_start: 0.7535 (ptm-80) cc_final: 0.7119 (ttp80) REVERT: L 110 ASP cc_start: 0.8503 (m-30) cc_final: 0.8248 (m-30) REVERT: M 27 GLN cc_start: 0.7266 (mm-40) cc_final: 0.6938 (tm-30) REVERT: M 50 LYS cc_start: 0.7282 (tptm) cc_final: 0.6996 (tppp) REVERT: M 83 LYS cc_start: 0.7877 (ttmt) cc_final: 0.7421 (mttm) REVERT: N 28 TRP cc_start: 0.7351 (t60) cc_final: 0.7150 (t60) REVERT: N 31 ARG cc_start: 0.7381 (mtm110) cc_final: 0.7035 (mtt-85) REVERT: N 67 ARG cc_start: 0.7610 (mtp85) cc_final: 0.7027 (ttm-80) REVERT: N 127 TYR cc_start: 0.8344 (m-80) cc_final: 0.8029 (m-80) REVERT: N 179 LYS cc_start: 0.7238 (mttt) cc_final: 0.7024 (mttt) REVERT: O 37 ARG cc_start: 0.8871 (mtp180) cc_final: 0.8631 (mtm180) REVERT: O 40 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8072 (mm-30) REVERT: O 46 GLU cc_start: 0.6849 (pt0) cc_final: 0.6569 (pt0) REVERT: O 73 PHE cc_start: 0.6589 (m-80) cc_final: 0.5775 (m-80) REVERT: O 170 LYS cc_start: 0.7706 (mtpt) cc_final: 0.6963 (mmmt) REVERT: O 182 ASN cc_start: 0.7209 (m-40) cc_final: 0.6944 (t0) REVERT: P 111 LYS cc_start: 0.7754 (mtmt) cc_final: 0.7254 (mtpp) REVERT: P 159 LYS cc_start: 0.7565 (mtpt) cc_final: 0.7218 (mttp) REVERT: Q 11 LYS cc_start: 0.8027 (tttt) cc_final: 0.7505 (ttpt) REVERT: Q 50 LYS cc_start: 0.8571 (tttm) cc_final: 0.8330 (ttmt) REVERT: Q 99 THR cc_start: 0.8062 (p) cc_final: 0.7809 (t) REVERT: R 92 GLN cc_start: 0.8774 (mt0) cc_final: 0.8572 (mt0) REVERT: R 129 GLU cc_start: 0.7323 (tt0) cc_final: 0.7047 (tt0) REVERT: R 142 LYS cc_start: 0.8523 (ttpt) cc_final: 0.8162 (ttmt) REVERT: R 150 ARG cc_start: 0.8114 (tpt170) cc_final: 0.7421 (ttp80) REVERT: S 8 GLN cc_start: 0.8265 (tt0) cc_final: 0.7949 (tt0) REVERT: S 27 MET cc_start: 0.8359 (mtp) cc_final: 0.8068 (mtp) REVERT: S 40 ARG cc_start: 0.7887 (mmm160) cc_final: 0.7566 (mtp180) REVERT: S 47 LYS cc_start: 0.6062 (ttpp) cc_final: 0.5426 (mtpm) REVERT: S 88 HIS cc_start: 0.6585 (m-70) cc_final: 0.6066 (m170) REVERT: S 96 ASP cc_start: 0.7748 (t0) cc_final: 0.7494 (t0) REVERT: S 124 LEU cc_start: 0.8413 (mt) cc_final: 0.7998 (mp) REVERT: S 125 LYS cc_start: 0.7770 (ttmt) cc_final: 0.7492 (tttp) REVERT: S 146 LYS cc_start: 0.7470 (tttt) cc_final: 0.7028 (mtmm) REVERT: S 159 SER cc_start: 0.6801 (p) cc_final: 0.6596 (t) REVERT: S 161 LYS cc_start: 0.8012 (mtmt) cc_final: 0.7677 (mtmm) REVERT: V 59 MET cc_start: 0.5467 (mmt) cc_final: 0.4214 (mmt) REVERT: W 152 GLU cc_start: 0.3939 (mp0) cc_final: 0.3393 (pm20) REVERT: W 153 GLU cc_start: 0.3799 (mt-10) cc_final: 0.3014 (tm-30) REVERT: W 165 MET cc_start: 0.5245 (ttt) cc_final: 0.4963 (ttp) REVERT: W 197 VAL cc_start: 0.4684 (t) cc_final: 0.4359 (m) REVERT: Y 38 GLU cc_start: 0.7759 (tt0) cc_final: 0.7389 (tm-30) REVERT: Y 69 LYS cc_start: 0.8327 (mttt) cc_final: 0.7970 (mtpm) REVERT: Z 37 ASN cc_start: 0.1223 (OUTLIER) cc_final: 0.0640 (m-40) REVERT: Z 203 MET cc_start: 0.3981 (mtm) cc_final: 0.3690 (ptp) REVERT: a 85 MET cc_start: 0.0914 (mtm) cc_final: 0.0493 (mpp) REVERT: b 1 MET cc_start: 0.1954 (mtp) cc_final: 0.1419 (mpp) REVERT: b 41 ARG cc_start: 0.5279 (mtp85) cc_final: 0.4393 (tpm170) REVERT: b 166 ASN cc_start: 0.5945 (m-40) cc_final: 0.5179 (m110) REVERT: b 209 PHE cc_start: 0.6385 (p90) cc_final: 0.5457 (p90) REVERT: b 237 MET cc_start: 0.6013 (mmp) cc_final: 0.5740 (mmp) REVERT: b 277 LEU cc_start: 0.5726 (mm) cc_final: 0.5325 (mm) REVERT: b 383 LYS cc_start: 0.5625 (ttpp) cc_final: 0.5184 (ptmt) REVERT: b 386 LYS cc_start: 0.4643 (ptpt) cc_final: 0.4413 (mtmt) REVERT: b 401 ASP cc_start: 0.6496 (m-30) cc_final: 0.6249 (m-30) REVERT: e 62 LYS cc_start: 0.8634 (mmtp) cc_final: 0.8210 (mttm) REVERT: f 33 GLU cc_start: 0.8046 (tt0) cc_final: 0.7843 (tt0) REVERT: f 54 ARG cc_start: 0.8039 (mtp180) cc_final: 0.7750 (mtt-85) REVERT: f 67 MET cc_start: 0.9170 (mtt) cc_final: 0.8876 (mtp) REVERT: f 86 ARG cc_start: 0.8293 (ttt90) cc_final: 0.8038 (tpp80) REVERT: h 17 LEU cc_start: 0.6991 (mt) cc_final: 0.6509 (mt) REVERT: h 61 GLN cc_start: 0.7897 (mt0) cc_final: 0.7623 (mt0) REVERT: h 74 LYS cc_start: 0.7205 (ttmt) cc_final: 0.6832 (ttmm) REVERT: h 102 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7717 (mm-30) REVERT: i 20 MET cc_start: 0.7285 (ptm) cc_final: 0.6769 (ptm) REVERT: i 50 LEU cc_start: 0.8165 (mt) cc_final: 0.7867 (mp) REVERT: i 56 ARG cc_start: 0.6795 (ttm-80) cc_final: 0.6468 (ttt180) REVERT: i 70 ARG cc_start: 0.8182 (mtp85) cc_final: 0.7934 (mtt-85) REVERT: i 71 LYS cc_start: 0.7910 (mtpp) cc_final: 0.7702 (mttp) REVERT: i 79 SER cc_start: 0.8422 (m) cc_final: 0.8199 (t) REVERT: i 86 LYS cc_start: 0.8094 (tppt) cc_final: 0.7809 (tppt) REVERT: i 88 GLU cc_start: 0.7392 (tp30) cc_final: 0.6905 (tp30) REVERT: i 89 GLU cc_start: 0.7893 (tt0) cc_final: 0.7669 (tt0) REVERT: i 90 MET cc_start: 0.8162 (mmp) cc_final: 0.7706 (mmm) REVERT: i 92 ASN cc_start: 0.7509 (m-40) cc_final: 0.7060 (m110) REVERT: l 24 ILE cc_start: 0.1810 (OUTLIER) cc_final: 0.1280 (mt) REVERT: m 242 PRO cc_start: 0.8098 (Cg_exo) cc_final: 0.7791 (Cg_endo) REVERT: n 62 PHE cc_start: 0.2857 (m-10) cc_final: 0.2641 (p90) REVERT: n 363 PHE cc_start: 0.2610 (OUTLIER) cc_final: 0.2267 (m-80) REVERT: n 366 TYR cc_start: 0.3316 (t80) cc_final: 0.3096 (t80) REVERT: o 152 MET cc_start: 0.6895 (mmm) cc_final: 0.6633 (tpt) REVERT: o 194 LYS cc_start: 0.4091 (mppt) cc_final: 0.3841 (pptt) REVERT: q 261 PHE cc_start: 0.1662 (t80) cc_final: 0.1323 (t80) REVERT: q 367 MET cc_start: 0.3096 (mtp) cc_final: 0.2795 (mtm) REVERT: q 392 ARG cc_start: 0.3541 (ttp-170) cc_final: 0.3326 (tpm-80) REVERT: r 110 LYS cc_start: 0.5173 (mtpp) cc_final: 0.4904 (mtpp) REVERT: r 259 LEU cc_start: 0.4450 (mt) cc_final: 0.4184 (mt) REVERT: t 88 ASN cc_start: 0.4503 (t0) cc_final: 0.4115 (t0) REVERT: t 211 ARG cc_start: 0.5925 (mtt-85) cc_final: 0.5682 (mtp85) REVERT: t 221 GLU cc_start: 0.3338 (mt-10) cc_final: 0.1322 (mm-30) REVERT: t 272 LYS cc_start: 0.5864 (mtpt) cc_final: 0.5217 (mmpt) REVERT: t 286 LEU cc_start: 0.7078 (tp) cc_final: 0.6744 (tp) REVERT: v 24 LYS cc_start: 0.8000 (mmtt) cc_final: 0.7661 (mttt) REVERT: v 197 LYS cc_start: 0.7315 (ttmt) cc_final: 0.6741 (ttpp) REVERT: v 203 LYS cc_start: 0.7860 (ptpt) cc_final: 0.7163 (mttt) REVERT: v 221 ARG cc_start: 0.7588 (mtt180) cc_final: 0.7370 (ttm-80) REVERT: w 4 SER cc_start: 0.7870 (t) cc_final: 0.7535 (m) REVERT: w 8 LYS cc_start: 0.8038 (mttt) cc_final: 0.7755 (mtmt) REVERT: w 38 LYS cc_start: 0.7892 (mttt) cc_final: 0.7568 (mtmm) REVERT: w 40 ILE cc_start: 0.7647 (tp) cc_final: 0.7400 (tp) REVERT: w 78 ASP cc_start: 0.6708 (t0) cc_final: 0.6081 (t0) REVERT: w 81 ASP cc_start: 0.7589 (m-30) cc_final: 0.7098 (m-30) REVERT: w 88 LEU cc_start: 0.8010 (mt) cc_final: 0.7503 (mp) REVERT: w 202 MET cc_start: 0.6947 (mtp) cc_final: 0.6691 (mtt) REVERT: w 232 LYS cc_start: 0.8139 (tttt) cc_final: 0.7802 (ttmt) REVERT: x 18 ILE cc_start: 0.8731 (mt) cc_final: 0.8525 (mm) REVERT: x 19 PHE cc_start: 0.8016 (m-80) cc_final: 0.6669 (t80) REVERT: x 23 LYS cc_start: 0.8622 (tttt) cc_final: 0.8366 (ttpm) REVERT: x 35 ARG cc_start: 0.7553 (mmp-170) cc_final: 0.7259 (mmp-170) REVERT: x 48 ARG cc_start: 0.7141 (ttt-90) cc_final: 0.6588 (ttt-90) REVERT: x 50 GLN cc_start: 0.6394 (tp40) cc_final: 0.5984 (mm110) REVERT: x 71 ASN cc_start: 0.7246 (m-40) cc_final: 0.6859 (m110) REVERT: x 79 ASP cc_start: 0.7581 (m-30) cc_final: 0.7289 (m-30) REVERT: x 82 MET cc_start: 0.7511 (ttp) cc_final: 0.7232 (ttt) REVERT: x 141 LYS cc_start: 0.7629 (ttpp) cc_final: 0.7288 (mptt) REVERT: x 142 ARG cc_start: 0.8120 (mtt180) cc_final: 0.7852 (mtt180) REVERT: x 189 ARG cc_start: 0.7616 (mmt180) cc_final: 0.7219 (mmt90) REVERT: x 201 ASN cc_start: 0.7590 (m-40) cc_final: 0.7368 (t0) REVERT: x 213 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.7856 (tp) REVERT: x 285 GLU cc_start: 0.7934 (tt0) cc_final: 0.7687 (tt0) REVERT: x 289 GLU cc_start: 0.7744 (tt0) cc_final: 0.7419 (tp30) REVERT: x 295 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8571 (mp) REVERT: y 8 GLU cc_start: 0.6161 (mm-30) cc_final: 0.5783 (mp0) REVERT: y 11 ASN cc_start: 0.6509 (m-40) cc_final: 0.6250 (m-40) REVERT: y 38 PHE cc_start: 0.7535 (m-80) cc_final: 0.7209 (m-80) outliers start: 24 outliers final: 10 residues processed: 1973 average time/residue: 2.0198 time to fit residues: 5430.6140 Evaluate side-chains 1172 residues out of total 8126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1158 time to evaluate : 7.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 261 ASP Chi-restraints excluded: chain Z residue 37 ASN Chi-restraints excluded: chain a residue 163 LEU Chi-restraints excluded: chain l residue 24 ILE Chi-restraints excluded: chain n residue 363 PHE Chi-restraints excluded: chain n residue 371 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 185 VAL Chi-restraints excluded: chain q residue 319 THR Chi-restraints excluded: chain r residue 223 VAL Chi-restraints excluded: chain v residue 21 ASN Chi-restraints excluded: chain x residue 65 VAL Chi-restraints excluded: chain x residue 213 LEU Chi-restraints excluded: chain x residue 295 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1127 random chunks: chunk 951 optimal weight: 9.9990 chunk 854 optimal weight: 3.9990 chunk 473 optimal weight: 20.0000 chunk 291 optimal weight: 0.0020 chunk 576 optimal weight: 9.9990 chunk 456 optimal weight: 0.0980 chunk 883 optimal weight: 20.0000 chunk 341 optimal weight: 4.9990 chunk 537 optimal weight: 20.0000 chunk 657 optimal weight: 4.9990 chunk 1023 optimal weight: 5.9990 overall best weight: 2.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 444 HIS 3 477 ASN 3 528 ASN 3 612 ASN 3 617 ASN 3 680 GLN 3 681 ASN 3 684 ASN A 29 ASN A 115 GLN A 118 HIS A 165 ASN A 195 HIS A 254 GLN B 163 HIS B 165 GLN ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 HIS C 260 GLN ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN F 225 GLN H 51 GLN I 293 GLN I 370 HIS J 221 GLN ** K 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN N 23 GLN ** P 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 15 HIS Q 73 GLN R 57 ASN S 8 GLN S 122 HIS Z 37 ASN b 272 HIS b 413 ASN h 20 GLN h 104 GLN h 108 GLN i 91 ASN l 117 HIS m 170 HIS ** n 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 20 HIS r 40 GLN t 269 GLN v 10 ASN v 21 ASN v 60 GLN v 210 GLN w 5 ASN x 58 GLN x 164 HIS ** x 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 21 ASN ** y 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 170 GLN y 187 ASN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 128121 Z= 0.184 Angle : 0.522 16.019 183401 Z= 0.266 Chirality : 0.036 0.249 22273 Planarity : 0.004 0.061 15165 Dihedral : 21.416 179.920 43833 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.87 % Allowed : 12.65 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.09), residues: 9119 helix: 2.28 (0.08), residues: 3814 sheet: 0.49 (0.14), residues: 1390 loop : -0.13 (0.10), residues: 3915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP w 54 HIS 0.007 0.001 HIS b 90 PHE 0.035 0.002 PHE D 96 TYR 0.024 0.002 TYR C 194 ARG 0.008 0.001 ARG 3 479 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18238 Ramachandran restraints generated. 9119 Oldfield, 0 Emsley, 9119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18238 Ramachandran restraints generated. 9119 Oldfield, 0 Emsley, 9119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1443 residues out of total 8126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 1210 time to evaluate : 7.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 703 MET cc_start: 0.4762 (OUTLIER) cc_final: 0.4230 (mmp) REVERT: 8 298 LYS cc_start: 0.6857 (mtpt) cc_final: 0.6206 (tppp) REVERT: 8 378 GLU cc_start: 0.7735 (tp30) cc_final: 0.7524 (mm-30) REVERT: A 50 GLN cc_start: 0.6581 (tp40) cc_final: 0.5999 (mt0) REVERT: A 95 GLN cc_start: 0.6174 (mt0) cc_final: 0.5929 (tt0) REVERT: A 125 PHE cc_start: 0.4348 (m-80) cc_final: 0.4131 (m-10) REVERT: B 56 ILE cc_start: 0.7886 (mt) cc_final: 0.7571 (pp) REVERT: B 113 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6744 (mt-10) REVERT: B 287 LYS cc_start: 0.6546 (mmmm) cc_final: 0.6109 (mmmt) REVERT: B 380 MET cc_start: 0.5435 (mmt) cc_final: 0.5198 (tpt) REVERT: C 18 ASN cc_start: 0.8156 (m110) cc_final: 0.7482 (t0) REVERT: C 55 LYS cc_start: 0.8165 (mttt) cc_final: 0.7875 (mtmm) REVERT: C 155 ASP cc_start: 0.7717 (m-30) cc_final: 0.7341 (m-30) REVERT: C 211 GLU cc_start: 0.8207 (tp30) cc_final: 0.7910 (mp0) REVERT: C 226 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8603 (mt-10) REVERT: C 257 LYS cc_start: 0.8654 (ttmm) cc_final: 0.8338 (mtpt) REVERT: C 265 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7397 (mp0) REVERT: C 304 GLN cc_start: 0.8442 (mt0) cc_final: 0.7836 (mt0) REVERT: C 338 LYS cc_start: 0.7733 (mmtt) cc_final: 0.7476 (mttm) REVERT: D 105 HIS cc_start: 0.4977 (t70) cc_final: 0.4601 (t70) REVERT: D 311 TYR cc_start: 0.7697 (t80) cc_final: 0.7488 (t80) REVERT: D 332 PHE cc_start: 0.5985 (t80) cc_final: 0.5677 (t80) REVERT: D 334 GLU cc_start: 0.6432 (OUTLIER) cc_final: 0.6009 (tp30) REVERT: D 365 ASP cc_start: 0.5999 (m-30) cc_final: 0.5703 (m-30) REVERT: E 29 LYS cc_start: 0.7862 (ptmm) cc_final: 0.7464 (tppt) REVERT: E 46 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8405 (ttt-90) REVERT: E 102 ASN cc_start: 0.8007 (p0) cc_final: 0.7771 (p0) REVERT: F 12 GLN cc_start: 0.8342 (tt0) cc_final: 0.8097 (mp10) REVERT: F 24 GLU cc_start: 0.7398 (tt0) cc_final: 0.7128 (mt-10) REVERT: F 25 GLN cc_start: 0.7427 (tt0) cc_final: 0.6886 (mt0) REVERT: F 38 LYS cc_start: 0.8358 (tppp) cc_final: 0.8071 (tttt) REVERT: F 76 TYR cc_start: 0.7744 (t80) cc_final: 0.7491 (t80) REVERT: F 98 LYS cc_start: 0.8291 (ttmm) cc_final: 0.7822 (ttmt) REVERT: F 233 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6887 (mt-10) REVERT: F 234 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8208 (mp0) REVERT: G 77 GLN cc_start: 0.8657 (pt0) cc_final: 0.8442 (pt0) REVERT: G 89 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7602 (mp0) REVERT: G 96 LYS cc_start: 0.8635 (mtmt) cc_final: 0.8329 (mttp) REVERT: G 100 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7249 (pt0) REVERT: G 111 LYS cc_start: 0.8216 (ttpp) cc_final: 0.7720 (mtmm) REVERT: H 17 THR cc_start: 0.8285 (p) cc_final: 0.7932 (m) REVERT: H 42 ASP cc_start: 0.8530 (m-30) cc_final: 0.8284 (m-30) REVERT: H 135 GLU cc_start: 0.7549 (pt0) cc_final: 0.7252 (pt0) REVERT: H 160 ASP cc_start: 0.7697 (m-30) cc_final: 0.7337 (m-30) REVERT: H 161 LEU cc_start: 0.8477 (tp) cc_final: 0.8199 (tp) REVERT: H 163 GLN cc_start: 0.8196 (mt0) cc_final: 0.7841 (mt0) REVERT: H 177 ASP cc_start: 0.7698 (m-30) cc_final: 0.7427 (m-30) REVERT: I 57 GLU cc_start: 0.7728 (tt0) cc_final: 0.7511 (tt0) REVERT: I 75 HIS cc_start: 0.5947 (m-70) cc_final: 0.5553 (m-70) REVERT: I 119 ASP cc_start: 0.6726 (t0) cc_final: 0.6255 (OUTLIER) REVERT: I 128 SER cc_start: 0.7197 (m) cc_final: 0.6894 (p) REVERT: I 134 THR cc_start: 0.8180 (p) cc_final: 0.7937 (m) REVERT: I 135 LYS cc_start: 0.7916 (ttpp) cc_final: 0.7488 (ttpm) REVERT: I 174 LYS cc_start: 0.7444 (mttt) cc_final: 0.6876 (mtpp) REVERT: I 218 GLU cc_start: 0.7521 (tt0) cc_final: 0.7238 (tt0) REVERT: I 224 GLN cc_start: 0.7534 (mm-40) cc_final: 0.7006 (mp10) REVERT: I 312 LYS cc_start: 0.8391 (mttt) cc_final: 0.7958 (mptm) REVERT: I 388 ASP cc_start: 0.8102 (t70) cc_final: 0.7792 (t0) REVERT: I 390 LYS cc_start: 0.8522 (tttt) cc_final: 0.8311 (tttm) REVERT: I 411 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.6904 (p0) REVERT: K 39 LYS cc_start: 0.3646 (ptpt) cc_final: 0.3210 (ttmt) REVERT: K 111 LYS cc_start: 0.5840 (ttmm) cc_final: 0.5496 (tttp) REVERT: K 237 LYS cc_start: 0.5476 (OUTLIER) cc_final: 0.4840 (mtpt) REVERT: K 244 LEU cc_start: 0.6447 (OUTLIER) cc_final: 0.6065 (tt) REVERT: K 250 ASN cc_start: 0.5370 (t0) cc_final: 0.5074 (t0) REVERT: L 23 LYS cc_start: 0.7536 (ptmt) cc_final: 0.7104 (ttpp) REVERT: L 46 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7631 (mp) REVERT: L 110 ASP cc_start: 0.8555 (m-30) cc_final: 0.8319 (m-30) REVERT: M 50 LYS cc_start: 0.7342 (tptm) cc_final: 0.7030 (tppp) REVERT: M 83 LYS cc_start: 0.7881 (ttmt) cc_final: 0.7430 (tttm) REVERT: M 102 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.7593 (tmtp) REVERT: N 8 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7251 (tt0) REVERT: N 28 TRP cc_start: 0.7408 (t60) cc_final: 0.7192 (t60) REVERT: N 31 ARG cc_start: 0.7299 (mtm110) cc_final: 0.6955 (ttt-90) REVERT: N 67 ARG cc_start: 0.7615 (mtp85) cc_final: 0.7028 (ttm-80) REVERT: N 127 TYR cc_start: 0.8296 (m-80) cc_final: 0.7976 (m-80) REVERT: O 73 PHE cc_start: 0.6686 (m-80) cc_final: 0.5930 (m-80) REVERT: O 130 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8199 (ttpm) REVERT: O 170 LYS cc_start: 0.7777 (mtpt) cc_final: 0.7036 (mmmt) REVERT: O 182 ASN cc_start: 0.7226 (m-40) cc_final: 0.6982 (t0) REVERT: P 23 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7921 (mtp-110) REVERT: P 53 ASP cc_start: 0.7485 (OUTLIER) cc_final: 0.7275 (m-30) REVERT: Q 11 LYS cc_start: 0.7869 (tttt) cc_final: 0.7359 (ttpt) REVERT: R 142 LYS cc_start: 0.8587 (ttpt) cc_final: 0.8190 (ttmt) REVERT: R 150 ARG cc_start: 0.8114 (tpt170) cc_final: 0.7459 (ttp80) REVERT: S 3 HIS cc_start: 0.6544 (OUTLIER) cc_final: 0.5779 (t-90) REVERT: S 27 MET cc_start: 0.8356 (mtp) cc_final: 0.8140 (mtp) REVERT: S 40 ARG cc_start: 0.7896 (mmm160) cc_final: 0.7675 (mtp180) REVERT: S 47 LYS cc_start: 0.6056 (ttpp) cc_final: 0.5430 (tttm) REVERT: S 88 HIS cc_start: 0.6778 (m-70) cc_final: 0.6285 (m170) REVERT: S 119 ARG cc_start: 0.6176 (mtm180) cc_final: 0.5479 (mtm-85) REVERT: S 125 LYS cc_start: 0.7750 (ttmt) cc_final: 0.7510 (tttp) REVERT: S 161 LYS cc_start: 0.8121 (mtmt) cc_final: 0.7814 (mtmm) REVERT: V 59 MET cc_start: 0.5572 (mmt) cc_final: 0.4488 (mmt) REVERT: W 152 GLU cc_start: 0.4083 (mp0) cc_final: 0.3600 (pm20) REVERT: W 165 MET cc_start: 0.5568 (ttt) cc_final: 0.5175 (ttp) REVERT: Y 38 GLU cc_start: 0.7783 (tt0) cc_final: 0.7405 (tm-30) REVERT: Y 69 LYS cc_start: 0.8199 (mttt) cc_final: 0.7931 (mtpm) REVERT: Z 203 MET cc_start: 0.3926 (mtm) cc_final: 0.3568 (ptp) REVERT: a 210 MET cc_start: 0.2102 (ttt) cc_final: 0.1899 (tpp) REVERT: b 1 MET cc_start: 0.1743 (mtp) cc_final: 0.1313 (mpp) REVERT: b 41 ARG cc_start: 0.5449 (mtp85) cc_final: 0.4452 (tpm170) REVERT: b 166 ASN cc_start: 0.5570 (m-40) cc_final: 0.5311 (m110) REVERT: b 209 PHE cc_start: 0.6213 (p90) cc_final: 0.5463 (p90) REVERT: b 214 LEU cc_start: 0.6057 (OUTLIER) cc_final: 0.5600 (tt) REVERT: b 383 LYS cc_start: 0.5620 (ttpp) cc_final: 0.5141 (ptmt) REVERT: b 401 ASP cc_start: 0.6685 (m-30) cc_final: 0.6484 (m-30) REVERT: b 434 GLU cc_start: 0.6326 (mt-10) cc_final: 0.5790 (mt-10) REVERT: e 62 LYS cc_start: 0.8641 (mmtp) cc_final: 0.8260 (mttm) REVERT: f 49 ILE cc_start: 0.8594 (mt) cc_final: 0.8369 (tt) REVERT: f 54 ARG cc_start: 0.8093 (mtp180) cc_final: 0.7839 (mtt-85) REVERT: f 67 MET cc_start: 0.9204 (mtt) cc_final: 0.8947 (mtp) REVERT: f 86 ARG cc_start: 0.8436 (ttt90) cc_final: 0.8137 (tpp80) REVERT: h 17 LEU cc_start: 0.7036 (mt) cc_final: 0.6574 (mt) REVERT: h 48 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7209 (ttp-170) REVERT: h 61 GLN cc_start: 0.7943 (mt0) cc_final: 0.7671 (mt0) REVERT: h 102 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7584 (mm-30) REVERT: i 20 MET cc_start: 0.7411 (ptm) cc_final: 0.7096 (ptm) REVERT: i 50 LEU cc_start: 0.8119 (mt) cc_final: 0.7870 (mp) REVERT: i 56 ARG cc_start: 0.6844 (ttm-80) cc_final: 0.6478 (ttp-170) REVERT: i 71 LYS cc_start: 0.8007 (mtpp) cc_final: 0.7707 (mttp) REVERT: i 86 LYS cc_start: 0.8134 (tppt) cc_final: 0.7847 (tppt) REVERT: i 88 GLU cc_start: 0.7508 (tp30) cc_final: 0.7281 (tp30) REVERT: i 89 GLU cc_start: 0.7883 (tt0) cc_final: 0.7646 (tt0) REVERT: i 90 MET cc_start: 0.8101 (mmp) cc_final: 0.7729 (mmm) REVERT: l 121 MET cc_start: 0.2587 (pp-130) cc_final: 0.1586 (mmm) REVERT: l 136 MET cc_start: 0.2193 (OUTLIER) cc_final: 0.1469 (tmm) REVERT: m 251 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7336 (tt0) REVERT: n 62 PHE cc_start: 0.3089 (m-10) cc_final: 0.2701 (p90) REVERT: o 152 MET cc_start: 0.7034 (mmm) cc_final: 0.6729 (tpt) REVERT: o 194 LYS cc_start: 0.4245 (mppt) cc_final: 0.4005 (pptt) REVERT: q 261 PHE cc_start: 0.1643 (t80) cc_final: 0.1363 (t80) REVERT: q 367 MET cc_start: 0.2915 (mtp) cc_final: 0.2681 (mtm) REVERT: r 13 GLN cc_start: 0.6862 (mm-40) cc_final: 0.6443 (mt0) REVERT: r 208 MET cc_start: 0.4803 (OUTLIER) cc_final: 0.4560 (tpt) REVERT: r 259 LEU cc_start: 0.4531 (mt) cc_final: 0.4265 (mt) REVERT: t 64 LYS cc_start: 0.6646 (OUTLIER) cc_final: 0.6082 (tppt) REVERT: t 88 ASN cc_start: 0.4878 (m-40) cc_final: 0.4320 (t0) REVERT: t 210 LYS cc_start: 0.5533 (mmtp) cc_final: 0.5202 (mmtm) REVERT: t 248 GLU cc_start: 0.5407 (mm-30) cc_final: 0.5202 (mp0) REVERT: t 251 ILE cc_start: 0.5536 (mt) cc_final: 0.5114 (mt) REVERT: u 1 MET cc_start: 0.5160 (OUTLIER) cc_final: 0.4857 (mtp) REVERT: v 24 LYS cc_start: 0.7955 (mmtt) cc_final: 0.7641 (mttt) REVERT: v 26 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7558 (tpp-160) REVERT: v 163 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7597 (mt-10) REVERT: v 197 LYS cc_start: 0.7350 (ttmt) cc_final: 0.6746 (ttpp) REVERT: v 203 LYS cc_start: 0.7890 (ptpt) cc_final: 0.7128 (mttt) REVERT: v 221 ARG cc_start: 0.7605 (mtt180) cc_final: 0.7386 (ttm-80) REVERT: w 4 SER cc_start: 0.7861 (t) cc_final: 0.7525 (m) REVERT: w 8 LYS cc_start: 0.8114 (mttt) cc_final: 0.7767 (mtmt) REVERT: w 38 LYS cc_start: 0.7918 (mttt) cc_final: 0.7587 (mtmt) REVERT: w 40 ILE cc_start: 0.7759 (tp) cc_final: 0.7491 (tp) REVERT: w 78 ASP cc_start: 0.6702 (t0) cc_final: 0.6210 (t0) REVERT: w 202 MET cc_start: 0.6761 (mtp) cc_final: 0.6508 (mtt) REVERT: w 232 LYS cc_start: 0.8292 (tttt) cc_final: 0.7832 (ttmt) REVERT: x 23 LYS cc_start: 0.8632 (tttt) cc_final: 0.8373 (ttpm) REVERT: x 48 ARG cc_start: 0.7154 (ttt-90) cc_final: 0.6599 (ttt-90) REVERT: x 50 GLN cc_start: 0.6474 (tp40) cc_final: 0.6052 (mm110) REVERT: x 71 ASN cc_start: 0.7298 (m-40) cc_final: 0.6948 (m110) REVERT: x 79 ASP cc_start: 0.7612 (m-30) cc_final: 0.7329 (m-30) REVERT: x 141 LYS cc_start: 0.7889 (ttpp) cc_final: 0.7471 (mttm) REVERT: x 142 ARG cc_start: 0.8109 (mtt180) cc_final: 0.7695 (mtt180) REVERT: x 189 ARG cc_start: 0.7650 (mmt180) cc_final: 0.7211 (mmt90) REVERT: x 223 ASP cc_start: 0.8262 (m-30) cc_final: 0.8045 (m-30) REVERT: x 275 LYS cc_start: 0.8612 (mttt) cc_final: 0.8409 (mttt) REVERT: x 285 GLU cc_start: 0.7971 (tt0) cc_final: 0.7724 (tt0) REVERT: y 8 GLU cc_start: 0.6202 (mm-30) cc_final: 0.5822 (mp0) REVERT: y 11 ASN cc_start: 0.6370 (m-40) cc_final: 0.6101 (m-40) REVERT: y 62 MET cc_start: 0.5359 (mmm) cc_final: 0.4992 (mmm) outliers start: 233 outliers final: 108 residues processed: 1347 average time/residue: 1.9740 time to fit residues: 3662.6317 Evaluate side-chains 1206 residues out of total 8126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1075 time to evaluate : 7.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 598 CYS Chi-restraints excluded: chain 3 residue 609 LEU Chi-restraints excluded: chain 3 residue 616 SER Chi-restraints excluded: chain 3 residue 703 MET Chi-restraints excluded: chain 8 residue 304 LEU Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 225 SER Chi-restraints excluded: chain I residue 391 THR Chi-restraints excluded: chain I residue 411 ASP Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain K residue 70 ASP Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain K residue 207 ILE Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 237 LYS Chi-restraints excluded: chain K residue 243 THR Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain M residue 12 TRP Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 118 SER Chi-restraints excluded: chain O residue 130 LYS Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain P residue 23 ARG Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain S residue 3 HIS Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 105 THR Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain W residue 100 THR Chi-restraints excluded: chain W residue 102 LEU Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 180 ILE Chi-restraints excluded: chain W residue 230 SER Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 84 MET Chi-restraints excluded: chain Z residue 159 VAL Chi-restraints excluded: chain a residue 163 LEU Chi-restraints excluded: chain a residue 208 SER Chi-restraints excluded: chain b residue 15 ASN Chi-restraints excluded: chain b residue 64 ILE Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 214 LEU Chi-restraints excluded: chain b residue 220 ASP Chi-restraints excluded: chain b residue 273 SER Chi-restraints excluded: chain b residue 308 SER Chi-restraints excluded: chain b residue 331 VAL Chi-restraints excluded: chain e residue 80 LYS Chi-restraints excluded: chain h residue 48 ARG Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain h residue 98 SER Chi-restraints excluded: chain i residue 81 THR Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain l residue 136 MET Chi-restraints excluded: chain m residue 244 ILE Chi-restraints excluded: chain m residue 251 GLU Chi-restraints excluded: chain m residue 254 MET Chi-restraints excluded: chain n residue 162 ILE Chi-restraints excluded: chain n residue 255 ILE Chi-restraints excluded: chain n residue 371 VAL Chi-restraints excluded: chain n residue 393 MET Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 162 LEU Chi-restraints excluded: chain o residue 185 VAL Chi-restraints excluded: chain q residue 303 THR Chi-restraints excluded: chain q residue 477 THR Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain r residue 107 ILE Chi-restraints excluded: chain r residue 208 MET Chi-restraints excluded: chain r residue 223 VAL Chi-restraints excluded: chain t residue 64 LYS Chi-restraints excluded: chain t residue 145 VAL Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 63 LEU Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain v residue 21 ASN Chi-restraints excluded: chain v residue 26 ARG Chi-restraints excluded: chain w residue 97 LYS Chi-restraints excluded: chain w residue 205 ILE Chi-restraints excluded: chain x residue 56 VAL Chi-restraints excluded: chain x residue 65 VAL Chi-restraints excluded: chain x residue 87 SER Chi-restraints excluded: chain y residue 36 SER Chi-restraints excluded: chain y residue 52 THR Chi-restraints excluded: chain y residue 92 VAL Chi-restraints excluded: chain y residue 216 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1127 random chunks: chunk 568 optimal weight: 1.9990 chunk 317 optimal weight: 10.0000 chunk 851 optimal weight: 0.0470 chunk 696 optimal weight: 20.0000 chunk 282 optimal weight: 20.0000 chunk 1025 optimal weight: 40.0000 chunk 1107 optimal weight: 5.9990 chunk 913 optimal weight: 5.9990 chunk 1016 optimal weight: 0.8980 chunk 349 optimal weight: 7.9990 chunk 822 optimal weight: 10.0000 overall best weight: 2.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 444 HIS A 106 ASN A 165 ASN B 319 ASN C 260 GLN ** D 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN F 19 GLN F 225 GLN H 51 GLN H 59 ASN I 63 ASN J 284 HIS K 295 GLN N 23 GLN Q 73 GLN S 122 HIS ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 98 ASN a 57 ASN h 104 GLN ** n 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 160 HIS u 17 HIS v 10 ASN v 210 GLN w 5 ASN x 58 GLN x 62 ASN x 151 ASN ** x 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 187 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 128121 Z= 0.185 Angle : 0.523 14.345 183401 Z= 0.267 Chirality : 0.036 0.298 22273 Planarity : 0.004 0.062 15165 Dihedral : 21.383 179.613 43820 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.63 % Allowed : 13.84 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.09), residues: 9119 helix: 2.19 (0.08), residues: 3802 sheet: 0.44 (0.14), residues: 1360 loop : -0.17 (0.10), residues: 3957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP e 32 HIS 0.025 0.001 HIS C 58 PHE 0.033 0.002 PHE D 96 TYR 0.024 0.002 TYR l 95 ARG 0.006 0.001 ARG 3 479 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18238 Ramachandran restraints generated. 9119 Oldfield, 0 Emsley, 9119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18238 Ramachandran restraints generated. 9119 Oldfield, 0 Emsley, 9119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1465 residues out of total 8126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 295 poor density : 1170 time to evaluate : 7.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 374 GLU cc_start: 0.2723 (OUTLIER) cc_final: 0.2392 (mp0) REVERT: 3 471 ARG cc_start: 0.3468 (ptp-110) cc_final: 0.3110 (ppp80) REVERT: 3 686 GLU cc_start: 0.3756 (OUTLIER) cc_final: 0.3303 (pt0) REVERT: 3 703 MET cc_start: 0.4749 (OUTLIER) cc_final: 0.4192 (mmp) REVERT: 3 729 MET cc_start: 0.1555 (tpp) cc_final: 0.1126 (ptt) REVERT: 8 298 LYS cc_start: 0.6819 (mtpt) cc_final: 0.6181 (tppp) REVERT: 8 302 LYS cc_start: 0.6537 (ttmt) cc_final: 0.6042 (tttp) REVERT: 8 378 GLU cc_start: 0.7789 (tp30) cc_final: 0.7557 (mm-30) REVERT: A 50 GLN cc_start: 0.6781 (tp40) cc_final: 0.6286 (mt0) REVERT: A 160 PHE cc_start: 0.6727 (m-80) cc_final: 0.6509 (m-80) REVERT: A 167 ARG cc_start: 0.6310 (mtt180) cc_final: 0.5936 (mtp180) REVERT: B 56 ILE cc_start: 0.7841 (mt) cc_final: 0.7494 (pp) REVERT: B 113 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6734 (mt-10) REVERT: B 287 LYS cc_start: 0.6585 (mmmm) cc_final: 0.6150 (mmmt) REVERT: C 14 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: C 18 ASN cc_start: 0.8213 (m110) cc_final: 0.7493 (t0) REVERT: C 55 LYS cc_start: 0.7985 (mttt) cc_final: 0.7765 (mtmm) REVERT: C 211 GLU cc_start: 0.8204 (tp30) cc_final: 0.7895 (mp0) REVERT: C 226 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8569 (mt-10) REVERT: C 257 LYS cc_start: 0.8620 (ttmm) cc_final: 0.8273 (mtpt) REVERT: C 265 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7498 (mp0) REVERT: C 304 GLN cc_start: 0.8462 (mt0) cc_final: 0.7828 (mt0) REVERT: C 338 LYS cc_start: 0.7772 (mmtt) cc_final: 0.7509 (mttm) REVERT: D 65 MET cc_start: 0.5499 (mtp) cc_final: 0.5028 (mtp) REVERT: D 311 TYR cc_start: 0.7699 (t80) cc_final: 0.7490 (t80) REVERT: D 332 PHE cc_start: 0.6093 (t80) cc_final: 0.5818 (t80) REVERT: E 29 LYS cc_start: 0.7900 (ptmm) cc_final: 0.7463 (tppt) REVERT: E 46 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8428 (ttt-90) REVERT: E 99 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6200 (mm-30) REVERT: F 12 GLN cc_start: 0.8352 (tt0) cc_final: 0.8106 (mp10) REVERT: F 24 GLU cc_start: 0.7431 (tt0) cc_final: 0.7140 (mt-10) REVERT: F 25 GLN cc_start: 0.7438 (tt0) cc_final: 0.6914 (mt0) REVERT: F 30 ARG cc_start: 0.7836 (ttt-90) cc_final: 0.7628 (tmt90) REVERT: F 38 LYS cc_start: 0.8405 (tppp) cc_final: 0.8087 (tttt) REVERT: F 59 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7287 (tm-30) REVERT: F 76 TYR cc_start: 0.7784 (t80) cc_final: 0.7510 (t80) REVERT: F 98 LYS cc_start: 0.8260 (ttmm) cc_final: 0.7798 (ttmt) REVERT: F 233 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6795 (mt-10) REVERT: F 234 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8078 (mp0) REVERT: G 84 ARG cc_start: 0.7044 (ttp-110) cc_final: 0.6633 (ttp80) REVERT: G 89 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7614 (mp0) REVERT: G 111 LYS cc_start: 0.8251 (ttpp) cc_final: 0.7772 (mtmm) REVERT: H 5 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7971 (tt0) REVERT: H 17 THR cc_start: 0.8323 (p) cc_final: 0.8017 (m) REVERT: H 42 ASP cc_start: 0.8551 (m-30) cc_final: 0.8300 (m-30) REVERT: H 135 GLU cc_start: 0.7765 (pt0) cc_final: 0.7437 (pt0) REVERT: H 160 ASP cc_start: 0.7785 (m-30) cc_final: 0.7380 (m-30) REVERT: H 161 LEU cc_start: 0.8417 (tp) cc_final: 0.8140 (tp) REVERT: H 163 GLN cc_start: 0.8163 (mt0) cc_final: 0.7904 (mt0) REVERT: H 177 ASP cc_start: 0.7716 (m-30) cc_final: 0.7403 (m-30) REVERT: H 180 TYR cc_start: 0.7813 (m-80) cc_final: 0.7303 (m-80) REVERT: I 44 LYS cc_start: 0.7433 (pttt) cc_final: 0.6992 (mmtp) REVERT: I 57 GLU cc_start: 0.7555 (tt0) cc_final: 0.7281 (tt0) REVERT: I 75 HIS cc_start: 0.5884 (m-70) cc_final: 0.5507 (m-70) REVERT: I 119 ASP cc_start: 0.6713 (t0) cc_final: 0.6237 (OUTLIER) REVERT: I 124 GLU cc_start: 0.7246 (tt0) cc_final: 0.6960 (tp30) REVERT: I 128 SER cc_start: 0.7164 (m) cc_final: 0.6852 (p) REVERT: I 135 LYS cc_start: 0.7973 (ttpp) cc_final: 0.7744 (ttpm) REVERT: I 174 LYS cc_start: 0.7410 (mttt) cc_final: 0.6916 (mtpp) REVERT: I 224 GLN cc_start: 0.7729 (mm-40) cc_final: 0.7430 (mm-40) REVERT: I 238 ASP cc_start: 0.8612 (p0) cc_final: 0.8197 (p0) REVERT: I 312 LYS cc_start: 0.8401 (mttt) cc_final: 0.7844 (mptm) REVERT: I 388 ASP cc_start: 0.8092 (t70) cc_final: 0.7741 (t0) REVERT: I 390 LYS cc_start: 0.8545 (tttt) cc_final: 0.8289 (tttm) REVERT: I 411 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.6887 (p0) REVERT: K 39 LYS cc_start: 0.3845 (ptpt) cc_final: 0.3308 (ttmt) REVERT: K 111 LYS cc_start: 0.5939 (ttmm) cc_final: 0.5549 (tttp) REVERT: K 144 LEU cc_start: 0.6228 (mp) cc_final: 0.5889 (mp) REVERT: K 237 LYS cc_start: 0.5538 (ttmt) cc_final: 0.4992 (mtpt) REVERT: K 250 ASN cc_start: 0.5489 (t0) cc_final: 0.5115 (t0) REVERT: L 23 LYS cc_start: 0.7493 (ptmt) cc_final: 0.7091 (ttpp) REVERT: L 110 ASP cc_start: 0.8546 (m-30) cc_final: 0.8320 (m-30) REVERT: M 37 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8245 (tt0) REVERT: M 83 LYS cc_start: 0.7955 (ttmt) cc_final: 0.7480 (mttm) REVERT: M 102 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.7634 (tmtp) REVERT: N 8 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7249 (tt0) REVERT: N 28 TRP cc_start: 0.7474 (t60) cc_final: 0.7268 (t60) REVERT: N 31 ARG cc_start: 0.7355 (mtm110) cc_final: 0.6986 (ttt-90) REVERT: N 67 ARG cc_start: 0.7648 (mtp85) cc_final: 0.7082 (ttm-80) REVERT: N 127 TYR cc_start: 0.8296 (m-80) cc_final: 0.7913 (m-80) REVERT: O 49 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.6613 (ttm170) REVERT: O 73 PHE cc_start: 0.6870 (m-80) cc_final: 0.6132 (m-80) REVERT: O 130 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8224 (ttpm) REVERT: O 170 LYS cc_start: 0.7841 (mtpt) cc_final: 0.7578 (mtpp) REVERT: O 182 ASN cc_start: 0.7220 (m-40) cc_final: 0.6995 (t0) REVERT: P 23 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7988 (mtp-110) REVERT: Q 11 LYS cc_start: 0.7886 (tttt) cc_final: 0.7675 (tptm) REVERT: R 129 GLU cc_start: 0.7499 (tt0) cc_final: 0.7158 (tt0) REVERT: R 142 LYS cc_start: 0.8673 (ttpt) cc_final: 0.8253 (ttmt) REVERT: R 150 ARG cc_start: 0.8090 (tpt170) cc_final: 0.7483 (ttp80) REVERT: S 3 HIS cc_start: 0.6656 (OUTLIER) cc_final: 0.5907 (t-90) REVERT: S 26 ARG cc_start: 0.7081 (mpp80) cc_final: 0.6837 (mpp80) REVERT: S 47 LYS cc_start: 0.6044 (ttpp) cc_final: 0.5442 (tptm) REVERT: S 66 GLU cc_start: 0.8215 (tp30) cc_final: 0.7854 (tp30) REVERT: S 88 HIS cc_start: 0.6804 (m-70) cc_final: 0.6596 (m170) REVERT: S 119 ARG cc_start: 0.6212 (mtm180) cc_final: 0.5380 (mtm-85) REVERT: S 124 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7784 (mp) REVERT: S 125 LYS cc_start: 0.7758 (ttmt) cc_final: 0.7498 (tttp) REVERT: S 161 LYS cc_start: 0.7960 (mtmt) cc_final: 0.7671 (mtmm) REVERT: V 59 MET cc_start: 0.5805 (mmt) cc_final: 0.4428 (mmt) REVERT: W 152 GLU cc_start: 0.3870 (mp0) cc_final: 0.3425 (pm20) REVERT: W 165 MET cc_start: 0.5667 (ttt) cc_final: 0.5254 (ttp) REVERT: Y 38 GLU cc_start: 0.7813 (tt0) cc_final: 0.7451 (tm-30) REVERT: Y 69 LYS cc_start: 0.8274 (mttt) cc_final: 0.7986 (mtpm) REVERT: a 85 MET cc_start: 0.0384 (mtm) cc_final: -0.0604 (pmt) REVERT: a 210 MET cc_start: 0.2119 (ttt) cc_final: 0.1903 (tpp) REVERT: b 1 MET cc_start: 0.1570 (mtp) cc_final: 0.1076 (mpp) REVERT: b 41 ARG cc_start: 0.5453 (mtp85) cc_final: 0.4481 (tpm170) REVERT: b 47 MET cc_start: 0.5570 (OUTLIER) cc_final: 0.5228 (mmt) REVERT: b 111 ASP cc_start: 0.5792 (t0) cc_final: 0.5436 (t70) REVERT: b 166 ASN cc_start: 0.5643 (m-40) cc_final: 0.5293 (m110) REVERT: b 209 PHE cc_start: 0.6138 (p90) cc_final: 0.5402 (p90) REVERT: b 383 LYS cc_start: 0.5626 (ttpp) cc_final: 0.5155 (ptmt) REVERT: e 21 HIS cc_start: 0.8888 (OUTLIER) cc_final: 0.7139 (m-70) REVERT: e 62 LYS cc_start: 0.8599 (mmtp) cc_final: 0.8253 (mttm) REVERT: f 54 ARG cc_start: 0.8154 (mtp180) cc_final: 0.7836 (mtt-85) REVERT: f 67 MET cc_start: 0.9195 (mtt) cc_final: 0.8969 (mtp) REVERT: f 86 ARG cc_start: 0.8441 (ttt90) cc_final: 0.8131 (tpp80) REVERT: h 48 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7119 (ttp-170) REVERT: h 61 GLN cc_start: 0.8096 (mt0) cc_final: 0.7806 (mt0) REVERT: h 102 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7512 (mm-30) REVERT: i 50 LEU cc_start: 0.8171 (mt) cc_final: 0.7933 (mp) REVERT: i 56 ARG cc_start: 0.6863 (ttm-80) cc_final: 0.6597 (ttt180) REVERT: i 71 LYS cc_start: 0.8010 (mtpp) cc_final: 0.7721 (mttp) REVERT: i 86 LYS cc_start: 0.8293 (tppt) cc_final: 0.8028 (tppt) REVERT: i 88 GLU cc_start: 0.7426 (tp30) cc_final: 0.6906 (tp30) REVERT: i 89 GLU cc_start: 0.7857 (tt0) cc_final: 0.7627 (tt0) REVERT: i 90 MET cc_start: 0.8213 (mmp) cc_final: 0.7856 (mmm) REVERT: l 63 LEU cc_start: 0.3808 (tt) cc_final: 0.3548 (mt) REVERT: l 136 MET cc_start: 0.2350 (mpp) cc_final: 0.1758 (tmm) REVERT: m 246 TRP cc_start: 0.7811 (p-90) cc_final: 0.7585 (p-90) REVERT: m 251 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7353 (tt0) REVERT: m 292 LYS cc_start: 0.5888 (OUTLIER) cc_final: 0.5597 (ptpt) REVERT: n 42 TYR cc_start: 0.2647 (OUTLIER) cc_final: 0.1996 (m-80) REVERT: n 62 PHE cc_start: 0.3292 (m-10) cc_final: 0.2784 (p90) REVERT: n 172 LYS cc_start: 0.3977 (OUTLIER) cc_final: 0.3766 (tptt) REVERT: n 364 VAL cc_start: 0.4277 (t) cc_final: 0.4062 (t) REVERT: o 102 PHE cc_start: 0.7098 (OUTLIER) cc_final: 0.6772 (t80) REVERT: o 117 LEU cc_start: 0.6300 (mt) cc_final: 0.5992 (mt) REVERT: o 194 LYS cc_start: 0.4471 (mppt) cc_final: 0.4177 (pptt) REVERT: o 200 MET cc_start: 0.3895 (OUTLIER) cc_final: 0.3652 (pp-130) REVERT: q 230 ARG cc_start: 0.2359 (OUTLIER) cc_final: 0.1680 (tpp80) REVERT: q 261 PHE cc_start: 0.1766 (t80) cc_final: 0.1480 (t80) REVERT: q 367 MET cc_start: 0.2884 (mtp) cc_final: 0.2623 (mtm) REVERT: r 13 GLN cc_start: 0.6927 (mm-40) cc_final: 0.6552 (mt0) REVERT: r 208 MET cc_start: 0.4757 (OUTLIER) cc_final: 0.4496 (tpt) REVERT: t 64 LYS cc_start: 0.6607 (OUTLIER) cc_final: 0.6069 (tppt) REVERT: t 85 LYS cc_start: 0.5590 (tppp) cc_final: 0.5192 (mmmt) REVERT: t 88 ASN cc_start: 0.4762 (m-40) cc_final: 0.4475 (t0) REVERT: t 170 GLU cc_start: 0.5395 (OUTLIER) cc_final: 0.5087 (mm-30) REVERT: t 210 LYS cc_start: 0.5492 (mmtp) cc_final: 0.5252 (mmtm) REVERT: t 248 GLU cc_start: 0.5573 (mm-30) cc_final: 0.5285 (mp0) REVERT: t 251 ILE cc_start: 0.5446 (mt) cc_final: 0.5109 (mt) REVERT: t 272 LYS cc_start: 0.5813 (OUTLIER) cc_final: 0.5604 (tttm) REVERT: v 24 LYS cc_start: 0.7987 (mmtt) cc_final: 0.7666 (mttt) REVERT: v 26 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7487 (tpp-160) REVERT: v 163 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7633 (mt-10) REVERT: v 191 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7245 (tptm) REVERT: v 197 LYS cc_start: 0.7358 (ttmt) cc_final: 0.6714 (ttpp) REVERT: v 203 LYS cc_start: 0.7848 (ptpt) cc_final: 0.7021 (mttt) REVERT: v 221 ARG cc_start: 0.7560 (mtt180) cc_final: 0.7317 (ttm-80) REVERT: w 4 SER cc_start: 0.7821 (t) cc_final: 0.7510 (m) REVERT: w 8 LYS cc_start: 0.8110 (mttt) cc_final: 0.7738 (mtmt) REVERT: w 38 LYS cc_start: 0.7959 (mttt) cc_final: 0.7624 (mtmt) REVERT: w 40 ILE cc_start: 0.7755 (tp) cc_final: 0.7453 (tp) REVERT: w 78 ASP cc_start: 0.6384 (t0) cc_final: 0.5986 (t0) REVERT: w 202 MET cc_start: 0.6926 (mtp) cc_final: 0.6668 (mtt) REVERT: w 204 LYS cc_start: 0.6801 (OUTLIER) cc_final: 0.6545 (tmtt) REVERT: x 23 LYS cc_start: 0.8674 (tttt) cc_final: 0.8407 (ttpm) REVERT: x 48 ARG cc_start: 0.7299 (ttt-90) cc_final: 0.6661 (ttt-90) REVERT: x 50 GLN cc_start: 0.6431 (tp40) cc_final: 0.6012 (mm110) REVERT: x 62 ASN cc_start: 0.7493 (m-40) cc_final: 0.7048 (m110) REVERT: x 71 ASN cc_start: 0.7310 (m-40) cc_final: 0.6974 (m110) REVERT: x 79 ASP cc_start: 0.7562 (m-30) cc_final: 0.7289 (m-30) REVERT: x 142 ARG cc_start: 0.8030 (mtt180) cc_final: 0.7731 (mtt180) REVERT: x 189 ARG cc_start: 0.7634 (mmt180) cc_final: 0.7200 (mmt90) REVERT: x 223 ASP cc_start: 0.8270 (m-30) cc_final: 0.8054 (m-30) REVERT: x 285 GLU cc_start: 0.7989 (tt0) cc_final: 0.7751 (tt0) REVERT: y 8 GLU cc_start: 0.6224 (mm-30) cc_final: 0.5835 (mp0) REVERT: y 11 ASN cc_start: 0.6341 (m-40) cc_final: 0.6031 (m-40) REVERT: y 62 MET cc_start: 0.5534 (mmm) cc_final: 0.5237 (mmm) outliers start: 295 outliers final: 127 residues processed: 1352 average time/residue: 2.0010 time to fit residues: 3723.0708 Evaluate side-chains 1220 residues out of total 8126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1057 time to evaluate : 7.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 374 GLU Chi-restraints excluded: chain 3 residue 448 ILE Chi-restraints excluded: chain 3 residue 598 CYS Chi-restraints excluded: chain 3 residue 609 LEU Chi-restraints excluded: chain 3 residue 616 SER Chi-restraints excluded: chain 3 residue 686 GLU Chi-restraints excluded: chain 3 residue 703 MET Chi-restraints excluded: chain 8 residue 304 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain I residue 55 GLU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 225 SER Chi-restraints excluded: chain I residue 391 THR Chi-restraints excluded: chain I residue 411 ASP Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain J residue 323 LEU Chi-restraints excluded: chain K residue 70 ASP Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 243 THR Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 261 ASP Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain M residue 12 TRP Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 118 SER Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 130 LYS Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain P residue 23 ARG Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain S residue 3 HIS Chi-restraints excluded: chain S residue 105 THR Chi-restraints excluded: chain S residue 124 LEU Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain W residue 100 THR Chi-restraints excluded: chain W residue 102 LEU Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 180 ILE Chi-restraints excluded: chain W residue 197 VAL Chi-restraints excluded: chain W residue 216 LYS Chi-restraints excluded: chain W residue 230 SER Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 84 MET Chi-restraints excluded: chain Z residue 159 VAL Chi-restraints excluded: chain Z residue 342 ILE Chi-restraints excluded: chain Z residue 348 SER Chi-restraints excluded: chain a residue 163 LEU Chi-restraints excluded: chain a residue 208 SER Chi-restraints excluded: chain b residue 15 ASN Chi-restraints excluded: chain b residue 47 MET Chi-restraints excluded: chain b residue 64 ILE Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 220 ASP Chi-restraints excluded: chain b residue 308 SER Chi-restraints excluded: chain b residue 331 VAL Chi-restraints excluded: chain e residue 21 HIS Chi-restraints excluded: chain e residue 80 LYS Chi-restraints excluded: chain h residue 9 LEU Chi-restraints excluded: chain h residue 46 THR Chi-restraints excluded: chain h residue 48 ARG Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain h residue 98 SER Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 81 THR Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain m residue 244 ILE Chi-restraints excluded: chain m residue 251 GLU Chi-restraints excluded: chain m residue 252 GLU Chi-restraints excluded: chain m residue 254 MET Chi-restraints excluded: chain m residue 292 LYS Chi-restraints excluded: chain n residue 42 TYR Chi-restraints excluded: chain n residue 172 LYS Chi-restraints excluded: chain n residue 255 ILE Chi-restraints excluded: chain n residue 371 VAL Chi-restraints excluded: chain n residue 393 MET Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 105 LYS Chi-restraints excluded: chain o residue 162 LEU Chi-restraints excluded: chain o residue 185 VAL Chi-restraints excluded: chain o residue 200 MET Chi-restraints excluded: chain q residue 230 ARG Chi-restraints excluded: chain q residue 303 THR Chi-restraints excluded: chain q residue 477 THR Chi-restraints excluded: chain r residue 21 GLU Chi-restraints excluded: chain r residue 208 MET Chi-restraints excluded: chain r residue 223 VAL Chi-restraints excluded: chain t residue 64 LYS Chi-restraints excluded: chain t residue 170 GLU Chi-restraints excluded: chain t residue 272 LYS Chi-restraints excluded: chain u residue 63 LEU Chi-restraints excluded: chain v residue 21 ASN Chi-restraints excluded: chain v residue 26 ARG Chi-restraints excluded: chain v residue 191 LYS Chi-restraints excluded: chain v residue 207 ILE Chi-restraints excluded: chain w residue 97 LYS Chi-restraints excluded: chain w residue 204 LYS Chi-restraints excluded: chain w residue 205 ILE Chi-restraints excluded: chain x residue 56 VAL Chi-restraints excluded: chain x residue 65 VAL Chi-restraints excluded: chain x residue 87 SER Chi-restraints excluded: chain y residue 36 SER Chi-restraints excluded: chain y residue 51 THR Chi-restraints excluded: chain y residue 52 THR Chi-restraints excluded: chain y residue 92 VAL Chi-restraints excluded: chain y residue 216 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1127 random chunks: chunk 1012 optimal weight: 6.9990 chunk 770 optimal weight: 5.9990 chunk 532 optimal weight: 20.0000 chunk 113 optimal weight: 10.0000 chunk 489 optimal weight: 10.0000 chunk 688 optimal weight: 4.9990 chunk 1028 optimal weight: 2.9990 chunk 1089 optimal weight: 4.9990 chunk 537 optimal weight: 0.3980 chunk 975 optimal weight: 0.0870 chunk 293 optimal weight: 0.8980 overall best weight: 1.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 444 HIS 3 581 GLN A 47 HIS A 95 GLN A 165 ASN B 319 ASN C 58 HIS C 260 GLN ** D 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN I 63 ASN J 284 HIS N 23 GLN Q 73 GLN T 205 GLN ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 98 ASN h 104 GLN m 365 ASN ** n 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 330 GLN u 17 HIS v 10 ASN v 210 GLN w 5 ASN x 62 ASN x 151 ASN ** x 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 187 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 128121 Z= 0.138 Angle : 0.481 13.998 183401 Z= 0.247 Chirality : 0.035 0.280 22273 Planarity : 0.004 0.061 15165 Dihedral : 21.305 179.683 43820 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.89 % Allowed : 15.33 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.09), residues: 9119 helix: 2.29 (0.08), residues: 3805 sheet: 0.42 (0.14), residues: 1379 loop : -0.14 (0.10), residues: 3935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP w 54 HIS 0.004 0.001 HIS l 92 PHE 0.035 0.001 PHE D 96 TYR 0.019 0.001 TYR l 95 ARG 0.009 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18238 Ramachandran restraints generated. 9119 Oldfield, 0 Emsley, 9119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18238 Ramachandran restraints generated. 9119 Oldfield, 0 Emsley, 9119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1360 residues out of total 8126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1125 time to evaluate : 7.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 729 MET cc_start: 0.1347 (tpp) cc_final: 0.1053 (ptt) REVERT: 8 298 LYS cc_start: 0.6864 (mtpt) cc_final: 0.6234 (tppp) REVERT: 8 302 LYS cc_start: 0.6535 (ttmt) cc_final: 0.6030 (tttp) REVERT: 8 332 MET cc_start: 0.6193 (ttm) cc_final: 0.5942 (ttt) REVERT: 8 378 GLU cc_start: 0.7777 (tp30) cc_final: 0.7549 (mm-30) REVERT: A 50 GLN cc_start: 0.6788 (tp40) cc_final: 0.6516 (tt0) REVERT: A 160 PHE cc_start: 0.6688 (m-80) cc_final: 0.6469 (m-80) REVERT: A 167 ARG cc_start: 0.6231 (mtt180) cc_final: 0.5845 (mtp180) REVERT: A 228 GLU cc_start: 0.5872 (tp30) cc_final: 0.5641 (mm-30) REVERT: B 56 ILE cc_start: 0.7753 (mt) cc_final: 0.7405 (pp) REVERT: B 113 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6770 (mt-10) REVERT: C 14 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7711 (mp0) REVERT: C 18 ASN cc_start: 0.8066 (m110) cc_final: 0.7326 (t0) REVERT: C 55 LYS cc_start: 0.8088 (mttt) cc_final: 0.7862 (mtmm) REVERT: C 155 ASP cc_start: 0.7911 (m-30) cc_final: 0.7538 (m-30) REVERT: C 211 GLU cc_start: 0.8218 (tp30) cc_final: 0.7904 (mp0) REVERT: C 226 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8616 (mt-10) REVERT: C 257 LYS cc_start: 0.8603 (ttmm) cc_final: 0.8297 (mtpt) REVERT: C 265 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7481 (mt-10) REVERT: C 304 GLN cc_start: 0.8418 (mt0) cc_final: 0.8107 (mt0) REVERT: C 338 LYS cc_start: 0.7652 (mmtt) cc_final: 0.7445 (mttt) REVERT: D 65 MET cc_start: 0.5519 (mtp) cc_final: 0.5063 (mtp) REVERT: D 105 HIS cc_start: 0.5030 (t70) cc_final: 0.4687 (t-170) REVERT: D 332 PHE cc_start: 0.6029 (t80) cc_final: 0.5778 (t80) REVERT: D 334 GLU cc_start: 0.6321 (OUTLIER) cc_final: 0.5947 (tp30) REVERT: D 365 ASP cc_start: 0.6199 (m-30) cc_final: 0.5869 (m-30) REVERT: D 409 LYS cc_start: 0.3757 (mptp) cc_final: 0.3390 (mptp) REVERT: E 29 LYS cc_start: 0.7980 (ptmm) cc_final: 0.7569 (tppt) REVERT: E 104 GLU cc_start: 0.7367 (mp0) cc_final: 0.7104 (mp0) REVERT: E 146 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7638 (tt) REVERT: F 12 GLN cc_start: 0.8304 (tt0) cc_final: 0.8072 (mp10) REVERT: F 24 GLU cc_start: 0.7408 (tt0) cc_final: 0.7135 (mt-10) REVERT: F 25 GLN cc_start: 0.7427 (tt0) cc_final: 0.6890 (mt0) REVERT: F 38 LYS cc_start: 0.8392 (tppp) cc_final: 0.8079 (tttt) REVERT: F 76 TYR cc_start: 0.7784 (t80) cc_final: 0.7500 (t80) REVERT: F 98 LYS cc_start: 0.8242 (ttmm) cc_final: 0.7753 (ttmt) REVERT: F 233 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6545 (mm-30) REVERT: F 234 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: G 77 GLN cc_start: 0.8603 (pt0) cc_final: 0.8328 (pt0) REVERT: G 84 ARG cc_start: 0.7029 (ttp-110) cc_final: 0.6625 (ttp80) REVERT: G 89 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7589 (mp0) REVERT: G 111 LYS cc_start: 0.8251 (ttpp) cc_final: 0.7750 (mtmm) REVERT: H 5 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7956 (tt0) REVERT: H 17 THR cc_start: 0.8322 (p) cc_final: 0.8031 (m) REVERT: H 42 ASP cc_start: 0.8518 (m-30) cc_final: 0.8269 (m-30) REVERT: H 69 ARG cc_start: 0.7993 (tpp80) cc_final: 0.7659 (tpp80) REVERT: H 135 GLU cc_start: 0.7628 (pt0) cc_final: 0.7300 (pt0) REVERT: H 160 ASP cc_start: 0.7825 (m-30) cc_final: 0.7438 (m-30) REVERT: H 161 LEU cc_start: 0.8414 (tp) cc_final: 0.8117 (tp) REVERT: H 163 GLN cc_start: 0.8167 (mt0) cc_final: 0.7885 (mt0) REVERT: H 177 ASP cc_start: 0.7689 (m-30) cc_final: 0.7386 (m-30) REVERT: I 44 LYS cc_start: 0.7521 (pttt) cc_final: 0.7025 (mmtp) REVERT: I 57 GLU cc_start: 0.7470 (tt0) cc_final: 0.7244 (tt0) REVERT: I 75 HIS cc_start: 0.5928 (m-70) cc_final: 0.5518 (m-70) REVERT: I 119 ASP cc_start: 0.6707 (t0) cc_final: 0.6246 (OUTLIER) REVERT: I 124 GLU cc_start: 0.7313 (tt0) cc_final: 0.6888 (tp30) REVERT: I 128 SER cc_start: 0.7129 (m) cc_final: 0.6790 (p) REVERT: I 135 LYS cc_start: 0.7966 (ttpp) cc_final: 0.7741 (ttpm) REVERT: I 174 LYS cc_start: 0.7411 (mttt) cc_final: 0.6827 (mtpt) REVERT: I 218 GLU cc_start: 0.7504 (tt0) cc_final: 0.7100 (tt0) REVERT: I 224 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7353 (mm-40) REVERT: I 236 LYS cc_start: 0.8146 (pttt) cc_final: 0.7839 (ptpp) REVERT: I 238 ASP cc_start: 0.8597 (p0) cc_final: 0.8376 (p0) REVERT: I 312 LYS cc_start: 0.8399 (mttt) cc_final: 0.7870 (mptm) REVERT: I 330 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7979 (mp0) REVERT: I 388 ASP cc_start: 0.8104 (t70) cc_final: 0.7768 (t0) REVERT: I 411 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.6704 (p0) REVERT: K 50 LYS cc_start: 0.4359 (tppp) cc_final: 0.4114 (tptm) REVERT: K 237 LYS cc_start: 0.5395 (OUTLIER) cc_final: 0.4813 (mtpt) REVERT: L 23 LYS cc_start: 0.7537 (ptmt) cc_final: 0.7132 (ttpp) REVERT: L 46 ILE cc_start: 0.7611 (OUTLIER) cc_final: 0.7367 (mp) REVERT: L 110 ASP cc_start: 0.8507 (m-30) cc_final: 0.8283 (m-30) REVERT: M 27 GLN cc_start: 0.7458 (tm-30) cc_final: 0.6806 (mt0) REVERT: M 83 LYS cc_start: 0.7926 (ttmt) cc_final: 0.7525 (ttmm) REVERT: M 102 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.7571 (tmtp) REVERT: N 31 ARG cc_start: 0.7311 (mtm110) cc_final: 0.6923 (mtt-85) REVERT: N 67 ARG cc_start: 0.7646 (mtp85) cc_final: 0.7089 (ttm-80) REVERT: N 127 TYR cc_start: 0.8229 (m-80) cc_final: 0.7843 (m-80) REVERT: O 73 PHE cc_start: 0.6826 (m-80) cc_final: 0.6097 (m-80) REVERT: O 78 ARG cc_start: 0.8395 (mmp-170) cc_final: 0.8026 (mmp-170) REVERT: O 130 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8249 (ttpm) REVERT: O 170 LYS cc_start: 0.7837 (mtpt) cc_final: 0.7575 (mtpp) REVERT: P 23 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7934 (mtp-110) REVERT: Q 11 LYS cc_start: 0.7849 (tttt) cc_final: 0.7633 (tptm) REVERT: R 142 LYS cc_start: 0.8629 (ttpt) cc_final: 0.8192 (ttmt) REVERT: R 145 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7678 (mp0) REVERT: R 150 ARG cc_start: 0.8088 (tpt170) cc_final: 0.7451 (ttp80) REVERT: S 3 HIS cc_start: 0.6596 (OUTLIER) cc_final: 0.5808 (t-90) REVERT: S 26 ARG cc_start: 0.7100 (mpp80) cc_final: 0.6881 (mpp80) REVERT: S 47 LYS cc_start: 0.6144 (ttpp) cc_final: 0.5523 (tptm) REVERT: S 66 GLU cc_start: 0.8229 (tp30) cc_final: 0.7872 (tp30) REVERT: S 88 HIS cc_start: 0.6849 (m-70) cc_final: 0.6399 (m170) REVERT: S 119 ARG cc_start: 0.6215 (mtm180) cc_final: 0.5629 (mtp-110) REVERT: S 124 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7717 (mp) REVERT: S 125 LYS cc_start: 0.7738 (ttmt) cc_final: 0.7490 (tttp) REVERT: V 59 MET cc_start: 0.5880 (mmt) cc_final: 0.4490 (mmt) REVERT: W 152 GLU cc_start: 0.4189 (mp0) cc_final: 0.3674 (pm20) REVERT: W 165 MET cc_start: 0.5650 (ttt) cc_final: 0.5180 (ttp) REVERT: W 196 ASP cc_start: 0.3702 (OUTLIER) cc_final: 0.2662 (m-30) REVERT: Y 38 GLU cc_start: 0.7636 (tt0) cc_final: 0.7282 (tm-30) REVERT: Y 69 LYS cc_start: 0.8259 (mttt) cc_final: 0.8034 (mtpm) REVERT: Z 67 LEU cc_start: 0.5232 (pt) cc_final: 0.4958 (pt) REVERT: Z 69 ASP cc_start: 0.2628 (OUTLIER) cc_final: 0.2106 (m-30) REVERT: a 85 MET cc_start: 0.0540 (mtm) cc_final: -0.0646 (pmt) REVERT: a 185 MET cc_start: 0.2268 (OUTLIER) cc_final: 0.1481 (pmt) REVERT: b 41 ARG cc_start: 0.5467 (mtp85) cc_final: 0.4457 (tpm170) REVERT: b 111 ASP cc_start: 0.5616 (t0) cc_final: 0.5348 (t70) REVERT: b 145 ASP cc_start: 0.6672 (OUTLIER) cc_final: 0.6405 (m-30) REVERT: b 166 ASN cc_start: 0.5701 (m-40) cc_final: 0.5346 (m110) REVERT: b 209 PHE cc_start: 0.6131 (p90) cc_final: 0.5472 (p90) REVERT: b 275 LYS cc_start: 0.6378 (OUTLIER) cc_final: 0.6110 (pttp) REVERT: b 383 LYS cc_start: 0.5616 (ttpp) cc_final: 0.5150 (ptmt) REVERT: e 62 LYS cc_start: 0.8629 (mmtp) cc_final: 0.8271 (mttm) REVERT: f 54 ARG cc_start: 0.8160 (mtp180) cc_final: 0.7798 (mtt-85) REVERT: f 67 MET cc_start: 0.9210 (mtt) cc_final: 0.8953 (mtp) REVERT: h 61 GLN cc_start: 0.8073 (mt0) cc_final: 0.7803 (mt0) REVERT: h 102 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7489 (mm-30) REVERT: i 50 LEU cc_start: 0.8172 (mt) cc_final: 0.7933 (mp) REVERT: i 56 ARG cc_start: 0.6893 (ttm-80) cc_final: 0.6628 (ttt180) REVERT: i 71 LYS cc_start: 0.7987 (mtpp) cc_final: 0.7692 (mttp) REVERT: i 86 LYS cc_start: 0.8276 (tppt) cc_final: 0.8044 (tppt) REVERT: i 89 GLU cc_start: 0.7818 (tt0) cc_final: 0.7595 (tt0) REVERT: i 90 MET cc_start: 0.8234 (mmp) cc_final: 0.7822 (mmm) REVERT: l 105 MET cc_start: 0.1944 (tmm) cc_final: 0.1681 (ttp) REVERT: l 136 MET cc_start: 0.2421 (OUTLIER) cc_final: 0.1827 (tmm) REVERT: m 246 TRP cc_start: 0.7735 (p-90) cc_final: 0.7496 (p-90) REVERT: m 251 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7298 (tt0) REVERT: m 292 LYS cc_start: 0.5865 (OUTLIER) cc_final: 0.5580 (ptpt) REVERT: n 42 TYR cc_start: 0.2706 (OUTLIER) cc_final: 0.2114 (m-80) REVERT: n 62 PHE cc_start: 0.3271 (m-10) cc_final: 0.2777 (p90) REVERT: o 102 PHE cc_start: 0.7053 (OUTLIER) cc_final: 0.6759 (t80) REVERT: o 117 LEU cc_start: 0.6208 (mt) cc_final: 0.5916 (mt) REVERT: o 194 LYS cc_start: 0.4496 (mppt) cc_final: 0.4201 (pptt) REVERT: q 261 PHE cc_start: 0.1826 (t80) cc_final: 0.1497 (t80) REVERT: q 352 MET cc_start: 0.2295 (ttm) cc_final: 0.2067 (ttm) REVERT: q 367 MET cc_start: 0.2854 (mtp) cc_final: 0.2605 (mtm) REVERT: r 13 GLN cc_start: 0.6931 (mm-40) cc_final: 0.6547 (mt0) REVERT: r 208 MET cc_start: 0.4733 (OUTLIER) cc_final: 0.4478 (tpt) REVERT: t 64 LYS cc_start: 0.6542 (OUTLIER) cc_final: 0.5983 (tppt) REVERT: t 85 LYS cc_start: 0.5535 (tppp) cc_final: 0.5142 (mmmt) REVERT: t 210 LYS cc_start: 0.5664 (mmtp) cc_final: 0.5404 (mmtm) REVERT: t 248 GLU cc_start: 0.5552 (mm-30) cc_final: 0.5235 (mp0) REVERT: u 49 LEU cc_start: 0.6915 (mm) cc_final: 0.6603 (mp) REVERT: u 103 ARG cc_start: 0.6267 (mmt90) cc_final: 0.5961 (mmm-85) REVERT: v 24 LYS cc_start: 0.7931 (mmtt) cc_final: 0.7624 (mttt) REVERT: v 26 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7489 (tpp-160) REVERT: v 197 LYS cc_start: 0.7332 (ttmt) cc_final: 0.6728 (ttpp) REVERT: v 203 LYS cc_start: 0.7838 (ptpt) cc_final: 0.7064 (mttt) REVERT: v 221 ARG cc_start: 0.7533 (mtt180) cc_final: 0.7305 (ttm-80) REVERT: w 8 LYS cc_start: 0.8085 (mttt) cc_final: 0.7730 (mtmt) REVERT: w 38 LYS cc_start: 0.7942 (mttt) cc_final: 0.7609 (mtmt) REVERT: w 40 ILE cc_start: 0.7673 (tp) cc_final: 0.7366 (tp) REVERT: w 78 ASP cc_start: 0.6377 (t0) cc_final: 0.5950 (t0) REVERT: w 202 MET cc_start: 0.6986 (mtp) cc_final: 0.6747 (mtt) REVERT: w 204 LYS cc_start: 0.6753 (OUTLIER) cc_final: 0.6525 (tmtt) REVERT: x 19 PHE cc_start: 0.8042 (m-80) cc_final: 0.6692 (t80) REVERT: x 23 LYS cc_start: 0.8647 (tttt) cc_final: 0.8399 (ttpm) REVERT: x 48 ARG cc_start: 0.7295 (ttt-90) cc_final: 0.6655 (ttt-90) REVERT: x 50 GLN cc_start: 0.6413 (tp40) cc_final: 0.6055 (mm110) REVERT: x 71 ASN cc_start: 0.7316 (m-40) cc_final: 0.6970 (m110) REVERT: x 79 ASP cc_start: 0.7581 (m-30) cc_final: 0.7327 (m-30) REVERT: x 141 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7072 (mttp) REVERT: x 142 ARG cc_start: 0.8063 (mtt180) cc_final: 0.7660 (mtt180) REVERT: x 189 ARG cc_start: 0.7635 (mmt180) cc_final: 0.7227 (mmt90) REVERT: x 213 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.7919 (tp) REVERT: x 275 LYS cc_start: 0.8634 (mttt) cc_final: 0.8381 (mttt) REVERT: x 277 GLU cc_start: 0.7930 (pm20) cc_final: 0.7545 (pm20) REVERT: x 285 GLU cc_start: 0.7960 (tt0) cc_final: 0.7750 (tt0) REVERT: y 8 GLU cc_start: 0.6246 (mm-30) cc_final: 0.5840 (mp0) REVERT: y 11 ASN cc_start: 0.6259 (m-40) cc_final: 0.5993 (m-40) REVERT: y 62 MET cc_start: 0.5479 (mmm) cc_final: 0.5171 (mmm) outliers start: 235 outliers final: 109 residues processed: 1275 average time/residue: 1.9350 time to fit residues: 3410.8293 Evaluate side-chains 1190 residues out of total 8126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1051 time to evaluate : 7.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 598 CYS Chi-restraints excluded: chain 3 residue 609 LEU Chi-restraints excluded: chain 3 residue 616 SER Chi-restraints excluded: chain 8 residue 304 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 225 SER Chi-restraints excluded: chain I residue 330 GLU Chi-restraints excluded: chain I residue 391 THR Chi-restraints excluded: chain I residue 411 ASP Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain J residue 323 LEU Chi-restraints excluded: chain K residue 70 ASP Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain K residue 131 ASP Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 237 LYS Chi-restraints excluded: chain K residue 243 THR Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain M residue 12 TRP Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain O residue 55 HIS Chi-restraints excluded: chain O residue 130 LYS Chi-restraints excluded: chain P residue 23 ARG Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain S residue 3 HIS Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 105 THR Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 124 LEU Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 180 ILE Chi-restraints excluded: chain W residue 196 ASP Chi-restraints excluded: chain W residue 197 VAL Chi-restraints excluded: chain W residue 216 LYS Chi-restraints excluded: chain W residue 230 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 69 ASP Chi-restraints excluded: chain Z residue 124 LEU Chi-restraints excluded: chain Z residue 159 VAL Chi-restraints excluded: chain Z residue 342 ILE Chi-restraints excluded: chain a residue 163 LEU Chi-restraints excluded: chain a residue 185 MET Chi-restraints excluded: chain a residue 208 SER Chi-restraints excluded: chain b residue 15 ASN Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain b residue 145 ASP Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 275 LYS Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 331 VAL Chi-restraints excluded: chain e residue 80 LYS Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain i residue 81 THR Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain l residue 136 MET Chi-restraints excluded: chain m residue 244 ILE Chi-restraints excluded: chain m residue 251 GLU Chi-restraints excluded: chain m residue 292 LYS Chi-restraints excluded: chain n residue 42 TYR Chi-restraints excluded: chain n residue 68 ILE Chi-restraints excluded: chain n residue 162 ILE Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 255 ILE Chi-restraints excluded: chain n residue 371 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 162 LEU Chi-restraints excluded: chain o residue 185 VAL Chi-restraints excluded: chain q residue 303 THR Chi-restraints excluded: chain q residue 366 MET Chi-restraints excluded: chain q residue 477 THR Chi-restraints excluded: chain r residue 21 GLU Chi-restraints excluded: chain r residue 208 MET Chi-restraints excluded: chain r residue 223 VAL Chi-restraints excluded: chain t residue 64 LYS Chi-restraints excluded: chain t residue 286 LEU Chi-restraints excluded: chain t residue 289 ILE Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain v residue 21 ASN Chi-restraints excluded: chain v residue 26 ARG Chi-restraints excluded: chain v residue 207 ILE Chi-restraints excluded: chain w residue 204 LYS Chi-restraints excluded: chain w residue 205 ILE Chi-restraints excluded: chain x residue 56 VAL Chi-restraints excluded: chain x residue 65 VAL Chi-restraints excluded: chain x residue 87 SER Chi-restraints excluded: chain x residue 213 LEU Chi-restraints excluded: chain y residue 52 THR Chi-restraints excluded: chain y residue 92 VAL Chi-restraints excluded: chain y residue 186 VAL Chi-restraints excluded: chain y residue 216 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1127 random chunks: chunk 907 optimal weight: 9.9990 chunk 618 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 chunk 811 optimal weight: 10.0000 chunk 449 optimal weight: 2.9990 chunk 929 optimal weight: 7.9990 chunk 753 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 556 optimal weight: 1.9990 chunk 977 optimal weight: 9.9990 chunk 274 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 444 HIS A 47 HIS A 95 GLN A 165 ASN B 319 ASN C 58 HIS C 260 GLN D 129 GLN ** D 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 GLN G 138 HIS H 51 GLN H 157 ASN I 63 ASN J 284 HIS N 23 GLN O 55 HIS Q 73 GLN ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 104 ASN Y 42 GLN Y 98 ASN h 104 GLN ** n 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 40 GLN u 17 HIS v 10 ASN v 210 GLN w 5 ASN ** x 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 62 ASN x 151 ASN x 201 ASN ** x 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 170 GLN y 187 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 128121 Z= 0.276 Angle : 0.620 16.435 183401 Z= 0.315 Chirality : 0.040 0.322 22273 Planarity : 0.005 0.063 15165 Dihedral : 21.499 178.549 43820 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.95 % Allowed : 15.48 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.09), residues: 9119 helix: 1.82 (0.08), residues: 3812 sheet: 0.37 (0.14), residues: 1347 loop : -0.33 (0.09), residues: 3960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP e 32 HIS 0.009 0.001 HIS b 75 PHE 0.033 0.002 PHE D 96 TYR 0.029 0.002 TYR C 194 ARG 0.010 0.001 ARG Z 334 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18238 Ramachandran restraints generated. 9119 Oldfield, 0 Emsley, 9119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18238 Ramachandran restraints generated. 9119 Oldfield, 0 Emsley, 9119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1457 residues out of total 8126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 1136 time to evaluate : 7.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 547 LEU cc_start: 0.0972 (OUTLIER) cc_final: 0.0702 (mt) REVERT: 3 614 MET cc_start: 0.4728 (tpp) cc_final: 0.4454 (tpp) REVERT: 3 635 TYR cc_start: 0.4558 (OUTLIER) cc_final: 0.4235 (m-10) REVERT: 3 703 MET cc_start: 0.4865 (OUTLIER) cc_final: 0.4287 (mmp) REVERT: 8 298 LYS cc_start: 0.6826 (mtpt) cc_final: 0.6272 (tppp) REVERT: 8 378 GLU cc_start: 0.7756 (tp30) cc_final: 0.7519 (mm-30) REVERT: A 228 GLU cc_start: 0.6232 (tp30) cc_final: 0.6004 (mm-30) REVERT: B 56 ILE cc_start: 0.7999 (mt) cc_final: 0.7672 (pp) REVERT: B 113 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6769 (mt-10) REVERT: B 211 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7096 (tt0) REVERT: B 287 LYS cc_start: 0.6326 (mmmm) cc_final: 0.5768 (mmmt) REVERT: C 18 ASN cc_start: 0.8067 (m110) cc_final: 0.7262 (t0) REVERT: C 55 LYS cc_start: 0.8139 (mttt) cc_final: 0.7911 (mtmm) REVERT: C 73 ARG cc_start: 0.7854 (mpp-170) cc_final: 0.7445 (mmt90) REVERT: C 93 MET cc_start: 0.8962 (pmm) cc_final: 0.8535 (pmm) REVERT: C 211 GLU cc_start: 0.8200 (tp30) cc_final: 0.7875 (mp0) REVERT: C 226 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8637 (mt-10) REVERT: C 257 LYS cc_start: 0.8618 (ttmm) cc_final: 0.8291 (mtpt) REVERT: C 265 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7531 (mt-10) REVERT: C 304 GLN cc_start: 0.8479 (mt0) cc_final: 0.8208 (mt0) REVERT: C 338 LYS cc_start: 0.7660 (mmtt) cc_final: 0.7446 (mttt) REVERT: D 65 MET cc_start: 0.5618 (mtp) cc_final: 0.5107 (mtp) REVERT: D 365 ASP cc_start: 0.6300 (m-30) cc_final: 0.5958 (m-30) REVERT: E 15 VAL cc_start: 0.8826 (m) cc_final: 0.8559 (t) REVERT: E 29 LYS cc_start: 0.7903 (ptmm) cc_final: 0.7590 (ptpp) REVERT: E 46 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8466 (ttt-90) REVERT: E 99 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6233 (mm-30) REVERT: E 108 LYS cc_start: 0.7311 (ptpt) cc_final: 0.7016 (ptpp) REVERT: E 146 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7618 (tt) REVERT: F 12 GLN cc_start: 0.8377 (tt0) cc_final: 0.8005 (mp10) REVERT: F 24 GLU cc_start: 0.7512 (tt0) cc_final: 0.7235 (mt-10) REVERT: F 25 GLN cc_start: 0.7493 (tt0) cc_final: 0.6957 (mt0) REVERT: F 30 ARG cc_start: 0.7893 (ttt-90) cc_final: 0.7547 (tmt90) REVERT: F 38 LYS cc_start: 0.8409 (tppp) cc_final: 0.8043 (tttt) REVERT: F 46 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7894 (tt0) REVERT: F 59 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7385 (tm-30) REVERT: F 76 TYR cc_start: 0.7755 (t80) cc_final: 0.7508 (t80) REVERT: F 233 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6830 (mt-10) REVERT: F 234 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8165 (mp0) REVERT: G 84 ARG cc_start: 0.6990 (ttp-110) cc_final: 0.6598 (ttp80) REVERT: G 111 LYS cc_start: 0.8355 (ttpp) cc_final: 0.7820 (mtmm) REVERT: G 211 LEU cc_start: 0.7602 (tp) cc_final: 0.7374 (tt) REVERT: H 42 ASP cc_start: 0.8595 (m-30) cc_final: 0.8348 (m-30) REVERT: H 157 ASN cc_start: 0.8507 (OUTLIER) cc_final: 0.8251 (t0) REVERT: H 160 ASP cc_start: 0.7744 (m-30) cc_final: 0.7339 (m-30) REVERT: H 161 LEU cc_start: 0.8432 (tp) cc_final: 0.8199 (tp) REVERT: H 163 GLN cc_start: 0.8196 (mt0) cc_final: 0.7939 (mt0) REVERT: H 177 ASP cc_start: 0.7639 (m-30) cc_final: 0.7265 (m-30) REVERT: H 180 TYR cc_start: 0.7866 (m-80) cc_final: 0.7504 (m-80) REVERT: I 44 LYS cc_start: 0.7475 (pttt) cc_final: 0.7233 (pttp) REVERT: I 57 GLU cc_start: 0.7654 (tt0) cc_final: 0.7426 (tt0) REVERT: I 75 HIS cc_start: 0.5877 (m-70) cc_final: 0.5514 (m-70) REVERT: I 119 ASP cc_start: 0.6683 (t0) cc_final: 0.6185 (OUTLIER) REVERT: I 124 GLU cc_start: 0.7342 (tt0) cc_final: 0.6925 (tp30) REVERT: I 128 SER cc_start: 0.7244 (m) cc_final: 0.6935 (p) REVERT: I 135 LYS cc_start: 0.8013 (ttpp) cc_final: 0.7771 (ttpm) REVERT: I 174 LYS cc_start: 0.7439 (mttt) cc_final: 0.6873 (mtpt) REVERT: I 224 GLN cc_start: 0.7623 (mm-40) cc_final: 0.7290 (mm-40) REVERT: I 236 LYS cc_start: 0.8263 (pttt) cc_final: 0.7920 (ptpp) REVERT: I 238 ASP cc_start: 0.8570 (p0) cc_final: 0.8142 (p0) REVERT: I 312 LYS cc_start: 0.8322 (mttt) cc_final: 0.7799 (mptm) REVERT: I 330 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8020 (mp0) REVERT: I 359 ASP cc_start: 0.8044 (t70) cc_final: 0.7817 (t70) REVERT: I 411 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.6769 (p0) REVERT: J 201 MET cc_start: 0.4659 (OUTLIER) cc_final: 0.4317 (mmt) REVERT: K 39 LYS cc_start: 0.3557 (pttt) cc_final: 0.3172 (ttmt) REVERT: K 237 LYS cc_start: 0.5533 (OUTLIER) cc_final: 0.4901 (mtpt) REVERT: L 23 LYS cc_start: 0.7551 (ptmt) cc_final: 0.7134 (ttpp) REVERT: L 110 ASP cc_start: 0.8682 (m-30) cc_final: 0.8462 (m-30) REVERT: M 27 GLN cc_start: 0.7462 (tm-30) cc_final: 0.6870 (mt0) REVERT: M 83 LYS cc_start: 0.7992 (ttmt) cc_final: 0.7512 (tttm) REVERT: M 102 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.7590 (tmtp) REVERT: N 8 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7320 (tt0) REVERT: N 31 ARG cc_start: 0.7445 (mtm110) cc_final: 0.7080 (ttt-90) REVERT: N 67 ARG cc_start: 0.7643 (mtp85) cc_final: 0.7154 (ttm-80) REVERT: N 127 TYR cc_start: 0.8366 (m-80) cc_final: 0.7990 (m-80) REVERT: O 49 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.6564 (ttm110) REVERT: O 73 PHE cc_start: 0.7005 (m-80) cc_final: 0.6225 (m-80) REVERT: O 130 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8175 (ttpm) REVERT: O 170 LYS cc_start: 0.7827 (mtpt) cc_final: 0.7553 (mtpp) REVERT: P 23 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8013 (mtp-110) REVERT: Q 11 LYS cc_start: 0.7893 (tttt) cc_final: 0.7672 (tptm) REVERT: Q 129 VAL cc_start: 0.8724 (OUTLIER) cc_final: 0.8301 (m) REVERT: R 142 LYS cc_start: 0.8740 (ttpt) cc_final: 0.8303 (ttmt) REVERT: R 150 ARG cc_start: 0.8046 (tpt170) cc_final: 0.7448 (ttp80) REVERT: S 3 HIS cc_start: 0.6593 (OUTLIER) cc_final: 0.5879 (t-90) REVERT: S 47 LYS cc_start: 0.6184 (ttpp) cc_final: 0.5529 (tptm) REVERT: S 66 GLU cc_start: 0.8249 (tp30) cc_final: 0.8023 (tp30) REVERT: S 88 HIS cc_start: 0.7043 (m-70) cc_final: 0.6630 (m170) REVERT: S 124 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7663 (mp) REVERT: S 125 LYS cc_start: 0.7722 (ttmt) cc_final: 0.7492 (tttp) REVERT: V 59 MET cc_start: 0.6002 (mmt) cc_final: 0.4726 (mmt) REVERT: W 8 LYS cc_start: 0.5977 (mmtt) cc_final: 0.5511 (tmtt) REVERT: W 52 VAL cc_start: 0.5537 (t) cc_final: 0.5193 (m) REVERT: W 79 GLU cc_start: 0.4225 (pm20) cc_final: 0.3959 (mm-30) REVERT: W 152 GLU cc_start: 0.4453 (mp0) cc_final: 0.3773 (mp0) REVERT: W 153 GLU cc_start: 0.4070 (OUTLIER) cc_final: 0.3313 (pt0) REVERT: W 165 MET cc_start: 0.5804 (ttt) cc_final: 0.5348 (ttp) REVERT: Y 26 GLN cc_start: 0.8206 (mt0) cc_final: 0.7991 (mp10) REVERT: Y 38 GLU cc_start: 0.7676 (tt0) cc_final: 0.7259 (tm-30) REVERT: Y 69 LYS cc_start: 0.8248 (mttt) cc_final: 0.7858 (mtmm) REVERT: Z 66 LYS cc_start: 0.3955 (mmpt) cc_final: 0.3328 (mttt) REVERT: Z 67 LEU cc_start: 0.5214 (pt) cc_final: 0.4802 (tt) REVERT: Z 69 ASP cc_start: 0.2949 (OUTLIER) cc_final: 0.2283 (m-30) REVERT: a 85 MET cc_start: 0.0516 (mtm) cc_final: -0.0662 (pmt) REVERT: a 102 LYS cc_start: 0.1623 (mmmt) cc_final: 0.0969 (mptt) REVERT: a 185 MET cc_start: 0.1956 (ppp) cc_final: 0.1308 (pmt) REVERT: a 210 MET cc_start: 0.3306 (ttt) cc_final: 0.2180 (tpp) REVERT: b 41 ARG cc_start: 0.5568 (mtp85) cc_final: 0.4843 (mpt180) REVERT: b 83 ASP cc_start: 0.5120 (t0) cc_final: 0.4887 (t70) REVERT: b 111 ASP cc_start: 0.5653 (t0) cc_final: 0.5407 (t70) REVERT: b 120 GLN cc_start: 0.4796 (mm-40) cc_final: 0.4439 (pp30) REVERT: b 166 ASN cc_start: 0.5749 (m-40) cc_final: 0.5438 (m110) REVERT: b 172 ILE cc_start: 0.5326 (OUTLIER) cc_final: 0.5040 (mm) REVERT: b 209 PHE cc_start: 0.6329 (p90) cc_final: 0.5718 (p90) REVERT: b 383 LYS cc_start: 0.5755 (ttpp) cc_final: 0.5301 (ptmt) REVERT: e 21 HIS cc_start: 0.8896 (OUTLIER) cc_final: 0.7198 (m-70) REVERT: f 54 ARG cc_start: 0.8268 (mtp180) cc_final: 0.7761 (mtt-85) REVERT: f 67 MET cc_start: 0.9213 (mtt) cc_final: 0.8923 (mtp) REVERT: h 48 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7137 (ttp-170) REVERT: h 61 GLN cc_start: 0.8203 (mt0) cc_final: 0.7933 (mt0) REVERT: h 102 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7461 (mm-30) REVERT: i 46 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.6857 (tp30) REVERT: i 56 ARG cc_start: 0.6831 (ttm-80) cc_final: 0.6583 (ttt180) REVERT: i 71 LYS cc_start: 0.7975 (mtpp) cc_final: 0.7704 (mttp) REVERT: i 86 LYS cc_start: 0.8315 (tppt) cc_final: 0.7996 (tppt) REVERT: i 89 GLU cc_start: 0.7745 (tt0) cc_final: 0.7491 (tt0) REVERT: i 90 MET cc_start: 0.8253 (mmp) cc_final: 0.8009 (mmm) REVERT: l 115 LYS cc_start: 0.2896 (tptt) cc_final: 0.2445 (mtmt) REVERT: l 136 MET cc_start: 0.2607 (OUTLIER) cc_final: 0.2001 (tmm) REVERT: m 138 PRO cc_start: 0.6303 (Cg_endo) cc_final: 0.6039 (Cg_exo) REVERT: m 292 LYS cc_start: 0.5832 (OUTLIER) cc_final: 0.5550 (ptpt) REVERT: n 42 TYR cc_start: 0.2910 (OUTLIER) cc_final: 0.2637 (m-80) REVERT: o 117 LEU cc_start: 0.6169 (mt) cc_final: 0.5807 (mt) REVERT: o 194 LYS cc_start: 0.4316 (mppt) cc_final: 0.3964 (pptt) REVERT: q 230 ARG cc_start: 0.2408 (OUTLIER) cc_final: 0.1352 (tpp80) REVERT: q 261 PHE cc_start: 0.1665 (t80) cc_final: 0.1424 (t80) REVERT: q 291 ASN cc_start: 0.5154 (m-40) cc_final: 0.4831 (m-40) REVERT: q 367 MET cc_start: 0.2880 (mtp) cc_final: 0.2633 (mtm) REVERT: r 13 GLN cc_start: 0.6964 (mm-40) cc_final: 0.6723 (mt0) REVERT: r 208 MET cc_start: 0.4879 (OUTLIER) cc_final: 0.4622 (tpt) REVERT: r 222 GLU cc_start: 0.2780 (tp30) cc_final: 0.2453 (tp30) REVERT: t 64 LYS cc_start: 0.6621 (OUTLIER) cc_final: 0.6330 (tppt) REVERT: t 170 GLU cc_start: 0.4174 (mm-30) cc_final: 0.3934 (mm-30) REVERT: t 248 GLU cc_start: 0.5569 (mm-30) cc_final: 0.5240 (mp0) REVERT: u 1 MET cc_start: 0.5630 (OUTLIER) cc_final: 0.5324 (mtp) REVERT: u 48 LYS cc_start: 0.5231 (mtmt) cc_final: 0.4826 (mmtp) REVERT: u 109 LYS cc_start: 0.3974 (OUTLIER) cc_final: 0.3589 (mptt) REVERT: v 24 LYS cc_start: 0.8004 (mmtt) cc_final: 0.7645 (mttt) REVERT: v 26 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7500 (tpp-160) REVERT: v 191 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7512 (ttpt) REVERT: v 197 LYS cc_start: 0.7303 (ttmt) cc_final: 0.6611 (ttpp) REVERT: v 203 LYS cc_start: 0.7808 (ptpt) cc_final: 0.6925 (mttt) REVERT: v 221 ARG cc_start: 0.7579 (mtt180) cc_final: 0.7352 (mmm-85) REVERT: w 4 SER cc_start: 0.7852 (t) cc_final: 0.7540 (m) REVERT: w 8 LYS cc_start: 0.8217 (mttt) cc_final: 0.7833 (mtmt) REVERT: w 22 LEU cc_start: 0.8819 (tp) cc_final: 0.8562 (tt) REVERT: w 38 LYS cc_start: 0.7847 (mttt) cc_final: 0.7521 (mtmt) REVERT: w 78 ASP cc_start: 0.6690 (t0) cc_final: 0.6234 (t0) REVERT: w 114 ASP cc_start: 0.6889 (m-30) cc_final: 0.6542 (m-30) REVERT: w 143 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7063 (mppt) REVERT: w 204 LYS cc_start: 0.6844 (OUTLIER) cc_final: 0.6598 (tmtt) REVERT: x 23 LYS cc_start: 0.8708 (tttt) cc_final: 0.8321 (ttpp) REVERT: x 48 ARG cc_start: 0.7314 (ttt-90) cc_final: 0.6605 (ttt-90) REVERT: x 50 GLN cc_start: 0.6411 (tp40) cc_final: 0.6085 (mm110) REVERT: x 62 ASN cc_start: 0.7460 (m-40) cc_final: 0.7106 (m110) REVERT: x 71 ASN cc_start: 0.7378 (m-40) cc_final: 0.7039 (m110) REVERT: x 79 ASP cc_start: 0.7584 (m-30) cc_final: 0.7349 (m-30) REVERT: x 142 ARG cc_start: 0.8124 (mtt180) cc_final: 0.7662 (mtt180) REVERT: x 189 ARG cc_start: 0.7738 (mmt180) cc_final: 0.7266 (mmm160) REVERT: x 213 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.7924 (tp) REVERT: x 277 GLU cc_start: 0.8115 (pm20) cc_final: 0.7798 (pm20) REVERT: y 8 GLU cc_start: 0.6329 (mm-30) cc_final: 0.5964 (mp0) REVERT: y 11 ASN cc_start: 0.5982 (m-40) cc_final: 0.5670 (m-40) outliers start: 321 outliers final: 156 residues processed: 1347 average time/residue: 1.9568 time to fit residues: 3644.4977 Evaluate side-chains 1258 residues out of total 8126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1060 time to evaluate : 7.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 354 MET Chi-restraints excluded: chain 3 residue 445 VAL Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 547 LEU Chi-restraints excluded: chain 3 residue 598 CYS Chi-restraints excluded: chain 3 residue 609 LEU Chi-restraints excluded: chain 3 residue 616 SER Chi-restraints excluded: chain 3 residue 635 TYR Chi-restraints excluded: chain 3 residue 703 MET Chi-restraints excluded: chain 8 residue 304 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 211 GLN Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 175 LYS Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain I residue 55 GLU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 225 SER Chi-restraints excluded: chain I residue 330 GLU Chi-restraints excluded: chain I residue 411 ASP Chi-restraints excluded: chain J residue 201 MET Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain J residue 323 LEU Chi-restraints excluded: chain K residue 70 ASP Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain K residue 131 ASP Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 237 LYS Chi-restraints excluded: chain K residue 243 THR Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 261 ASP Chi-restraints excluded: chain M residue 12 TRP Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 104 GLU Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 55 HIS Chi-restraints excluded: chain O residue 130 LYS Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain P residue 23 ARG Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain S residue 3 HIS Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 105 THR Chi-restraints excluded: chain S residue 124 LEU Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain W residue 100 THR Chi-restraints excluded: chain W residue 102 LEU Chi-restraints excluded: chain W residue 153 GLU Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 180 ILE Chi-restraints excluded: chain W residue 196 ASP Chi-restraints excluded: chain W residue 197 VAL Chi-restraints excluded: chain W residue 216 LYS Chi-restraints excluded: chain W residue 230 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 71 SER Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 22 ILE Chi-restraints excluded: chain Z residue 69 ASP Chi-restraints excluded: chain Z residue 84 MET Chi-restraints excluded: chain Z residue 124 LEU Chi-restraints excluded: chain Z residue 159 VAL Chi-restraints excluded: chain Z residue 342 ILE Chi-restraints excluded: chain Z residue 348 SER Chi-restraints excluded: chain a residue 163 LEU Chi-restraints excluded: chain a residue 208 SER Chi-restraints excluded: chain b residue 15 ASN Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 172 ILE Chi-restraints excluded: chain b residue 220 ASP Chi-restraints excluded: chain b residue 273 SER Chi-restraints excluded: chain b residue 308 SER Chi-restraints excluded: chain b residue 309 VAL Chi-restraints excluded: chain b residue 331 VAL Chi-restraints excluded: chain e residue 21 HIS Chi-restraints excluded: chain e residue 80 LYS Chi-restraints excluded: chain h residue 9 LEU Chi-restraints excluded: chain h residue 46 THR Chi-restraints excluded: chain h residue 48 ARG Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain l residue 136 MET Chi-restraints excluded: chain m residue 244 ILE Chi-restraints excluded: chain m residue 252 GLU Chi-restraints excluded: chain m residue 254 MET Chi-restraints excluded: chain m residue 276 VAL Chi-restraints excluded: chain m residue 292 LYS Chi-restraints excluded: chain m residue 384 ILE Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 42 TYR Chi-restraints excluded: chain n residue 120 GLU Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 255 ILE Chi-restraints excluded: chain n residue 371 VAL Chi-restraints excluded: chain n residue 375 ILE Chi-restraints excluded: chain o residue 105 LYS Chi-restraints excluded: chain o residue 162 LEU Chi-restraints excluded: chain o residue 185 VAL Chi-restraints excluded: chain q residue 230 ARG Chi-restraints excluded: chain q residue 303 THR Chi-restraints excluded: chain q residue 477 THR Chi-restraints excluded: chain r residue 208 MET Chi-restraints excluded: chain r residue 223 VAL Chi-restraints excluded: chain t residue 64 LYS Chi-restraints excluded: chain t residue 286 LEU Chi-restraints excluded: chain t residue 289 ILE Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 63 LEU Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain u residue 109 LYS Chi-restraints excluded: chain v residue 21 ASN Chi-restraints excluded: chain v residue 26 ARG Chi-restraints excluded: chain v residue 165 LEU Chi-restraints excluded: chain v residue 191 LYS Chi-restraints excluded: chain w residue 30 THR Chi-restraints excluded: chain w residue 97 LYS Chi-restraints excluded: chain w residue 143 LYS Chi-restraints excluded: chain w residue 204 LYS Chi-restraints excluded: chain w residue 205 ILE Chi-restraints excluded: chain x residue 56 VAL Chi-restraints excluded: chain x residue 65 VAL Chi-restraints excluded: chain x residue 87 SER Chi-restraints excluded: chain x residue 213 LEU Chi-restraints excluded: chain y residue 36 SER Chi-restraints excluded: chain y residue 51 THR Chi-restraints excluded: chain y residue 52 THR Chi-restraints excluded: chain y residue 74 THR Chi-restraints excluded: chain y residue 92 VAL Chi-restraints excluded: chain y residue 186 VAL Chi-restraints excluded: chain y residue 216 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1127 random chunks: chunk 366 optimal weight: 10.0000 chunk 981 optimal weight: 0.7980 chunk 215 optimal weight: 8.9990 chunk 639 optimal weight: 7.9990 chunk 268 optimal weight: 30.0000 chunk 1090 optimal weight: 2.9990 chunk 905 optimal weight: 10.0000 chunk 504 optimal weight: 6.9990 chunk 90 optimal weight: 20.0000 chunk 360 optimal weight: 9.9990 chunk 572 optimal weight: 7.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 444 HIS A 165 ASN C 58 HIS ** D 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN H 50 ASN H 51 GLN H 59 ASN H 157 ASN I 63 ASN J 284 HIS J 320 ASN N 23 GLN Q 73 GLN ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 98 ASN Z 137 ASN Z 184 ASN a 140 HIS b 107 GLN l 166 GLN ** n 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 191 ASN ** n 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 10 ASN v 210 GLN w 5 ASN ** x 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 55 ASN ** x 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 128121 Z= 0.287 Angle : 0.625 17.970 183401 Z= 0.318 Chirality : 0.041 0.331 22273 Planarity : 0.005 0.062 15165 Dihedral : 21.543 177.815 43818 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.17 % Allowed : 16.37 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.09), residues: 9119 helix: 1.61 (0.08), residues: 3802 sheet: 0.26 (0.14), residues: 1353 loop : -0.44 (0.09), residues: 3964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP e 32 HIS 0.035 0.002 HIS O 55 PHE 0.034 0.002 PHE D 96 TYR 0.026 0.002 TYR C 194 ARG 0.009 0.001 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18238 Ramachandran restraints generated. 9119 Oldfield, 0 Emsley, 9119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18238 Ramachandran restraints generated. 9119 Oldfield, 0 Emsley, 9119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1456 residues out of total 8126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 339 poor density : 1117 time to evaluate : 7.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 633 LEU cc_start: 0.4868 (OUTLIER) cc_final: 0.4570 (mp) REVERT: 3 646 LEU cc_start: 0.3113 (OUTLIER) cc_final: 0.2513 (tp) REVERT: 3 703 MET cc_start: 0.4797 (OUTLIER) cc_final: 0.4325 (mmp) REVERT: 8 298 LYS cc_start: 0.6889 (mtpt) cc_final: 0.6361 (tppp) REVERT: 8 378 GLU cc_start: 0.7759 (tp30) cc_final: 0.7474 (mm-30) REVERT: A 49 ILE cc_start: 0.6943 (mt) cc_final: 0.6592 (pt) REVERT: A 167 ARG cc_start: 0.6553 (mtt180) cc_final: 0.6131 (mtp180) REVERT: A 253 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7783 (mttp) REVERT: B 56 ILE cc_start: 0.8041 (mt) cc_final: 0.7667 (pp) REVERT: B 58 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7690 (ptm160) REVERT: B 113 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6788 (mt-10) REVERT: B 211 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7131 (tt0) REVERT: B 287 LYS cc_start: 0.6298 (mmmm) cc_final: 0.5728 (mmmt) REVERT: C 14 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: C 18 ASN cc_start: 0.8043 (m110) cc_final: 0.7239 (t0) REVERT: C 55 LYS cc_start: 0.8156 (mttt) cc_final: 0.7912 (mtmm) REVERT: C 73 ARG cc_start: 0.7895 (mpp-170) cc_final: 0.7471 (mmt90) REVERT: C 93 MET cc_start: 0.8958 (pmm) cc_final: 0.8396 (pmm) REVERT: C 211 GLU cc_start: 0.8198 (tp30) cc_final: 0.7898 (mp0) REVERT: C 226 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8648 (mt-10) REVERT: C 257 LYS cc_start: 0.8615 (ttmm) cc_final: 0.8316 (tttt) REVERT: C 265 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7646 (mm-30) REVERT: C 304 GLN cc_start: 0.8489 (mt0) cc_final: 0.8229 (mt0) REVERT: C 338 LYS cc_start: 0.7643 (mmtt) cc_final: 0.7429 (mttt) REVERT: D 65 MET cc_start: 0.5679 (mtp) cc_final: 0.5232 (mtp) REVERT: D 365 ASP cc_start: 0.6241 (m-30) cc_final: 0.5958 (m-30) REVERT: E 15 VAL cc_start: 0.8821 (m) cc_final: 0.8586 (t) REVERT: E 29 LYS cc_start: 0.7988 (ptmm) cc_final: 0.7671 (ptpp) REVERT: E 46 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8429 (ttt-90) REVERT: E 99 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6213 (mm-30) REVERT: E 108 LYS cc_start: 0.7341 (ptpt) cc_final: 0.7016 (ptpp) REVERT: E 146 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7604 (tt) REVERT: F 12 GLN cc_start: 0.8324 (tt0) cc_final: 0.7996 (mp10) REVERT: F 24 GLU cc_start: 0.7489 (tt0) cc_final: 0.7268 (mt-10) REVERT: F 25 GLN cc_start: 0.7512 (tt0) cc_final: 0.7034 (mt0) REVERT: F 30 ARG cc_start: 0.7924 (ttt-90) cc_final: 0.7574 (tmt90) REVERT: F 38 LYS cc_start: 0.8429 (tppp) cc_final: 0.8044 (tttt) REVERT: F 46 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7883 (tt0) REVERT: F 47 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8399 (mtt180) REVERT: F 59 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7387 (tm-30) REVERT: F 76 TYR cc_start: 0.7672 (t80) cc_final: 0.7424 (t80) REVERT: F 233 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6815 (mt-10) REVERT: F 234 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8051 (mp0) REVERT: G 84 ARG cc_start: 0.7046 (ttp-110) cc_final: 0.6627 (ttp80) REVERT: G 111 LYS cc_start: 0.8351 (ttpp) cc_final: 0.7813 (mtmm) REVERT: G 211 LEU cc_start: 0.7597 (tp) cc_final: 0.7378 (tt) REVERT: H 42 ASP cc_start: 0.8610 (m-30) cc_final: 0.8384 (m-30) REVERT: H 160 ASP cc_start: 0.7559 (m-30) cc_final: 0.7196 (m-30) REVERT: H 177 ASP cc_start: 0.7651 (m-30) cc_final: 0.7303 (m-30) REVERT: I 1 MET cc_start: 0.6908 (ttm) cc_final: 0.6687 (ttm) REVERT: I 15 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7784 (tt0) REVERT: I 44 LYS cc_start: 0.7421 (pttt) cc_final: 0.7185 (pttp) REVERT: I 75 HIS cc_start: 0.5811 (m-70) cc_final: 0.5465 (m-70) REVERT: I 119 ASP cc_start: 0.6682 (t0) cc_final: 0.6191 (OUTLIER) REVERT: I 124 GLU cc_start: 0.7320 (tt0) cc_final: 0.6912 (tp30) REVERT: I 128 SER cc_start: 0.7290 (m) cc_final: 0.6948 (p) REVERT: I 135 LYS cc_start: 0.8096 (ttpp) cc_final: 0.7865 (ttpm) REVERT: I 172 ASP cc_start: 0.5531 (OUTLIER) cc_final: 0.5235 (p0) REVERT: I 174 LYS cc_start: 0.7431 (mttt) cc_final: 0.6865 (mtpt) REVERT: I 218 GLU cc_start: 0.7308 (tt0) cc_final: 0.6902 (tt0) REVERT: I 224 GLN cc_start: 0.7558 (mm-40) cc_final: 0.7299 (mm-40) REVERT: I 236 LYS cc_start: 0.8284 (pttt) cc_final: 0.7935 (ptpp) REVERT: I 312 LYS cc_start: 0.8281 (mttt) cc_final: 0.7744 (mptm) REVERT: I 330 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8011 (mp0) REVERT: I 359 ASP cc_start: 0.8156 (t70) cc_final: 0.7884 (t70) REVERT: I 411 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.6729 (p0) REVERT: K 237 LYS cc_start: 0.5470 (OUTLIER) cc_final: 0.4812 (mtpt) REVERT: K 244 LEU cc_start: 0.6677 (OUTLIER) cc_final: 0.6107 (tt) REVERT: K 254 LEU cc_start: 0.5229 (mp) cc_final: 0.4612 (mt) REVERT: L 23 LYS cc_start: 0.7543 (ptmt) cc_final: 0.7129 (ttpp) REVERT: L 67 ARG cc_start: 0.7722 (ptm-80) cc_final: 0.7455 (ptm-80) REVERT: M 27 GLN cc_start: 0.7423 (tm-30) cc_final: 0.6924 (mt0) REVERT: M 83 LYS cc_start: 0.7992 (ttmt) cc_final: 0.7505 (tttm) REVERT: M 102 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.7622 (tmtp) REVERT: N 8 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7329 (tt0) REVERT: N 31 ARG cc_start: 0.7552 (mtm110) cc_final: 0.7120 (ttt-90) REVERT: N 67 ARG cc_start: 0.7630 (mtp85) cc_final: 0.7131 (ttm-80) REVERT: N 127 TYR cc_start: 0.8340 (m-80) cc_final: 0.7958 (m-80) REVERT: O 49 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6488 (ttm110) REVERT: O 73 PHE cc_start: 0.7057 (m-80) cc_final: 0.6284 (m-80) REVERT: O 130 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8197 (ttpm) REVERT: O 170 LYS cc_start: 0.7833 (mtpt) cc_final: 0.7556 (mtpp) REVERT: O 177 LYS cc_start: 0.6515 (mtpt) cc_final: 0.6276 (ttmt) REVERT: P 23 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8011 (mtp-110) REVERT: Q 11 LYS cc_start: 0.7875 (tttt) cc_final: 0.7660 (tptm) REVERT: R 142 LYS cc_start: 0.8720 (ttpt) cc_final: 0.8297 (ttmt) REVERT: R 150 ARG cc_start: 0.8119 (tpt170) cc_final: 0.7521 (ttp80) REVERT: S 3 HIS cc_start: 0.6470 (OUTLIER) cc_final: 0.5752 (t-90) REVERT: S 6 GLU cc_start: 0.8429 (tp30) cc_final: 0.8185 (tp30) REVERT: S 47 LYS cc_start: 0.6138 (ttpp) cc_final: 0.5460 (tptm) REVERT: S 57 GLU cc_start: 0.7173 (tt0) cc_final: 0.6838 (pt0) REVERT: S 88 HIS cc_start: 0.6946 (m-70) cc_final: 0.6582 (m170) REVERT: S 124 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7746 (mp) REVERT: S 125 LYS cc_start: 0.7696 (ttmt) cc_final: 0.7477 (tttp) REVERT: V 59 MET cc_start: 0.5946 (mmt) cc_final: 0.4699 (mmt) REVERT: V 83 LYS cc_start: 0.6584 (tttt) cc_final: 0.5946 (mppt) REVERT: W 8 LYS cc_start: 0.5989 (mmtt) cc_final: 0.5531 (tmtt) REVERT: W 52 VAL cc_start: 0.5942 (t) cc_final: 0.5578 (m) REVERT: W 79 GLU cc_start: 0.4310 (pm20) cc_final: 0.3993 (mm-30) REVERT: W 152 GLU cc_start: 0.4254 (mp0) cc_final: 0.3805 (mp0) REVERT: W 153 GLU cc_start: 0.3969 (OUTLIER) cc_final: 0.3118 (pt0) REVERT: Y 38 GLU cc_start: 0.7806 (tt0) cc_final: 0.7387 (tm-30) REVERT: Y 69 LYS cc_start: 0.8223 (mttt) cc_final: 0.7874 (mtmm) REVERT: Y 115 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.8134 (tpt-90) REVERT: Z 67 LEU cc_start: 0.5244 (pt) cc_final: 0.4848 (tt) REVERT: Z 69 ASP cc_start: 0.3004 (OUTLIER) cc_final: 0.2285 (m-30) REVERT: Z 187 LYS cc_start: 0.5295 (OUTLIER) cc_final: 0.4590 (tppp) REVERT: a 102 LYS cc_start: 0.1686 (mmmt) cc_final: 0.1241 (pttt) REVERT: a 185 MET cc_start: 0.2052 (OUTLIER) cc_final: 0.1291 (pmt) REVERT: a 210 MET cc_start: 0.3459 (ttt) cc_final: 0.2173 (tpp) REVERT: b 41 ARG cc_start: 0.5498 (mtp85) cc_final: 0.4854 (mpt180) REVERT: b 83 ASP cc_start: 0.5097 (t0) cc_final: 0.4838 (t70) REVERT: b 111 ASP cc_start: 0.5575 (t0) cc_final: 0.5341 (t70) REVERT: b 166 ASN cc_start: 0.5721 (m-40) cc_final: 0.5453 (m110) REVERT: b 209 PHE cc_start: 0.6316 (p90) cc_final: 0.5769 (p90) REVERT: b 220 ASP cc_start: 0.6090 (OUTLIER) cc_final: 0.5840 (p0) REVERT: b 247 ARG cc_start: 0.6101 (OUTLIER) cc_final: 0.5704 (ptm-80) REVERT: b 275 LYS cc_start: 0.6321 (OUTLIER) cc_final: 0.6013 (pttp) REVERT: b 383 LYS cc_start: 0.5728 (ttpp) cc_final: 0.5249 (ptmt) REVERT: b 425 ASP cc_start: 0.4399 (OUTLIER) cc_final: 0.3736 (m-30) REVERT: e 16 LYS cc_start: 0.8431 (mmtt) cc_final: 0.8126 (mmmm) REVERT: e 21 HIS cc_start: 0.8883 (OUTLIER) cc_final: 0.7215 (m-70) REVERT: f 21 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.6880 (mtt90) REVERT: f 54 ARG cc_start: 0.8254 (mtp180) cc_final: 0.7762 (mtt-85) REVERT: f 67 MET cc_start: 0.9210 (mtt) cc_final: 0.8933 (mtp) REVERT: h 48 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7078 (ttp-170) REVERT: h 61 GLN cc_start: 0.8182 (mt0) cc_final: 0.7908 (mt0) REVERT: h 102 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7483 (mm-30) REVERT: i 46 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.6865 (tp30) REVERT: i 56 ARG cc_start: 0.7059 (ttm-80) cc_final: 0.6568 (ttt180) REVERT: i 71 LYS cc_start: 0.7889 (mtpp) cc_final: 0.7627 (mttp) REVERT: i 86 LYS cc_start: 0.8303 (tppt) cc_final: 0.7978 (tppt) REVERT: i 89 GLU cc_start: 0.7747 (tt0) cc_final: 0.7500 (tt0) REVERT: i 90 MET cc_start: 0.8267 (mmp) cc_final: 0.8016 (mmm) REVERT: l 53 LYS cc_start: 0.2258 (mttt) cc_final: 0.1676 (tmmt) REVERT: l 105 MET cc_start: 0.1951 (tmm) cc_final: 0.1732 (ttp) REVERT: l 115 LYS cc_start: 0.2955 (tptt) cc_final: 0.2560 (mtmt) REVERT: l 136 MET cc_start: 0.2603 (OUTLIER) cc_final: 0.2034 (tmm) REVERT: m 138 PRO cc_start: 0.6557 (Cg_endo) cc_final: 0.6203 (Cg_exo) REVERT: m 245 ASP cc_start: 0.7875 (p0) cc_final: 0.7614 (p0) REVERT: m 292 LYS cc_start: 0.5862 (OUTLIER) cc_final: 0.5573 (ptpt) REVERT: n 42 TYR cc_start: 0.2998 (OUTLIER) cc_final: 0.2727 (m-80) REVERT: n 363 PHE cc_start: 0.3369 (OUTLIER) cc_final: 0.2922 (m-80) REVERT: o 194 LYS cc_start: 0.4328 (mppt) cc_final: 0.4080 (pptt) REVERT: q 230 ARG cc_start: 0.2616 (OUTLIER) cc_final: 0.1726 (tpp80) REVERT: q 261 PHE cc_start: 0.1754 (t80) cc_final: 0.1491 (t80) REVERT: q 291 ASN cc_start: 0.5335 (m-40) cc_final: 0.4985 (m-40) REVERT: q 346 ASN cc_start: 0.3890 (OUTLIER) cc_final: 0.3081 (p0) REVERT: r 13 GLN cc_start: 0.7067 (mm-40) cc_final: 0.6826 (mt0) REVERT: r 133 MET cc_start: 0.3797 (ttt) cc_final: 0.3522 (ttm) REVERT: r 208 MET cc_start: 0.4829 (OUTLIER) cc_final: 0.4590 (tpt) REVERT: r 222 GLU cc_start: 0.3003 (tp30) cc_final: 0.2541 (tp30) REVERT: t 64 LYS cc_start: 0.6617 (OUTLIER) cc_final: 0.6324 (tppt) REVERT: t 248 GLU cc_start: 0.5561 (mm-30) cc_final: 0.5123 (mp0) REVERT: u 48 LYS cc_start: 0.5293 (mtmt) cc_final: 0.4842 (mmtp) REVERT: u 109 LYS cc_start: 0.4064 (OUTLIER) cc_final: 0.3660 (mptt) REVERT: v 24 LYS cc_start: 0.8011 (mmtt) cc_final: 0.7661 (mttt) REVERT: v 26 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7446 (tpp-160) REVERT: v 186 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7655 (tt0) REVERT: v 197 LYS cc_start: 0.7537 (ttmt) cc_final: 0.6805 (ttpp) REVERT: v 203 LYS cc_start: 0.7848 (ptpt) cc_final: 0.6953 (mttt) REVERT: v 221 ARG cc_start: 0.7623 (mtt180) cc_final: 0.7270 (ttm-80) REVERT: w 4 SER cc_start: 0.7868 (t) cc_final: 0.7550 (m) REVERT: w 8 LYS cc_start: 0.8229 (mttt) cc_final: 0.7849 (mtmt) REVERT: w 22 LEU cc_start: 0.8818 (tp) cc_final: 0.8566 (tt) REVERT: w 37 ASN cc_start: 0.8087 (OUTLIER) cc_final: 0.7810 (m110) REVERT: w 38 LYS cc_start: 0.7892 (mttt) cc_final: 0.7602 (mtmm) REVERT: w 78 ASP cc_start: 0.6684 (t0) cc_final: 0.6224 (t0) REVERT: w 114 ASP cc_start: 0.6886 (m-30) cc_final: 0.6545 (m-30) REVERT: w 143 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7119 (mppt) REVERT: w 204 LYS cc_start: 0.6862 (OUTLIER) cc_final: 0.6582 (tmtt) REVERT: x 23 LYS cc_start: 0.8745 (tttt) cc_final: 0.8450 (ttpm) REVERT: x 48 ARG cc_start: 0.7301 (ttt-90) cc_final: 0.6584 (ttt-90) REVERT: x 50 GLN cc_start: 0.6430 (tp40) cc_final: 0.6074 (mm110) REVERT: x 62 ASN cc_start: 0.7546 (m-40) cc_final: 0.7172 (m110) REVERT: x 71 ASN cc_start: 0.7415 (m-40) cc_final: 0.7050 (m110) REVERT: x 79 ASP cc_start: 0.7600 (m-30) cc_final: 0.7359 (m-30) REVERT: x 142 ARG cc_start: 0.8098 (mtt180) cc_final: 0.7597 (mtt90) REVERT: x 189 ARG cc_start: 0.7868 (mmt180) cc_final: 0.7420 (mmt90) REVERT: x 213 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.7947 (tp) REVERT: x 277 GLU cc_start: 0.8138 (pm20) cc_final: 0.7813 (pm20) REVERT: y 8 GLU cc_start: 0.6295 (mm-30) cc_final: 0.5925 (mp0) REVERT: y 11 ASN cc_start: 0.5793 (m-40) cc_final: 0.5586 (m-40) outliers start: 339 outliers final: 173 residues processed: 1339 average time/residue: 1.9526 time to fit residues: 3612.5457 Evaluate side-chains 1305 residues out of total 8126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1077 time to evaluate : 7.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 354 MET Chi-restraints excluded: chain 3 residue 374 GLU Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 598 CYS Chi-restraints excluded: chain 3 residue 609 LEU Chi-restraints excluded: chain 3 residue 616 SER Chi-restraints excluded: chain 3 residue 628 MET Chi-restraints excluded: chain 3 residue 633 LEU Chi-restraints excluded: chain 3 residue 646 LEU Chi-restraints excluded: chain 3 residue 703 MET Chi-restraints excluded: chain 8 residue 304 LEU Chi-restraints excluded: chain 8 residue 311 MET Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 211 GLN Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 348 ARG Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain F residue 47 ARG Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 175 LYS Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 15 GLU Chi-restraints excluded: chain I residue 55 GLU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 172 ASP Chi-restraints excluded: chain I residue 225 SER Chi-restraints excluded: chain I residue 330 GLU Chi-restraints excluded: chain I residue 411 ASP Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain J residue 323 LEU Chi-restraints excluded: chain K residue 70 ASP Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain K residue 131 ASP Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 237 LYS Chi-restraints excluded: chain K residue 243 THR Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain M residue 12 TRP Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 130 LYS Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain P residue 23 ARG Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 164 LYS Chi-restraints excluded: chain R residue 182 VAL Chi-restraints excluded: chain S residue 3 HIS Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 105 THR Chi-restraints excluded: chain S residue 124 LEU Chi-restraints excluded: chain V residue 91 VAL Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain W residue 80 LYS Chi-restraints excluded: chain W residue 102 LEU Chi-restraints excluded: chain W residue 153 GLU Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 196 ASP Chi-restraints excluded: chain W residue 197 VAL Chi-restraints excluded: chain W residue 216 LYS Chi-restraints excluded: chain W residue 230 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 71 SER Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Y residue 115 ARG Chi-restraints excluded: chain Z residue 22 ILE Chi-restraints excluded: chain Z residue 69 ASP Chi-restraints excluded: chain Z residue 84 MET Chi-restraints excluded: chain Z residue 124 LEU Chi-restraints excluded: chain Z residue 159 VAL Chi-restraints excluded: chain Z residue 187 LYS Chi-restraints excluded: chain Z residue 342 ILE Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 163 LEU Chi-restraints excluded: chain a residue 185 MET Chi-restraints excluded: chain a residue 208 SER Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 15 ASN Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 194 VAL Chi-restraints excluded: chain b residue 220 ASP Chi-restraints excluded: chain b residue 247 ARG Chi-restraints excluded: chain b residue 273 SER Chi-restraints excluded: chain b residue 275 LYS Chi-restraints excluded: chain b residue 308 SER Chi-restraints excluded: chain b residue 331 VAL Chi-restraints excluded: chain b residue 422 LEU Chi-restraints excluded: chain b residue 425 ASP Chi-restraints excluded: chain e residue 21 HIS Chi-restraints excluded: chain e residue 80 LYS Chi-restraints excluded: chain f residue 21 ARG Chi-restraints excluded: chain h residue 9 LEU Chi-restraints excluded: chain h residue 46 THR Chi-restraints excluded: chain h residue 48 ARG Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain h residue 98 SER Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain l residue 121 MET Chi-restraints excluded: chain l residue 136 MET Chi-restraints excluded: chain m residue 244 ILE Chi-restraints excluded: chain m residue 252 GLU Chi-restraints excluded: chain m residue 254 MET Chi-restraints excluded: chain m residue 276 VAL Chi-restraints excluded: chain m residue 292 LYS Chi-restraints excluded: chain m residue 384 ILE Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 42 TYR Chi-restraints excluded: chain n residue 68 ILE Chi-restraints excluded: chain n residue 120 GLU Chi-restraints excluded: chain n residue 162 ILE Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 255 ILE Chi-restraints excluded: chain n residue 363 PHE Chi-restraints excluded: chain n residue 371 VAL Chi-restraints excluded: chain n residue 375 ILE Chi-restraints excluded: chain o residue 162 LEU Chi-restraints excluded: chain o residue 185 VAL Chi-restraints excluded: chain o residue 193 VAL Chi-restraints excluded: chain o residue 197 LYS Chi-restraints excluded: chain q residue 230 ARG Chi-restraints excluded: chain q residue 303 THR Chi-restraints excluded: chain q residue 346 ASN Chi-restraints excluded: chain q residue 477 THR Chi-restraints excluded: chain r residue 21 GLU Chi-restraints excluded: chain r residue 208 MET Chi-restraints excluded: chain r residue 223 VAL Chi-restraints excluded: chain t residue 64 LYS Chi-restraints excluded: chain t residue 286 LEU Chi-restraints excluded: chain t residue 289 ILE Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain u residue 109 LYS Chi-restraints excluded: chain v residue 21 ASN Chi-restraints excluded: chain v residue 26 ARG Chi-restraints excluded: chain v residue 156 THR Chi-restraints excluded: chain v residue 165 LEU Chi-restraints excluded: chain v residue 186 GLU Chi-restraints excluded: chain v residue 207 ILE Chi-restraints excluded: chain w residue 30 THR Chi-restraints excluded: chain w residue 37 ASN Chi-restraints excluded: chain w residue 97 LYS Chi-restraints excluded: chain w residue 143 LYS Chi-restraints excluded: chain w residue 204 LYS Chi-restraints excluded: chain w residue 205 ILE Chi-restraints excluded: chain x residue 54 GLU Chi-restraints excluded: chain x residue 56 VAL Chi-restraints excluded: chain x residue 65 VAL Chi-restraints excluded: chain x residue 87 SER Chi-restraints excluded: chain x residue 213 LEU Chi-restraints excluded: chain x residue 295 LEU Chi-restraints excluded: chain y residue 36 SER Chi-restraints excluded: chain y residue 51 THR Chi-restraints excluded: chain y residue 52 THR Chi-restraints excluded: chain y residue 92 VAL Chi-restraints excluded: chain y residue 186 VAL Chi-restraints excluded: chain y residue 216 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1127 random chunks: chunk 1051 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 621 optimal weight: 2.9990 chunk 796 optimal weight: 20.0000 chunk 616 optimal weight: 5.9990 chunk 917 optimal weight: 20.0000 chunk 608 optimal weight: 3.9990 chunk 1086 optimal weight: 5.9990 chunk 679 optimal weight: 3.9990 chunk 662 optimal weight: 3.9990 chunk 501 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 444 HIS A 165 ASN C 58 HIS C 260 GLN ** D 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN H 163 GLN I 63 ASN J 284 HIS J 320 ASN N 23 GLN O 55 HIS Q 73 GLN ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 98 ASN Z 137 ASN h 16 GLN ** n 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 10 ASN v 210 GLN w 5 ASN ** x 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 62 ASN ** x 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 128121 Z= 0.221 Angle : 0.573 17.772 183401 Z= 0.293 Chirality : 0.038 0.299 22273 Planarity : 0.005 0.060 15165 Dihedral : 21.487 178.276 43818 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.80 % Allowed : 17.40 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.09), residues: 9119 helix: 1.73 (0.08), residues: 3804 sheet: 0.22 (0.13), residues: 1393 loop : -0.42 (0.09), residues: 3922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP e 32 HIS 0.015 0.001 HIS Z 205 PHE 0.039 0.002 PHE D 96 TYR 0.024 0.002 TYR C 194 ARG 0.009 0.001 ARG Z 204 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18238 Ramachandran restraints generated. 9119 Oldfield, 0 Emsley, 9119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18238 Ramachandran restraints generated. 9119 Oldfield, 0 Emsley, 9119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1400 residues out of total 8126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 309 poor density : 1091 time to evaluate : 7.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 633 LEU cc_start: 0.4638 (OUTLIER) cc_final: 0.4340 (mp) REVERT: 3 646 LEU cc_start: 0.2970 (OUTLIER) cc_final: 0.2415 (tp) REVERT: 8 298 LYS cc_start: 0.6825 (mtpt) cc_final: 0.6463 (tppt) REVERT: 8 378 GLU cc_start: 0.7747 (tp30) cc_final: 0.7473 (mm-30) REVERT: A 49 ILE cc_start: 0.6944 (mt) cc_final: 0.6592 (pt) REVERT: A 167 ARG cc_start: 0.6490 (mtt180) cc_final: 0.6066 (mtp180) REVERT: A 177 MET cc_start: 0.5020 (OUTLIER) cc_final: 0.4585 (ttm) REVERT: A 228 GLU cc_start: 0.6827 (tm-30) cc_final: 0.6524 (mm-30) REVERT: B 34 LYS cc_start: 0.7092 (tmtt) cc_final: 0.6669 (tttm) REVERT: B 56 ILE cc_start: 0.8107 (mt) cc_final: 0.7586 (pp) REVERT: B 58 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7681 (ptm160) REVERT: B 113 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6831 (mt-10) REVERT: B 211 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.7110 (tt0) REVERT: B 287 LYS cc_start: 0.6442 (mmmm) cc_final: 0.5866 (mmmt) REVERT: C 14 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: C 18 ASN cc_start: 0.8031 (m110) cc_final: 0.7238 (t0) REVERT: C 55 LYS cc_start: 0.8137 (mttt) cc_final: 0.7903 (mtmm) REVERT: C 73 ARG cc_start: 0.7890 (mpp-170) cc_final: 0.7453 (mmt90) REVERT: C 93 MET cc_start: 0.8938 (pmm) cc_final: 0.8465 (pmm) REVERT: C 211 GLU cc_start: 0.8209 (tp30) cc_final: 0.7906 (mp0) REVERT: C 226 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8651 (mt-10) REVERT: C 257 LYS cc_start: 0.8595 (ttmm) cc_final: 0.8310 (tttt) REVERT: C 265 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7508 (mt-10) REVERT: C 304 GLN cc_start: 0.8506 (mt0) cc_final: 0.8272 (mt0) REVERT: C 338 LYS cc_start: 0.7627 (mmtt) cc_final: 0.7406 (mttt) REVERT: D 65 MET cc_start: 0.5644 (mtp) cc_final: 0.5173 (mtp) REVERT: D 183 LYS cc_start: 0.6934 (OUTLIER) cc_final: 0.6714 (mtmt) REVERT: D 365 ASP cc_start: 0.6267 (m-30) cc_final: 0.6020 (m-30) REVERT: E 15 VAL cc_start: 0.8812 (m) cc_final: 0.8592 (t) REVERT: E 29 LYS cc_start: 0.7981 (ptmm) cc_final: 0.7663 (ptpp) REVERT: E 46 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8439 (ttt-90) REVERT: E 99 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6164 (mm-30) REVERT: E 108 LYS cc_start: 0.7335 (ptpt) cc_final: 0.7021 (ptpp) REVERT: E 146 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7604 (tt) REVERT: F 12 GLN cc_start: 0.8318 (tt0) cc_final: 0.7997 (mp10) REVERT: F 24 GLU cc_start: 0.7518 (tt0) cc_final: 0.7265 (mt-10) REVERT: F 25 GLN cc_start: 0.7470 (tt0) cc_final: 0.7052 (mt0) REVERT: F 30 ARG cc_start: 0.7868 (ttt-90) cc_final: 0.7514 (tmt90) REVERT: F 38 LYS cc_start: 0.8420 (tppp) cc_final: 0.8024 (tttt) REVERT: F 47 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8380 (mtt180) REVERT: F 59 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7350 (tm-30) REVERT: F 76 TYR cc_start: 0.7696 (t80) cc_final: 0.7460 (t80) REVERT: F 233 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6645 (mt-10) REVERT: F 234 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8031 (mp0) REVERT: G 84 ARG cc_start: 0.7068 (ttp-110) cc_final: 0.6642 (ttp80) REVERT: G 89 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7627 (mp0) REVERT: G 111 LYS cc_start: 0.8340 (ttpp) cc_final: 0.7806 (mtmm) REVERT: H 42 ASP cc_start: 0.8599 (m-30) cc_final: 0.8368 (m-30) REVERT: H 160 ASP cc_start: 0.7745 (m-30) cc_final: 0.7313 (m-30) REVERT: H 161 LEU cc_start: 0.8399 (tp) cc_final: 0.8173 (tp) REVERT: H 177 ASP cc_start: 0.7614 (m-30) cc_final: 0.7290 (m-30) REVERT: H 180 TYR cc_start: 0.7655 (m-80) cc_final: 0.7309 (m-80) REVERT: I 1 MET cc_start: 0.6810 (ttm) cc_final: 0.6566 (ttm) REVERT: I 15 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7649 (tt0) REVERT: I 44 LYS cc_start: 0.7415 (pttt) cc_final: 0.7177 (pttp) REVERT: I 75 HIS cc_start: 0.5788 (m-70) cc_final: 0.5441 (m-70) REVERT: I 119 ASP cc_start: 0.6631 (t0) cc_final: 0.6229 (OUTLIER) REVERT: I 124 GLU cc_start: 0.7274 (tt0) cc_final: 0.6875 (tp30) REVERT: I 128 SER cc_start: 0.7243 (m) cc_final: 0.6894 (p) REVERT: I 135 LYS cc_start: 0.8097 (ttpp) cc_final: 0.7873 (ttpm) REVERT: I 172 ASP cc_start: 0.5622 (OUTLIER) cc_final: 0.5323 (p0) REVERT: I 174 LYS cc_start: 0.7424 (mttt) cc_final: 0.6860 (mtpt) REVERT: I 218 GLU cc_start: 0.7283 (tt0) cc_final: 0.6986 (tt0) REVERT: I 224 GLN cc_start: 0.7542 (mm-40) cc_final: 0.7236 (mm-40) REVERT: I 236 LYS cc_start: 0.8283 (pttt) cc_final: 0.7919 (ptpp) REVERT: I 312 LYS cc_start: 0.8278 (mttt) cc_final: 0.7746 (mptm) REVERT: I 330 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8021 (mp0) REVERT: I 359 ASP cc_start: 0.8148 (t70) cc_final: 0.7858 (t70) REVERT: I 411 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.6697 (p0) REVERT: J 201 MET cc_start: 0.4634 (mmt) cc_final: 0.3838 (mmt) REVERT: K 39 LYS cc_start: 0.3663 (pttt) cc_final: 0.3349 (ptpp) REVERT: K 237 LYS cc_start: 0.5458 (OUTLIER) cc_final: 0.4802 (mtpt) REVERT: K 244 LEU cc_start: 0.6706 (OUTLIER) cc_final: 0.6119 (tt) REVERT: K 254 LEU cc_start: 0.5459 (mp) cc_final: 0.4735 (mt) REVERT: K 259 PHE cc_start: 0.4412 (m-80) cc_final: 0.4161 (m-10) REVERT: L 23 LYS cc_start: 0.7563 (ptmt) cc_final: 0.7148 (ttpp) REVERT: L 67 ARG cc_start: 0.7734 (ptm-80) cc_final: 0.7474 (ptm-80) REVERT: M 27 GLN cc_start: 0.7356 (tm-30) cc_final: 0.6886 (mt0) REVERT: M 83 LYS cc_start: 0.7983 (ttmt) cc_final: 0.7496 (tttm) REVERT: M 102 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.7642 (tmtp) REVERT: N 8 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7297 (tt0) REVERT: N 31 ARG cc_start: 0.7534 (mtm110) cc_final: 0.7115 (ttt-90) REVERT: N 67 ARG cc_start: 0.7623 (mtp85) cc_final: 0.7111 (ttm-80) REVERT: N 127 TYR cc_start: 0.8317 (m-80) cc_final: 0.7886 (m-80) REVERT: O 73 PHE cc_start: 0.7024 (m-80) cc_final: 0.6267 (m-80) REVERT: O 130 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8214 (ttpm) REVERT: O 170 LYS cc_start: 0.7836 (mtpt) cc_final: 0.7568 (mtpp) REVERT: O 177 LYS cc_start: 0.6532 (mtpt) cc_final: 0.6267 (ttmt) REVERT: P 23 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7987 (mtp-110) REVERT: Q 11 LYS cc_start: 0.7897 (tttt) cc_final: 0.7675 (tptm) REVERT: R 142 LYS cc_start: 0.8655 (ttpt) cc_final: 0.8242 (ttmt) REVERT: R 150 ARG cc_start: 0.8142 (tpt170) cc_final: 0.7543 (ttp80) REVERT: S 3 HIS cc_start: 0.6380 (OUTLIER) cc_final: 0.5640 (t-90) REVERT: S 8 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.8058 (tt0) REVERT: S 47 LYS cc_start: 0.6132 (ttpp) cc_final: 0.5440 (tptm) REVERT: S 57 GLU cc_start: 0.7136 (tt0) cc_final: 0.6810 (pt0) REVERT: S 88 HIS cc_start: 0.6965 (m-70) cc_final: 0.6559 (m170) REVERT: S 124 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7705 (mp) REVERT: S 125 LYS cc_start: 0.7652 (ttmt) cc_final: 0.7404 (tttp) REVERT: V 83 LYS cc_start: 0.6596 (tttt) cc_final: 0.5997 (mppt) REVERT: W 8 LYS cc_start: 0.6003 (mmtt) cc_final: 0.5545 (tmtt) REVERT: W 52 VAL cc_start: 0.5909 (t) cc_final: 0.5536 (m) REVERT: W 79 GLU cc_start: 0.4265 (pm20) cc_final: 0.3923 (mm-30) REVERT: W 152 GLU cc_start: 0.4205 (mp0) cc_final: 0.3788 (mp0) REVERT: W 153 GLU cc_start: 0.3983 (OUTLIER) cc_final: 0.3047 (pt0) REVERT: W 162 GLU cc_start: 0.6025 (tp30) cc_final: 0.5707 (tp30) REVERT: Y 38 GLU cc_start: 0.7789 (tt0) cc_final: 0.7375 (tm-30) REVERT: Y 69 LYS cc_start: 0.8267 (mttt) cc_final: 0.7907 (mtmm) REVERT: Z 66 LYS cc_start: 0.3940 (mmpt) cc_final: 0.3223 (mtpt) REVERT: Z 67 LEU cc_start: 0.5243 (pt) cc_final: 0.4849 (tt) REVERT: Z 69 ASP cc_start: 0.2881 (OUTLIER) cc_final: 0.2238 (m-30) REVERT: Z 187 LYS cc_start: 0.5294 (OUTLIER) cc_final: 0.4597 (tppp) REVERT: Z 204 ARG cc_start: 0.4642 (tpp-160) cc_final: 0.3937 (mtp-110) REVERT: a 85 MET cc_start: 0.0798 (mtm) cc_final: -0.0410 (pmt) REVERT: a 102 LYS cc_start: 0.1727 (mmmt) cc_final: 0.1009 (mptt) REVERT: a 185 MET cc_start: 0.1972 (OUTLIER) cc_final: 0.1305 (pmt) REVERT: a 210 MET cc_start: 0.3383 (ttt) cc_final: 0.2174 (tpp) REVERT: b 1 MET cc_start: 0.2006 (OUTLIER) cc_final: 0.1785 (mpp) REVERT: b 41 ARG cc_start: 0.5480 (mtp85) cc_final: 0.4828 (mpt180) REVERT: b 111 ASP cc_start: 0.5550 (t0) cc_final: 0.5287 (t70) REVERT: b 166 ASN cc_start: 0.5732 (m-40) cc_final: 0.5409 (m110) REVERT: b 209 PHE cc_start: 0.6298 (p90) cc_final: 0.5803 (p90) REVERT: b 275 LYS cc_start: 0.6576 (OUTLIER) cc_final: 0.6252 (pttp) REVERT: b 383 LYS cc_start: 0.5729 (ttpp) cc_final: 0.5267 (ptmt) REVERT: b 384 ASN cc_start: 0.3197 (p0) cc_final: 0.2938 (p0) REVERT: b 425 ASP cc_start: 0.4274 (OUTLIER) cc_final: 0.3749 (m-30) REVERT: b 434 GLU cc_start: 0.6301 (mt-10) cc_final: 0.6083 (pt0) REVERT: e 16 LYS cc_start: 0.8474 (mmtt) cc_final: 0.8039 (mmmm) REVERT: e 21 HIS cc_start: 0.8899 (OUTLIER) cc_final: 0.7206 (m-70) REVERT: f 54 ARG cc_start: 0.8261 (mtp180) cc_final: 0.7753 (mtt-85) REVERT: f 67 MET cc_start: 0.9197 (mtt) cc_final: 0.8905 (mtp) REVERT: h 48 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7075 (ttp-170) REVERT: h 61 GLN cc_start: 0.8172 (mt0) cc_final: 0.7873 (mt0) REVERT: h 102 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7481 (mm-30) REVERT: i 46 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.6843 (tp30) REVERT: i 56 ARG cc_start: 0.6941 (ttm-80) cc_final: 0.6574 (ttt180) REVERT: i 62 ARG cc_start: 0.5964 (mtm180) cc_final: 0.5522 (mtt180) REVERT: i 71 LYS cc_start: 0.7876 (mtpp) cc_final: 0.7620 (mttp) REVERT: i 86 LYS cc_start: 0.8255 (tppt) cc_final: 0.7979 (tppt) REVERT: i 89 GLU cc_start: 0.7750 (tt0) cc_final: 0.7542 (tt0) REVERT: i 90 MET cc_start: 0.8306 (mmp) cc_final: 0.7999 (mmm) REVERT: l 136 MET cc_start: 0.2489 (OUTLIER) cc_final: 0.1926 (tmm) REVERT: m 138 PRO cc_start: 0.6529 (Cg_endo) cc_final: 0.6172 (Cg_exo) REVERT: m 292 LYS cc_start: 0.5822 (OUTLIER) cc_final: 0.5540 (ptpt) REVERT: m 334 ASN cc_start: 0.3893 (OUTLIER) cc_final: 0.3636 (m-40) REVERT: n 42 TYR cc_start: 0.2948 (OUTLIER) cc_final: 0.2692 (m-80) REVERT: n 72 MET cc_start: 0.5847 (tpp) cc_final: 0.5555 (tpp) REVERT: n 363 PHE cc_start: 0.3313 (OUTLIER) cc_final: 0.2874 (m-80) REVERT: o 127 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.7263 (mttp) REVERT: o 194 LYS cc_start: 0.4224 (mppt) cc_final: 0.3999 (pptt) REVERT: q 291 ASN cc_start: 0.5355 (m-40) cc_final: 0.5018 (m-40) REVERT: q 346 ASN cc_start: 0.3787 (OUTLIER) cc_final: 0.2988 (p0) REVERT: r 13 GLN cc_start: 0.7060 (mm-40) cc_final: 0.6700 (mt0) REVERT: r 208 MET cc_start: 0.4705 (OUTLIER) cc_final: 0.4482 (tpt) REVERT: r 222 GLU cc_start: 0.3125 (tp30) cc_final: 0.2643 (tp30) REVERT: t 64 LYS cc_start: 0.6566 (OUTLIER) cc_final: 0.6272 (tppt) REVERT: t 170 GLU cc_start: 0.4301 (mm-30) cc_final: 0.4038 (mm-30) REVERT: u 48 LYS cc_start: 0.5243 (mtmt) cc_final: 0.4807 (mmtp) REVERT: u 109 LYS cc_start: 0.3962 (OUTLIER) cc_final: 0.3585 (mptt) REVERT: v 24 LYS cc_start: 0.7967 (mmtt) cc_final: 0.7643 (mttt) REVERT: v 26 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7438 (tpp-160) REVERT: v 163 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7783 (mt-10) REVERT: v 197 LYS cc_start: 0.7334 (ttmt) cc_final: 0.6645 (ttpp) REVERT: v 203 LYS cc_start: 0.7869 (ptpt) cc_final: 0.7035 (mttt) REVERT: v 221 ARG cc_start: 0.7544 (mtt180) cc_final: 0.7229 (ttm-80) REVERT: w 4 SER cc_start: 0.7846 (t) cc_final: 0.7532 (m) REVERT: w 8 LYS cc_start: 0.8107 (mttt) cc_final: 0.7738 (mtmt) REVERT: w 22 LEU cc_start: 0.8808 (tp) cc_final: 0.8548 (tt) REVERT: w 37 ASN cc_start: 0.8079 (OUTLIER) cc_final: 0.7807 (m110) REVERT: w 38 LYS cc_start: 0.7863 (mttt) cc_final: 0.7578 (mtmm) REVERT: w 78 ASP cc_start: 0.6504 (t0) cc_final: 0.6037 (t0) REVERT: w 114 ASP cc_start: 0.6850 (m-30) cc_final: 0.6533 (m-30) REVERT: w 143 LYS cc_start: 0.7569 (mppt) cc_final: 0.7339 (mmtp) REVERT: w 204 LYS cc_start: 0.6852 (OUTLIER) cc_final: 0.6581 (tmtt) REVERT: x 19 PHE cc_start: 0.8125 (m-80) cc_final: 0.6657 (t80) REVERT: x 23 LYS cc_start: 0.8701 (tttt) cc_final: 0.8429 (ttpm) REVERT: x 48 ARG cc_start: 0.7324 (ttt-90) cc_final: 0.6635 (ttt-90) REVERT: x 50 GLN cc_start: 0.6386 (tp40) cc_final: 0.6044 (mm110) REVERT: x 71 ASN cc_start: 0.7451 (m-40) cc_final: 0.7049 (m110) REVERT: x 79 ASP cc_start: 0.7594 (m-30) cc_final: 0.7359 (m-30) REVERT: x 142 ARG cc_start: 0.8053 (mtt180) cc_final: 0.7536 (mtt90) REVERT: x 189 ARG cc_start: 0.7836 (mmt180) cc_final: 0.7416 (mmt90) REVERT: x 213 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.7913 (tp) REVERT: x 277 GLU cc_start: 0.8143 (pm20) cc_final: 0.7822 (pm20) REVERT: y 8 GLU cc_start: 0.6303 (mm-30) cc_final: 0.5919 (mp0) REVERT: y 11 ASN cc_start: 0.5700 (m-40) cc_final: 0.5477 (m-40) outliers start: 309 outliers final: 173 residues processed: 1301 average time/residue: 1.9326 time to fit residues: 3479.8967 Evaluate side-chains 1293 residues out of total 8126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1069 time to evaluate : 7.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 354 MET Chi-restraints excluded: chain 3 residue 371 ILE Chi-restraints excluded: chain 3 residue 374 GLU Chi-restraints excluded: chain 3 residue 448 ILE Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 609 LEU Chi-restraints excluded: chain 3 residue 616 SER Chi-restraints excluded: chain 3 residue 633 LEU Chi-restraints excluded: chain 3 residue 646 LEU Chi-restraints excluded: chain 8 residue 304 LEU Chi-restraints excluded: chain 8 residue 311 MET Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 211 GLN Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 348 ARG Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain F residue 47 ARG Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 175 LYS Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 15 GLU Chi-restraints excluded: chain I residue 55 GLU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 172 ASP Chi-restraints excluded: chain I residue 225 SER Chi-restraints excluded: chain I residue 330 GLU Chi-restraints excluded: chain I residue 411 ASP Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain K residue 70 ASP Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain K residue 131 ASP Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 209 ILE Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 237 LYS Chi-restraints excluded: chain K residue 243 THR Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain M residue 12 TRP Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain N residue 175 ASN Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 130 LYS Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain P residue 23 ARG Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 153 LYS Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 182 VAL Chi-restraints excluded: chain S residue 3 HIS Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 105 THR Chi-restraints excluded: chain S residue 124 LEU Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain W residue 80 LYS Chi-restraints excluded: chain W residue 102 LEU Chi-restraints excluded: chain W residue 153 GLU Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 196 ASP Chi-restraints excluded: chain W residue 197 VAL Chi-restraints excluded: chain W residue 216 LYS Chi-restraints excluded: chain W residue 228 VAL Chi-restraints excluded: chain W residue 230 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 22 ILE Chi-restraints excluded: chain Z residue 69 ASP Chi-restraints excluded: chain Z residue 84 MET Chi-restraints excluded: chain Z residue 94 VAL Chi-restraints excluded: chain Z residue 124 LEU Chi-restraints excluded: chain Z residue 159 VAL Chi-restraints excluded: chain Z residue 187 LYS Chi-restraints excluded: chain Z residue 342 ILE Chi-restraints excluded: chain a residue 163 LEU Chi-restraints excluded: chain a residue 185 MET Chi-restraints excluded: chain a residue 208 SER Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 15 ASN Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 194 VAL Chi-restraints excluded: chain b residue 275 LYS Chi-restraints excluded: chain b residue 308 SER Chi-restraints excluded: chain b residue 309 VAL Chi-restraints excluded: chain b residue 331 VAL Chi-restraints excluded: chain b residue 425 ASP Chi-restraints excluded: chain e residue 21 HIS Chi-restraints excluded: chain e residue 80 LYS Chi-restraints excluded: chain h residue 9 LEU Chi-restraints excluded: chain h residue 48 ARG Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain h residue 98 SER Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain l residue 121 MET Chi-restraints excluded: chain l residue 136 MET Chi-restraints excluded: chain m residue 244 ILE Chi-restraints excluded: chain m residue 254 MET Chi-restraints excluded: chain m residue 276 VAL Chi-restraints excluded: chain m residue 292 LYS Chi-restraints excluded: chain m residue 299 GLU Chi-restraints excluded: chain m residue 334 ASN Chi-restraints excluded: chain m residue 384 ILE Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 42 TYR Chi-restraints excluded: chain n residue 68 ILE Chi-restraints excluded: chain n residue 162 ILE Chi-restraints excluded: chain n residue 213 VAL Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 255 ILE Chi-restraints excluded: chain n residue 363 PHE Chi-restraints excluded: chain n residue 371 VAL Chi-restraints excluded: chain n residue 375 ILE Chi-restraints excluded: chain n residue 453 LEU Chi-restraints excluded: chain o residue 127 LYS Chi-restraints excluded: chain o residue 162 LEU Chi-restraints excluded: chain o residue 185 VAL Chi-restraints excluded: chain o residue 193 VAL Chi-restraints excluded: chain o residue 197 LYS Chi-restraints excluded: chain q residue 303 THR Chi-restraints excluded: chain q residue 346 ASN Chi-restraints excluded: chain q residue 477 THR Chi-restraints excluded: chain r residue 106 SER Chi-restraints excluded: chain r residue 208 MET Chi-restraints excluded: chain r residue 223 VAL Chi-restraints excluded: chain t residue 64 LYS Chi-restraints excluded: chain t residue 104 THR Chi-restraints excluded: chain t residue 286 LEU Chi-restraints excluded: chain t residue 289 ILE Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain u residue 109 LYS Chi-restraints excluded: chain v residue 21 ASN Chi-restraints excluded: chain v residue 26 ARG Chi-restraints excluded: chain v residue 156 THR Chi-restraints excluded: chain v residue 165 LEU Chi-restraints excluded: chain v residue 207 ILE Chi-restraints excluded: chain w residue 30 THR Chi-restraints excluded: chain w residue 37 ASN Chi-restraints excluded: chain w residue 97 LYS Chi-restraints excluded: chain w residue 204 LYS Chi-restraints excluded: chain w residue 205 ILE Chi-restraints excluded: chain x residue 54 GLU Chi-restraints excluded: chain x residue 56 VAL Chi-restraints excluded: chain x residue 65 VAL Chi-restraints excluded: chain x residue 87 SER Chi-restraints excluded: chain x residue 213 LEU Chi-restraints excluded: chain y residue 52 THR Chi-restraints excluded: chain y residue 92 VAL Chi-restraints excluded: chain y residue 129 ILE Chi-restraints excluded: chain y residue 186 VAL Chi-restraints excluded: chain y residue 216 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1127 random chunks: chunk 672 optimal weight: 0.6980 chunk 433 optimal weight: 0.9990 chunk 648 optimal weight: 0.5980 chunk 327 optimal weight: 0.9980 chunk 213 optimal weight: 10.0000 chunk 210 optimal weight: 10.0000 chunk 690 optimal weight: 0.0070 chunk 740 optimal weight: 6.9990 chunk 537 optimal weight: 0.0980 chunk 101 optimal weight: 30.0000 chunk 853 optimal weight: 7.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 444 HIS A 165 ASN B 319 ASN C 58 HIS D 141 HIS H 51 GLN H 163 GLN I 63 ASN J 284 HIS J 320 ASN N 23 GLN O 55 HIS Q 73 GLN ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 98 ASN Z 137 ASN h 16 GLN n 157 ASN ** n 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 40 GLN v 10 ASN v 210 GLN w 5 ASN ** x 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 62 ASN x 151 ASN ** x 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.095 128121 Z= 0.118 Angle : 0.484 15.484 183401 Z= 0.249 Chirality : 0.034 0.257 22273 Planarity : 0.004 0.058 15165 Dihedral : 21.283 178.679 43818 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.12 % Allowed : 19.09 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.09), residues: 9119 helix: 2.13 (0.08), residues: 3809 sheet: 0.36 (0.14), residues: 1386 loop : -0.23 (0.10), residues: 3924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 120 HIS 0.011 0.001 HIS Z 205 PHE 0.040 0.001 PHE D 96 TYR 0.013 0.001 TYR h 7 ARG 0.010 0.000 ARG 3 519 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18238 Ramachandran restraints generated. 9119 Oldfield, 0 Emsley, 9119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18238 Ramachandran restraints generated. 9119 Oldfield, 0 Emsley, 9119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1332 residues out of total 8126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1160 time to evaluate : 7.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 438 PHE cc_start: 0.3524 (m-80) cc_final: 0.3084 (m-80) REVERT: 3 471 ARG cc_start: 0.3714 (ptp-110) cc_final: 0.3261 (ptm-80) REVERT: 3 633 LEU cc_start: 0.4951 (OUTLIER) cc_final: 0.4616 (mp) REVERT: 3 646 LEU cc_start: 0.2923 (OUTLIER) cc_final: 0.2475 (tp) REVERT: 3 729 MET cc_start: 0.1791 (mmp) cc_final: 0.1217 (ptt) REVERT: 8 298 LYS cc_start: 0.6790 (mtpt) cc_final: 0.6262 (tppp) REVERT: 8 302 LYS cc_start: 0.6697 (ttmt) cc_final: 0.6205 (tttp) REVERT: 8 327 LYS cc_start: 0.5105 (mtpp) cc_final: 0.4740 (mmtm) REVERT: A 49 ILE cc_start: 0.6669 (mt) cc_final: 0.6400 (pt) REVERT: A 167 ARG cc_start: 0.6379 (mtt180) cc_final: 0.6050 (mtp180) REVERT: A 177 MET cc_start: 0.5009 (OUTLIER) cc_final: 0.4585 (ttm) REVERT: A 228 GLU cc_start: 0.6781 (tm-30) cc_final: 0.6279 (mm-30) REVERT: B 74 GLU cc_start: 0.6712 (pm20) cc_final: 0.6488 (mp0) REVERT: B 287 LYS cc_start: 0.6332 (mmmm) cc_final: 0.5781 (mmmt) REVERT: B 353 GLU cc_start: 0.6754 (mt-10) cc_final: 0.6374 (mt-10) REVERT: C 18 ASN cc_start: 0.8010 (m110) cc_final: 0.7263 (t0) REVERT: C 55 LYS cc_start: 0.7942 (mttt) cc_final: 0.7723 (mtmm) REVERT: C 73 ARG cc_start: 0.7794 (mpp-170) cc_final: 0.7423 (mmt90) REVERT: C 155 ASP cc_start: 0.7866 (m-30) cc_final: 0.7386 (m-30) REVERT: C 211 GLU cc_start: 0.8210 (tp30) cc_final: 0.7914 (mp0) REVERT: C 226 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8577 (mt-10) REVERT: C 257 LYS cc_start: 0.8544 (ttmm) cc_final: 0.8265 (ttpt) REVERT: C 265 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7532 (mt-10) REVERT: C 304 GLN cc_start: 0.8483 (mt0) cc_final: 0.8197 (mt0) REVERT: C 338 LYS cc_start: 0.7658 (mmtt) cc_final: 0.7445 (mttt) REVERT: D 65 MET cc_start: 0.5439 (mtp) cc_final: 0.5022 (mtp) REVERT: D 365 ASP cc_start: 0.6306 (m-30) cc_final: 0.6054 (m-30) REVERT: E 15 VAL cc_start: 0.8751 (m) cc_final: 0.8550 (t) REVERT: E 29 LYS cc_start: 0.7964 (ptmm) cc_final: 0.7517 (tppt) REVERT: E 108 LYS cc_start: 0.7121 (ptpt) cc_final: 0.6887 (ptpp) REVERT: E 146 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7694 (tt) REVERT: F 12 GLN cc_start: 0.8121 (tt0) cc_final: 0.7901 (mp10) REVERT: F 24 GLU cc_start: 0.7433 (tt0) cc_final: 0.7117 (mt-10) REVERT: F 25 GLN cc_start: 0.7464 (tt0) cc_final: 0.6964 (mt0) REVERT: F 38 LYS cc_start: 0.8352 (tppp) cc_final: 0.8017 (tttt) REVERT: F 76 TYR cc_start: 0.7765 (t80) cc_final: 0.7418 (t80) REVERT: F 233 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6524 (mm-30) REVERT: F 234 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: G 84 ARG cc_start: 0.6982 (ttp-110) cc_final: 0.6551 (ttp80) REVERT: G 89 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7549 (mp0) REVERT: G 111 LYS cc_start: 0.8369 (ttpp) cc_final: 0.7828 (mtmm) REVERT: H 42 ASP cc_start: 0.8522 (m-30) cc_final: 0.8291 (m-30) REVERT: H 135 GLU cc_start: 0.7723 (pt0) cc_final: 0.7376 (pt0) REVERT: H 160 ASP cc_start: 0.7701 (m-30) cc_final: 0.7291 (m-30) REVERT: H 161 LEU cc_start: 0.8396 (tp) cc_final: 0.8150 (tp) REVERT: H 177 ASP cc_start: 0.7521 (m-30) cc_final: 0.7192 (m-30) REVERT: H 180 TYR cc_start: 0.7627 (m-80) cc_final: 0.7342 (m-80) REVERT: I 1 MET cc_start: 0.6642 (ttm) cc_final: 0.6350 (ttm) REVERT: I 15 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7977 (tt0) REVERT: I 75 HIS cc_start: 0.5798 (m-70) cc_final: 0.5445 (m-70) REVERT: I 119 ASP cc_start: 0.6572 (t0) cc_final: 0.6273 (OUTLIER) REVERT: I 124 GLU cc_start: 0.7270 (tt0) cc_final: 0.6873 (tp30) REVERT: I 128 SER cc_start: 0.6960 (m) cc_final: 0.6565 (p) REVERT: I 135 LYS cc_start: 0.8003 (ttpp) cc_final: 0.7732 (ttpm) REVERT: I 218 GLU cc_start: 0.7193 (tt0) cc_final: 0.6960 (tt0) REVERT: I 224 GLN cc_start: 0.7497 (mm-40) cc_final: 0.7282 (mm-40) REVERT: I 236 LYS cc_start: 0.8161 (pttt) cc_final: 0.7866 (ptpp) REVERT: I 238 ASP cc_start: 0.8534 (p0) cc_final: 0.8073 (p0) REVERT: I 263 LYS cc_start: 0.6450 (mttt) cc_final: 0.5683 (mppt) REVERT: I 312 LYS cc_start: 0.8259 (mttt) cc_final: 0.7754 (mptm) REVERT: I 411 ASP cc_start: 0.7473 (m-30) cc_final: 0.6517 (p0) REVERT: J 201 MET cc_start: 0.4689 (mmt) cc_final: 0.4113 (mmt) REVERT: K 144 LEU cc_start: 0.5983 (mp) cc_final: 0.5665 (mt) REVERT: K 237 LYS cc_start: 0.5315 (OUTLIER) cc_final: 0.4781 (mtpt) REVERT: K 254 LEU cc_start: 0.5276 (mp) cc_final: 0.4595 (mt) REVERT: K 259 PHE cc_start: 0.4208 (m-80) cc_final: 0.3985 (m-10) REVERT: L 23 LYS cc_start: 0.7558 (ptmt) cc_final: 0.7172 (ttpp) REVERT: L 67 ARG cc_start: 0.7673 (ptm-80) cc_final: 0.7450 (ptm-80) REVERT: L 114 GLN cc_start: 0.7957 (tp40) cc_final: 0.7163 (mp10) REVERT: M 27 GLN cc_start: 0.7289 (tm-30) cc_final: 0.7005 (mt0) REVERT: M 37 GLU cc_start: 0.8409 (tt0) cc_final: 0.8125 (mt-10) REVERT: M 83 LYS cc_start: 0.7963 (ttmt) cc_final: 0.7469 (tttm) REVERT: M 102 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.7580 (tmtp) REVERT: N 28 TRP cc_start: 0.7635 (t60) cc_final: 0.7327 (t-100) REVERT: N 31 ARG cc_start: 0.7292 (mtm110) cc_final: 0.6920 (mtt-85) REVERT: N 67 ARG cc_start: 0.7625 (mtp85) cc_final: 0.6925 (mtt-85) REVERT: N 127 TYR cc_start: 0.8217 (m-80) cc_final: 0.7714 (m-80) REVERT: O 73 PHE cc_start: 0.6930 (m-80) cc_final: 0.6144 (m-80) REVERT: O 78 ARG cc_start: 0.8441 (mmp-170) cc_final: 0.8157 (mmp-170) REVERT: O 130 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8288 (ttpm) REVERT: O 170 LYS cc_start: 0.7850 (mtpt) cc_final: 0.7588 (mtpp) REVERT: P 23 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7915 (mtp-110) REVERT: P 55 GLN cc_start: 0.7929 (mp10) cc_final: 0.7716 (mm110) REVERT: Q 11 LYS cc_start: 0.7844 (tttt) cc_final: 0.7627 (tptm) REVERT: R 142 LYS cc_start: 0.8492 (ttpt) cc_final: 0.8083 (ttmt) REVERT: R 150 ARG cc_start: 0.8008 (tpt170) cc_final: 0.7415 (ttp80) REVERT: R 159 GLU cc_start: 0.7859 (mp0) cc_final: 0.7458 (mp0) REVERT: S 3 HIS cc_start: 0.6335 (OUTLIER) cc_final: 0.5551 (t-90) REVERT: S 57 GLU cc_start: 0.7085 (tt0) cc_final: 0.6779 (pt0) REVERT: S 88 HIS cc_start: 0.6974 (m-70) cc_final: 0.6540 (m170) REVERT: S 124 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7579 (mp) REVERT: V 83 LYS cc_start: 0.6544 (tttt) cc_final: 0.6045 (mppt) REVERT: W 8 LYS cc_start: 0.5870 (mmtt) cc_final: 0.5500 (tmtt) REVERT: W 152 GLU cc_start: 0.4422 (mp0) cc_final: 0.3890 (mp0) REVERT: W 162 GLU cc_start: 0.6112 (tp30) cc_final: 0.5728 (tp30) REVERT: Y 38 GLU cc_start: 0.7488 (tt0) cc_final: 0.7120 (tm-30) REVERT: Y 42 GLN cc_start: 0.8455 (tt0) cc_final: 0.8229 (tt0) REVERT: Y 69 LYS cc_start: 0.8201 (mttt) cc_final: 0.7897 (mtmm) REVERT: Z 48 ARG cc_start: 0.3687 (mtm-85) cc_final: 0.3237 (mmm160) REVERT: Z 66 LYS cc_start: 0.3811 (mmpt) cc_final: 0.3266 (mttt) REVERT: Z 67 LEU cc_start: 0.5078 (OUTLIER) cc_final: 0.4774 (tt) REVERT: Z 69 ASP cc_start: 0.2434 (OUTLIER) cc_final: 0.1841 (m-30) REVERT: Z 124 LEU cc_start: 0.2684 (OUTLIER) cc_final: 0.1947 (mt) REVERT: Z 125 LYS cc_start: 0.2552 (mtpp) cc_final: 0.1694 (mptt) REVERT: Z 187 LYS cc_start: 0.5057 (tppp) cc_final: 0.4828 (tppt) REVERT: Z 191 MET cc_start: 0.4156 (tpp) cc_final: 0.3790 (mtp) REVERT: a 85 MET cc_start: 0.0675 (mtm) cc_final: -0.0734 (pmt) REVERT: a 102 LYS cc_start: 0.1560 (mmmt) cc_final: 0.0997 (mptt) REVERT: a 124 LEU cc_start: 0.1335 (OUTLIER) cc_final: 0.1102 (tt) REVERT: a 185 MET cc_start: 0.2121 (ppp) cc_final: 0.1380 (pmt) REVERT: a 210 MET cc_start: 0.3390 (ttt) cc_final: 0.2816 (tpp) REVERT: b 15 ASN cc_start: 0.4811 (OUTLIER) cc_final: 0.4543 (p0) REVERT: b 41 ARG cc_start: 0.5444 (mtp85) cc_final: 0.4801 (mpt180) REVERT: b 111 ASP cc_start: 0.5496 (t0) cc_final: 0.5248 (t70) REVERT: b 166 ASN cc_start: 0.5739 (m-40) cc_final: 0.5365 (m110) REVERT: b 209 PHE cc_start: 0.6286 (p90) cc_final: 0.5786 (p90) REVERT: b 383 LYS cc_start: 0.5708 (ttpp) cc_final: 0.5295 (ptmt) REVERT: b 384 ASN cc_start: 0.3054 (p0) cc_final: 0.2777 (p0) REVERT: b 425 ASP cc_start: 0.4260 (OUTLIER) cc_final: 0.3769 (m-30) REVERT: f 21 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.6749 (mtt90) REVERT: f 54 ARG cc_start: 0.8258 (mtp180) cc_final: 0.7768 (mtt-85) REVERT: h 61 GLN cc_start: 0.8131 (mt0) cc_final: 0.7855 (mt0) REVERT: h 62 GLN cc_start: 0.7649 (tt0) cc_final: 0.7348 (tt0) REVERT: i 56 ARG cc_start: 0.6825 (ttm-80) cc_final: 0.6501 (ttt180) REVERT: i 62 ARG cc_start: 0.5933 (mtm180) cc_final: 0.5523 (mtt180) REVERT: i 71 LYS cc_start: 0.7871 (mtpp) cc_final: 0.7625 (mttp) REVERT: i 75 LYS cc_start: 0.8090 (tptp) cc_final: 0.7739 (tmtt) REVERT: i 86 LYS cc_start: 0.8277 (tppt) cc_final: 0.7980 (tppt) REVERT: i 89 GLU cc_start: 0.7902 (tt0) cc_final: 0.7596 (tt0) REVERT: i 90 MET cc_start: 0.8119 (mmp) cc_final: 0.7744 (mmm) REVERT: j 25 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8270 (tmm-80) REVERT: l 63 LEU cc_start: 0.3985 (tp) cc_final: 0.3548 (mt) REVERT: l 156 MET cc_start: 0.2271 (mmm) cc_final: 0.1971 (mmm) REVERT: m 278 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8299 (tttp) REVERT: m 292 LYS cc_start: 0.5776 (OUTLIER) cc_final: 0.5511 (ptpt) REVERT: n 42 TYR cc_start: 0.2806 (OUTLIER) cc_final: 0.2596 (m-80) REVERT: n 72 MET cc_start: 0.5784 (tpp) cc_final: 0.5512 (tpp) REVERT: o 127 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.7254 (mttp) REVERT: o 178 LYS cc_start: 0.6953 (OUTLIER) cc_final: 0.6554 (mtmt) REVERT: q 291 ASN cc_start: 0.5289 (m-40) cc_final: 0.4988 (m-40) REVERT: q 346 ASN cc_start: 0.3697 (OUTLIER) cc_final: 0.3008 (p0) REVERT: r 133 MET cc_start: 0.2751 (ttt) cc_final: 0.2289 (tpt) REVERT: r 208 MET cc_start: 0.4794 (OUTLIER) cc_final: 0.4515 (tpt) REVERT: r 222 GLU cc_start: 0.2962 (tp30) cc_final: 0.2554 (tp30) REVERT: u 48 LYS cc_start: 0.5158 (mtmt) cc_final: 0.4769 (mmtp) REVERT: u 49 LEU cc_start: 0.6709 (mm) cc_final: 0.6433 (mp) REVERT: v 24 LYS cc_start: 0.7961 (mmtt) cc_final: 0.7531 (mttt) REVERT: v 163 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7672 (mt-10) REVERT: v 197 LYS cc_start: 0.7333 (ttmt) cc_final: 0.6695 (ttpp) REVERT: v 203 LYS cc_start: 0.7854 (ptpt) cc_final: 0.7033 (mtpt) REVERT: v 221 ARG cc_start: 0.7411 (mtt180) cc_final: 0.7183 (ttm-80) REVERT: w 8 LYS cc_start: 0.8082 (mttt) cc_final: 0.7718 (mtmt) REVERT: w 22 LEU cc_start: 0.8745 (tp) cc_final: 0.8463 (tt) REVERT: w 37 ASN cc_start: 0.8028 (OUTLIER) cc_final: 0.7699 (m110) REVERT: w 38 LYS cc_start: 0.7853 (mttt) cc_final: 0.7537 (mtmt) REVERT: w 78 ASP cc_start: 0.6500 (t0) cc_final: 0.6024 (t0) REVERT: w 143 LYS cc_start: 0.7602 (mppt) cc_final: 0.7399 (mmtp) REVERT: w 204 LYS cc_start: 0.6792 (OUTLIER) cc_final: 0.6564 (tmtt) REVERT: w 228 TYR cc_start: 0.7251 (m-80) cc_final: 0.6878 (m-10) REVERT: x 19 PHE cc_start: 0.7896 (m-80) cc_final: 0.6730 (t80) REVERT: x 48 ARG cc_start: 0.7225 (ttt-90) cc_final: 0.6726 (ttt-90) REVERT: x 50 GLN cc_start: 0.6306 (tp40) cc_final: 0.5996 (mm110) REVERT: x 62 ASN cc_start: 0.7399 (m-40) cc_final: 0.6967 (m110) REVERT: x 71 ASN cc_start: 0.7384 (m-40) cc_final: 0.7009 (m110) REVERT: x 79 ASP cc_start: 0.7589 (m-30) cc_final: 0.7343 (m-30) REVERT: x 141 LYS cc_start: 0.8218 (ttmm) cc_final: 0.7233 (mttm) REVERT: x 142 ARG cc_start: 0.8093 (mtt180) cc_final: 0.7585 (mtt90) REVERT: x 189 ARG cc_start: 0.7707 (mmt180) cc_final: 0.7289 (mmm160) REVERT: x 277 GLU cc_start: 0.8062 (pm20) cc_final: 0.7773 (pm20) REVERT: y 8 GLU cc_start: 0.6265 (mm-30) cc_final: 0.5814 (mp0) REVERT: y 62 MET cc_start: 0.5661 (mmm) cc_final: 0.5364 (mmm) outliers start: 172 outliers final: 68 residues processed: 1273 average time/residue: 1.9785 time to fit residues: 3478.8241 Evaluate side-chains 1183 residues out of total 8126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1085 time to evaluate : 7.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 363 ASP Chi-restraints excluded: chain 3 residue 435 THR Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 609 LEU Chi-restraints excluded: chain 3 residue 616 SER Chi-restraints excluded: chain 3 residue 633 LEU Chi-restraints excluded: chain 3 residue 646 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 15 GLU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 237 LYS Chi-restraints excluded: chain K residue 243 THR Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain M residue 12 TRP Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain O residue 130 LYS Chi-restraints excluded: chain P residue 23 ARG Chi-restraints excluded: chain S residue 3 HIS Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 124 LEU Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain W residue 196 ASP Chi-restraints excluded: chain W residue 197 VAL Chi-restraints excluded: chain W residue 216 LYS Chi-restraints excluded: chain W residue 228 VAL Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Z residue 67 LEU Chi-restraints excluded: chain Z residue 69 ASP Chi-restraints excluded: chain Z residue 124 LEU Chi-restraints excluded: chain Z residue 342 ILE Chi-restraints excluded: chain a residue 124 LEU Chi-restraints excluded: chain a residue 147 LYS Chi-restraints excluded: chain a residue 163 LEU Chi-restraints excluded: chain b residue 15 ASN Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 309 VAL Chi-restraints excluded: chain b residue 425 ASP Chi-restraints excluded: chain e residue 80 LYS Chi-restraints excluded: chain f residue 21 ARG Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 25 ARG Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain l residue 121 MET Chi-restraints excluded: chain m residue 278 LYS Chi-restraints excluded: chain m residue 292 LYS Chi-restraints excluded: chain n residue 42 TYR Chi-restraints excluded: chain n residue 142 PHE Chi-restraints excluded: chain n residue 162 ILE Chi-restraints excluded: chain n residue 255 ILE Chi-restraints excluded: chain n residue 263 ILE Chi-restraints excluded: chain n residue 371 VAL Chi-restraints excluded: chain n residue 453 LEU Chi-restraints excluded: chain o residue 127 LYS Chi-restraints excluded: chain o residue 162 LEU Chi-restraints excluded: chain o residue 178 LYS Chi-restraints excluded: chain o residue 185 VAL Chi-restraints excluded: chain o residue 193 VAL Chi-restraints excluded: chain o residue 197 LYS Chi-restraints excluded: chain q residue 346 ASN Chi-restraints excluded: chain q residue 517 ARG Chi-restraints excluded: chain r residue 208 MET Chi-restraints excluded: chain r residue 223 VAL Chi-restraints excluded: chain t residue 104 THR Chi-restraints excluded: chain t residue 286 LEU Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain v residue 21 ASN Chi-restraints excluded: chain v residue 207 ILE Chi-restraints excluded: chain w residue 37 ASN Chi-restraints excluded: chain w residue 204 LYS Chi-restraints excluded: chain w residue 205 ILE Chi-restraints excluded: chain x residue 56 VAL Chi-restraints excluded: chain x residue 65 VAL Chi-restraints excluded: chain x residue 87 SER Chi-restraints excluded: chain y residue 52 THR Chi-restraints excluded: chain y residue 186 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1127 random chunks: chunk 988 optimal weight: 20.0000 chunk 1040 optimal weight: 4.9990 chunk 949 optimal weight: 30.0000 chunk 1012 optimal weight: 5.9990 chunk 609 optimal weight: 0.0980 chunk 440 optimal weight: 0.9990 chunk 794 optimal weight: 1.9990 chunk 310 optimal weight: 1.9990 chunk 914 optimal weight: 20.0000 chunk 957 optimal weight: 5.9990 chunk 1008 optimal weight: 0.0670 overall best weight: 1.0324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 444 HIS 3 714 GLN A 165 ASN B 319 ASN C 58 HIS D 105 HIS D 141 HIS H 51 GLN H 59 ASN H 163 GLN I 63 ASN J 284 HIS J 320 ASN N 23 GLN O 55 HIS P 92 GLN Y 98 ASN Z 137 ASN b 90 HIS h 16 GLN h 104 GLN ** n 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 10 ASN ** v 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 210 GLN w 5 ASN ** x 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 151 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 128121 Z= 0.118 Angle : 0.480 15.578 183401 Z= 0.244 Chirality : 0.034 0.230 22273 Planarity : 0.004 0.057 15165 Dihedral : 21.216 179.973 43818 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.94 % Allowed : 19.85 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.09), residues: 9119 helix: 2.21 (0.08), residues: 3810 sheet: 0.45 (0.14), residues: 1394 loop : -0.19 (0.10), residues: 3915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP w 54 HIS 0.008 0.001 HIS D 105 PHE 0.040 0.001 PHE D 96 TYR 0.026 0.001 TYR l 95 ARG 0.011 0.000 ARG 3 519 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18238 Ramachandran restraints generated. 9119 Oldfield, 0 Emsley, 9119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18238 Ramachandran restraints generated. 9119 Oldfield, 0 Emsley, 9119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1264 residues out of total 8126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1106 time to evaluate : 7.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 471 ARG cc_start: 0.3747 (ptp-110) cc_final: 0.3281 (ptm-80) REVERT: 3 633 LEU cc_start: 0.4925 (OUTLIER) cc_final: 0.4581 (mp) REVERT: 3 646 LEU cc_start: 0.3066 (OUTLIER) cc_final: 0.2583 (tp) REVERT: 3 729 MET cc_start: 0.1720 (mmp) cc_final: 0.1287 (ptt) REVERT: 8 298 LYS cc_start: 0.6805 (mtpt) cc_final: 0.6380 (tppt) REVERT: 8 302 LYS cc_start: 0.6556 (ttmt) cc_final: 0.6088 (tttp) REVERT: 8 327 LYS cc_start: 0.5127 (mtpp) cc_final: 0.4751 (mmtm) REVERT: A 49 ILE cc_start: 0.6642 (mt) cc_final: 0.6413 (pt) REVERT: A 167 ARG cc_start: 0.6405 (mtt180) cc_final: 0.6056 (mtp180) REVERT: A 228 GLU cc_start: 0.6729 (tm-30) cc_final: 0.6279 (mm-30) REVERT: B 287 LYS cc_start: 0.6317 (mmmm) cc_final: 0.5772 (mmmt) REVERT: B 353 GLU cc_start: 0.6684 (mt-10) cc_final: 0.6283 (mt-10) REVERT: C 18 ASN cc_start: 0.8012 (m110) cc_final: 0.7263 (t0) REVERT: C 55 LYS cc_start: 0.7949 (mttt) cc_final: 0.7732 (mtmm) REVERT: C 73 ARG cc_start: 0.7803 (mpp-170) cc_final: 0.7420 (mmt90) REVERT: C 155 ASP cc_start: 0.7840 (m-30) cc_final: 0.7324 (m-30) REVERT: C 211 GLU cc_start: 0.8217 (tp30) cc_final: 0.7943 (mp0) REVERT: C 226 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8594 (mt-10) REVERT: C 257 LYS cc_start: 0.8535 (ttmm) cc_final: 0.8263 (ttpt) REVERT: C 265 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7528 (mt-10) REVERT: C 304 GLN cc_start: 0.8469 (mt0) cc_final: 0.8194 (mt0) REVERT: C 338 LYS cc_start: 0.7636 (mmtt) cc_final: 0.7420 (mttt) REVERT: D 65 MET cc_start: 0.5444 (mtp) cc_final: 0.5012 (mtp) REVERT: D 365 ASP cc_start: 0.6298 (m-30) cc_final: 0.6063 (m-30) REVERT: D 415 TYR cc_start: 0.6051 (m-80) cc_final: 0.5849 (m-10) REVERT: E 29 LYS cc_start: 0.7958 (ptmm) cc_final: 0.7511 (tppt) REVERT: E 104 GLU cc_start: 0.7172 (mp0) cc_final: 0.6801 (pm20) REVERT: E 146 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7699 (tt) REVERT: F 24 GLU cc_start: 0.7392 (tt0) cc_final: 0.7105 (mt-10) REVERT: F 25 GLN cc_start: 0.7470 (tt0) cc_final: 0.6925 (mt0) REVERT: F 38 LYS cc_start: 0.8317 (tppp) cc_final: 0.7989 (tttt) REVERT: F 76 TYR cc_start: 0.7721 (t80) cc_final: 0.7419 (t80) REVERT: F 233 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6537 (mm-30) REVERT: F 234 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7913 (mp0) REVERT: G 84 ARG cc_start: 0.6991 (ttp-110) cc_final: 0.6604 (ttp80) REVERT: G 89 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7554 (mp0) REVERT: G 111 LYS cc_start: 0.8378 (ttpp) cc_final: 0.7829 (mtmm) REVERT: H 42 ASP cc_start: 0.8533 (m-30) cc_final: 0.8303 (m-30) REVERT: H 135 GLU cc_start: 0.7712 (pt0) cc_final: 0.7377 (pt0) REVERT: H 160 ASP cc_start: 0.7707 (m-30) cc_final: 0.7267 (m-30) REVERT: H 161 LEU cc_start: 0.8418 (tp) cc_final: 0.8170 (tp) REVERT: H 177 ASP cc_start: 0.7534 (m-30) cc_final: 0.7196 (m-30) REVERT: H 180 TYR cc_start: 0.7634 (m-80) cc_final: 0.7340 (m-80) REVERT: I 1 MET cc_start: 0.6745 (ttm) cc_final: 0.6445 (ttm) REVERT: I 15 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8014 (tt0) REVERT: I 75 HIS cc_start: 0.5784 (m-70) cc_final: 0.5428 (m-70) REVERT: I 119 ASP cc_start: 0.6510 (t0) cc_final: 0.6219 (OUTLIER) REVERT: I 124 GLU cc_start: 0.7275 (tt0) cc_final: 0.6876 (tp30) REVERT: I 128 SER cc_start: 0.6999 (m) cc_final: 0.6612 (p) REVERT: I 135 LYS cc_start: 0.8061 (ttpp) cc_final: 0.7801 (ttpm) REVERT: I 166 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8221 (mm) REVERT: I 174 LYS cc_start: 0.7347 (mttt) cc_final: 0.6814 (mtpt) REVERT: I 218 GLU cc_start: 0.7294 (tt0) cc_final: 0.7007 (tt0) REVERT: I 224 GLN cc_start: 0.7496 (mm-40) cc_final: 0.7270 (mm-40) REVERT: I 236 LYS cc_start: 0.8158 (pttt) cc_final: 0.7868 (ptpp) REVERT: I 238 ASP cc_start: 0.8549 (p0) cc_final: 0.8131 (p0) REVERT: I 263 LYS cc_start: 0.6508 (mttt) cc_final: 0.5728 (mppt) REVERT: I 312 LYS cc_start: 0.8258 (mttt) cc_final: 0.7757 (mptm) REVERT: I 411 ASP cc_start: 0.7506 (m-30) cc_final: 0.6558 (p0) REVERT: J 201 MET cc_start: 0.4723 (mmt) cc_final: 0.4113 (mmt) REVERT: K 144 LEU cc_start: 0.5887 (mp) cc_final: 0.5602 (mt) REVERT: K 237 LYS cc_start: 0.5265 (OUTLIER) cc_final: 0.4822 (mtpt) REVERT: K 259 PHE cc_start: 0.4212 (m-80) cc_final: 0.3984 (m-10) REVERT: L 23 LYS cc_start: 0.7542 (ptmt) cc_final: 0.7155 (ttpp) REVERT: L 67 ARG cc_start: 0.7682 (ptm-80) cc_final: 0.7453 (ptm-80) REVERT: L 114 GLN cc_start: 0.7972 (tp40) cc_final: 0.7178 (mp10) REVERT: M 27 GLN cc_start: 0.7274 (tm-30) cc_final: 0.7003 (mt0) REVERT: M 83 LYS cc_start: 0.7959 (ttmt) cc_final: 0.7461 (tttm) REVERT: M 102 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.7605 (tmtp) REVERT: N 28 TRP cc_start: 0.7495 (t60) cc_final: 0.7216 (t-100) REVERT: N 31 ARG cc_start: 0.7264 (mtm110) cc_final: 0.6902 (mtt-85) REVERT: N 67 ARG cc_start: 0.7639 (mtp85) cc_final: 0.6926 (mtt-85) REVERT: N 127 TYR cc_start: 0.8190 (m-80) cc_final: 0.7675 (m-80) REVERT: O 73 PHE cc_start: 0.6873 (m-80) cc_final: 0.6093 (m-80) REVERT: O 78 ARG cc_start: 0.8429 (mmp-170) cc_final: 0.8135 (mmp-170) REVERT: O 170 LYS cc_start: 0.7844 (mtpt) cc_final: 0.7579 (mtpp) REVERT: P 23 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7901 (mtp-110) REVERT: P 55 GLN cc_start: 0.7920 (mp10) cc_final: 0.7676 (mm110) REVERT: Q 11 LYS cc_start: 0.7856 (tttt) cc_final: 0.7648 (tptm) REVERT: R 142 LYS cc_start: 0.8545 (ttpt) cc_final: 0.8126 (ttmt) REVERT: R 150 ARG cc_start: 0.8039 (tpt170) cc_final: 0.7441 (ttp80) REVERT: R 159 GLU cc_start: 0.7882 (mp0) cc_final: 0.7480 (mp0) REVERT: S 3 HIS cc_start: 0.6393 (OUTLIER) cc_final: 0.5641 (t-90) REVERT: S 26 ARG cc_start: 0.6872 (mtt90) cc_final: 0.6608 (mtt90) REVERT: S 47 LYS cc_start: 0.6948 (ttmt) cc_final: 0.6051 (mttm) REVERT: S 57 GLU cc_start: 0.7140 (tt0) cc_final: 0.6839 (pt0) REVERT: S 88 HIS cc_start: 0.6976 (m-70) cc_final: 0.6542 (m170) REVERT: V 59 MET cc_start: 0.5641 (mmm) cc_final: 0.4804 (mmm) REVERT: V 61 THR cc_start: 0.5482 (OUTLIER) cc_final: 0.5260 (p) REVERT: V 83 LYS cc_start: 0.6642 (tttt) cc_final: 0.6059 (mppt) REVERT: W 8 LYS cc_start: 0.5896 (mmtt) cc_final: 0.5515 (tmtt) REVERT: W 47 ASP cc_start: 0.3914 (t0) cc_final: 0.3679 (t0) REVERT: W 152 GLU cc_start: 0.4391 (mp0) cc_final: 0.3891 (mp0) REVERT: W 162 GLU cc_start: 0.6092 (tp30) cc_final: 0.5657 (tp30) REVERT: W 196 ASP cc_start: 0.4006 (OUTLIER) cc_final: 0.2898 (m-30) REVERT: Y 38 GLU cc_start: 0.7489 (tt0) cc_final: 0.7136 (tm-30) REVERT: Y 42 GLN cc_start: 0.8455 (tt0) cc_final: 0.8206 (tt0) REVERT: Y 69 LYS cc_start: 0.8222 (mttt) cc_final: 0.7885 (mtmm) REVERT: Y 115 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.8169 (tpt-90) REVERT: Z 66 LYS cc_start: 0.3720 (mmpt) cc_final: 0.3139 (mttt) REVERT: Z 67 LEU cc_start: 0.5081 (OUTLIER) cc_final: 0.4747 (tt) REVERT: Z 69 ASP cc_start: 0.2404 (OUTLIER) cc_final: 0.1792 (m-30) REVERT: Z 124 LEU cc_start: 0.2506 (OUTLIER) cc_final: 0.1754 (mt) REVERT: Z 125 LYS cc_start: 0.2580 (mtpp) cc_final: 0.1688 (mptt) REVERT: Z 187 LYS cc_start: 0.5057 (tppp) cc_final: 0.4734 (tppt) REVERT: Z 191 MET cc_start: 0.4166 (tpp) cc_final: 0.3833 (mtp) REVERT: a 85 MET cc_start: 0.0651 (mtm) cc_final: -0.0685 (pmt) REVERT: a 102 LYS cc_start: 0.1577 (mmmt) cc_final: 0.1009 (mptt) REVERT: a 185 MET cc_start: 0.2180 (ppp) cc_final: 0.1438 (pmt) REVERT: a 210 MET cc_start: 0.3294 (ttt) cc_final: 0.2717 (tpp) REVERT: b 15 ASN cc_start: 0.4921 (m-40) cc_final: 0.4605 (p0) REVERT: b 41 ARG cc_start: 0.5391 (mtp85) cc_final: 0.4779 (mpt180) REVERT: b 111 ASP cc_start: 0.5454 (t0) cc_final: 0.5239 (t70) REVERT: b 166 ASN cc_start: 0.5667 (m-40) cc_final: 0.5319 (m110) REVERT: b 209 PHE cc_start: 0.6298 (p90) cc_final: 0.5835 (p90) REVERT: b 383 LYS cc_start: 0.5716 (ttpp) cc_final: 0.5296 (ptmt) REVERT: b 384 ASN cc_start: 0.3057 (p0) cc_final: 0.2786 (p0) REVERT: b 392 ASP cc_start: 0.3409 (t0) cc_final: 0.2841 (t70) REVERT: b 425 ASP cc_start: 0.4287 (OUTLIER) cc_final: 0.3818 (m-30) REVERT: f 21 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.6778 (mtt90) REVERT: f 54 ARG cc_start: 0.8267 (mtp180) cc_final: 0.7778 (mtt-85) REVERT: h 61 GLN cc_start: 0.8063 (mt0) cc_final: 0.7802 (mt0) REVERT: h 62 GLN cc_start: 0.7662 (tt0) cc_final: 0.7373 (tt0) REVERT: i 56 ARG cc_start: 0.6916 (ttm-80) cc_final: 0.6578 (ttt180) REVERT: i 62 ARG cc_start: 0.5946 (mtm180) cc_final: 0.5558 (mtt180) REVERT: i 71 LYS cc_start: 0.7900 (mtpp) cc_final: 0.7644 (mttp) REVERT: i 75 LYS cc_start: 0.8102 (tptp) cc_final: 0.7734 (tmtt) REVERT: i 79 SER cc_start: 0.8402 (OUTLIER) cc_final: 0.8127 (t) REVERT: i 86 LYS cc_start: 0.8293 (tppt) cc_final: 0.8017 (tppt) REVERT: i 89 GLU cc_start: 0.7898 (tt0) cc_final: 0.7607 (tt0) REVERT: i 90 MET cc_start: 0.8243 (mmp) cc_final: 0.7868 (mmm) REVERT: l 1 MET cc_start: 0.2903 (OUTLIER) cc_final: 0.1732 (ttm) REVERT: m 278 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8299 (tttp) REVERT: m 292 LYS cc_start: 0.5803 (OUTLIER) cc_final: 0.5540 (ptpt) REVERT: n 42 TYR cc_start: 0.2896 (OUTLIER) cc_final: 0.2683 (m-80) REVERT: o 127 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.7241 (mttp) REVERT: o 178 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.6583 (mtmt) REVERT: o 194 LYS cc_start: 0.4324 (pptt) cc_final: 0.3777 (ttmt) REVERT: q 227 TYR cc_start: 0.2755 (m-10) cc_final: 0.2549 (m-80) REVERT: q 261 PHE cc_start: 0.1861 (t80) cc_final: 0.1575 (t80) REVERT: q 322 TYR cc_start: 0.2362 (t80) cc_final: 0.2146 (t80) REVERT: q 346 ASN cc_start: 0.3705 (OUTLIER) cc_final: 0.3023 (p0) REVERT: q 531 TYR cc_start: 0.1702 (OUTLIER) cc_final: 0.0874 (m-80) REVERT: r 13 GLN cc_start: 0.6865 (mm-40) cc_final: 0.6543 (mt0) REVERT: r 133 MET cc_start: 0.2363 (ttt) cc_final: 0.2071 (tpt) REVERT: r 208 MET cc_start: 0.4822 (OUTLIER) cc_final: 0.4570 (tpt) REVERT: r 222 GLU cc_start: 0.2885 (tp30) cc_final: 0.2438 (tp30) REVERT: t 289 ILE cc_start: 0.7351 (mm) cc_final: 0.7147 (mp) REVERT: u 48 LYS cc_start: 0.5197 (mtmt) cc_final: 0.4800 (mmtp) REVERT: u 49 LEU cc_start: 0.6692 (mm) cc_final: 0.6423 (mp) REVERT: v 9 MET cc_start: 0.8684 (mmm) cc_final: 0.8455 (mmp) REVERT: v 24 LYS cc_start: 0.7945 (mmtt) cc_final: 0.7529 (mttt) REVERT: v 197 LYS cc_start: 0.7353 (ttmt) cc_final: 0.6685 (ttpp) REVERT: v 203 LYS cc_start: 0.7850 (ptpt) cc_final: 0.7039 (mttt) REVERT: v 221 ARG cc_start: 0.7412 (mtt180) cc_final: 0.7188 (ttm-80) REVERT: w 4 SER cc_start: 0.7795 (t) cc_final: 0.7495 (m) REVERT: w 8 LYS cc_start: 0.8076 (mttt) cc_final: 0.7706 (mtmt) REVERT: w 22 LEU cc_start: 0.8759 (tp) cc_final: 0.8473 (tt) REVERT: w 37 ASN cc_start: 0.8002 (OUTLIER) cc_final: 0.7678 (m110) REVERT: w 38 LYS cc_start: 0.7939 (mttt) cc_final: 0.7611 (mtmt) REVERT: w 78 ASP cc_start: 0.6511 (t0) cc_final: 0.6037 (t0) REVERT: w 143 LYS cc_start: 0.7569 (mppt) cc_final: 0.7342 (mmtp) REVERT: w 204 LYS cc_start: 0.6745 (OUTLIER) cc_final: 0.6500 (tmtt) REVERT: w 228 TYR cc_start: 0.7264 (m-80) cc_final: 0.6912 (m-10) REVERT: x 19 PHE cc_start: 0.7942 (m-80) cc_final: 0.6757 (t80) REVERT: x 48 ARG cc_start: 0.7187 (ttt-90) cc_final: 0.6656 (ttt-90) REVERT: x 50 GLN cc_start: 0.6367 (tp40) cc_final: 0.6052 (mm110) REVERT: x 62 ASN cc_start: 0.7353 (m-40) cc_final: 0.6908 (m110) REVERT: x 71 ASN cc_start: 0.7342 (m-40) cc_final: 0.6985 (m110) REVERT: x 79 ASP cc_start: 0.7617 (m-30) cc_final: 0.7375 (m-30) REVERT: x 141 LYS cc_start: 0.8252 (ttmm) cc_final: 0.7166 (mttm) REVERT: x 142 ARG cc_start: 0.8143 (mtt180) cc_final: 0.7764 (mtt180) REVERT: x 189 ARG cc_start: 0.7696 (mmt180) cc_final: 0.7271 (mmm160) REVERT: x 277 GLU cc_start: 0.8110 (pm20) cc_final: 0.7813 (pm20) REVERT: y 8 GLU cc_start: 0.6232 (mm-30) cc_final: 0.5787 (mp0) REVERT: y 206 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7569 (t) outliers start: 158 outliers final: 72 residues processed: 1216 average time/residue: 1.9678 time to fit residues: 3307.0346 Evaluate side-chains 1149 residues out of total 8126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1045 time to evaluate : 7.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 363 ASP Chi-restraints excluded: chain 3 residue 609 LEU Chi-restraints excluded: chain 3 residue 633 LEU Chi-restraints excluded: chain 3 residue 646 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 15 GLU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 166 ILE Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain K residue 70 ASP Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 237 LYS Chi-restraints excluded: chain K residue 243 THR Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain M residue 12 TRP Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain P residue 23 ARG Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain S residue 3 HIS Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain T residue 240 LEU Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain W residue 196 ASP Chi-restraints excluded: chain W residue 197 VAL Chi-restraints excluded: chain W residue 216 LYS Chi-restraints excluded: chain W residue 228 VAL Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 115 ARG Chi-restraints excluded: chain Z residue 67 LEU Chi-restraints excluded: chain Z residue 69 ASP Chi-restraints excluded: chain Z residue 124 LEU Chi-restraints excluded: chain Z residue 342 ILE Chi-restraints excluded: chain a residue 147 LYS Chi-restraints excluded: chain a residue 163 LEU Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 287 ILE Chi-restraints excluded: chain b residue 309 VAL Chi-restraints excluded: chain b residue 425 ASP Chi-restraints excluded: chain e residue 80 LYS Chi-restraints excluded: chain f residue 21 ARG Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 9 THR Chi-restraints excluded: chain m residue 156 THR Chi-restraints excluded: chain m residue 278 LYS Chi-restraints excluded: chain m residue 292 LYS Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 42 TYR Chi-restraints excluded: chain n residue 142 PHE Chi-restraints excluded: chain n residue 162 ILE Chi-restraints excluded: chain n residue 255 ILE Chi-restraints excluded: chain n residue 263 ILE Chi-restraints excluded: chain n residue 371 VAL Chi-restraints excluded: chain n residue 453 LEU Chi-restraints excluded: chain o residue 127 LYS Chi-restraints excluded: chain o residue 162 LEU Chi-restraints excluded: chain o residue 178 LYS Chi-restraints excluded: chain o residue 185 VAL Chi-restraints excluded: chain o residue 193 VAL Chi-restraints excluded: chain o residue 197 LYS Chi-restraints excluded: chain q residue 346 ASN Chi-restraints excluded: chain q residue 531 TYR Chi-restraints excluded: chain r residue 208 MET Chi-restraints excluded: chain r residue 223 VAL Chi-restraints excluded: chain t residue 104 THR Chi-restraints excluded: chain t residue 214 ILE Chi-restraints excluded: chain t residue 286 LEU Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain v residue 21 ASN Chi-restraints excluded: chain w residue 37 ASN Chi-restraints excluded: chain w residue 204 LYS Chi-restraints excluded: chain w residue 205 ILE Chi-restraints excluded: chain x residue 56 VAL Chi-restraints excluded: chain x residue 65 VAL Chi-restraints excluded: chain x residue 87 SER Chi-restraints excluded: chain y residue 52 THR Chi-restraints excluded: chain y residue 186 VAL Chi-restraints excluded: chain y residue 206 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1127 random chunks: chunk 664 optimal weight: 2.9990 chunk 1070 optimal weight: 4.9990 chunk 653 optimal weight: 6.9990 chunk 507 optimal weight: 5.9990 chunk 744 optimal weight: 8.9990 chunk 1122 optimal weight: 3.9990 chunk 1033 optimal weight: 0.0670 chunk 894 optimal weight: 7.9990 chunk 92 optimal weight: 30.0000 chunk 690 optimal weight: 10.0000 chunk 548 optimal weight: 20.0000 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 444 HIS A 165 ASN B 319 ASN C 58 HIS D 141 HIS H 51 GLN H 59 ASN H 163 GLN I 63 ASN J 284 HIS J 320 ASN N 23 GLN O 55 HIS P 92 GLN S 63 GLN ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 98 ASN h 16 GLN h 104 GLN ** n 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 40 GLN v 10 ASN ** v 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 210 GLN w 5 ASN ** x 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 128121 Z= 0.214 Angle : 0.567 16.829 183401 Z= 0.288 Chirality : 0.038 0.303 22273 Planarity : 0.005 0.077 15165 Dihedral : 21.332 179.753 43818 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.73 % Favored : 97.26 % Rotamer: Outliers : 1.81 % Allowed : 20.15 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.09), residues: 9119 helix: 1.97 (0.08), residues: 3821 sheet: 0.33 (0.14), residues: 1380 loop : -0.29 (0.10), residues: 3918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP w 54 HIS 0.036 0.001 HIS C 58 PHE 0.044 0.002 PHE D 96 TYR 0.025 0.002 TYR C 194 ARG 0.011 0.001 ARG N 50 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18238 Ramachandran restraints generated. 9119 Oldfield, 0 Emsley, 9119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18238 Ramachandran restraints generated. 9119 Oldfield, 0 Emsley, 9119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1208 residues out of total 8126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1061 time to evaluate : 7.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 633 LEU cc_start: 0.4867 (OUTLIER) cc_final: 0.4491 (mp) REVERT: 3 646 LEU cc_start: 0.2865 (OUTLIER) cc_final: 0.2355 (pp) REVERT: 8 294 LYS cc_start: 0.7169 (ttmt) cc_final: 0.6533 (tttt) REVERT: 8 298 LYS cc_start: 0.6851 (mtpt) cc_final: 0.6472 (tppt) REVERT: 8 302 LYS cc_start: 0.6474 (ttmt) cc_final: 0.6021 (tttp) REVERT: 8 327 LYS cc_start: 0.5209 (mtpp) cc_final: 0.4841 (mmtm) REVERT: A 49 ILE cc_start: 0.6677 (mt) cc_final: 0.6414 (pt) REVERT: A 167 ARG cc_start: 0.6423 (mtt180) cc_final: 0.6021 (mtp180) REVERT: B 56 ILE cc_start: 0.7957 (mt) cc_final: 0.7438 (pp) REVERT: B 287 LYS cc_start: 0.6405 (mmmm) cc_final: 0.5849 (mmmt) REVERT: B 300 ARG cc_start: 0.5919 (mtp180) cc_final: 0.5505 (tpp80) REVERT: C 18 ASN cc_start: 0.8007 (m110) cc_final: 0.7226 (t0) REVERT: C 73 ARG cc_start: 0.7878 (mpp-170) cc_final: 0.7457 (mmt90) REVERT: C 155 ASP cc_start: 0.7864 (m-30) cc_final: 0.7353 (m-30) REVERT: C 211 GLU cc_start: 0.8209 (tp30) cc_final: 0.7901 (mp0) REVERT: C 226 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8651 (mt-10) REVERT: C 257 LYS cc_start: 0.8585 (ttmm) cc_final: 0.8301 (mtpt) REVERT: C 265 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7509 (mt-10) REVERT: C 304 GLN cc_start: 0.8500 (mt0) cc_final: 0.8257 (mt0) REVERT: C 338 LYS cc_start: 0.7542 (mmtt) cc_final: 0.7299 (mttt) REVERT: D 65 MET cc_start: 0.5606 (mtp) cc_final: 0.5145 (mtp) REVERT: D 334 GLU cc_start: 0.6406 (OUTLIER) cc_final: 0.6198 (mm-30) REVERT: D 415 TYR cc_start: 0.6075 (m-80) cc_final: 0.5860 (m-10) REVERT: E 29 LYS cc_start: 0.7965 (ptmm) cc_final: 0.7583 (pttm) REVERT: E 146 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7671 (tt) REVERT: F 24 GLU cc_start: 0.7416 (tt0) cc_final: 0.7138 (mt-10) REVERT: F 25 GLN cc_start: 0.7494 (tt0) cc_final: 0.6985 (mt0) REVERT: F 30 ARG cc_start: 0.7706 (ttt-90) cc_final: 0.7379 (tmt90) REVERT: F 38 LYS cc_start: 0.8367 (tppp) cc_final: 0.7998 (tttt) REVERT: F 76 TYR cc_start: 0.7641 (t80) cc_final: 0.7339 (t80) REVERT: F 233 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6695 (mt-10) REVERT: F 234 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8039 (mp0) REVERT: G 84 ARG cc_start: 0.7055 (ttp-110) cc_final: 0.6657 (ttp80) REVERT: G 89 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7633 (mp0) REVERT: G 111 LYS cc_start: 0.8382 (ttpp) cc_final: 0.7850 (mtmm) REVERT: H 42 ASP cc_start: 0.8599 (m-30) cc_final: 0.8363 (m-30) REVERT: H 135 GLU cc_start: 0.7817 (pt0) cc_final: 0.7438 (pt0) REVERT: H 146 LEU cc_start: 0.7983 (mt) cc_final: 0.7587 (mp) REVERT: H 160 ASP cc_start: 0.7734 (m-30) cc_final: 0.7362 (m-30) REVERT: H 177 ASP cc_start: 0.7549 (m-30) cc_final: 0.7234 (m-30) REVERT: I 1 MET cc_start: 0.6777 (ttm) cc_final: 0.6519 (ttm) REVERT: I 15 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8030 (tt0) REVERT: I 75 HIS cc_start: 0.5722 (m-70) cc_final: 0.5405 (m-70) REVERT: I 119 ASP cc_start: 0.6680 (t0) cc_final: 0.6196 (OUTLIER) REVERT: I 124 GLU cc_start: 0.7293 (tt0) cc_final: 0.6884 (tp30) REVERT: I 128 SER cc_start: 0.7207 (m) cc_final: 0.6848 (p) REVERT: I 135 LYS cc_start: 0.8090 (ttpp) cc_final: 0.7884 (ttpm) REVERT: I 174 LYS cc_start: 0.7401 (mttt) cc_final: 0.6842 (mtpt) REVERT: I 218 GLU cc_start: 0.7290 (tt0) cc_final: 0.7075 (tt0) REVERT: I 224 GLN cc_start: 0.7535 (mm-40) cc_final: 0.7313 (mm-40) REVERT: I 236 LYS cc_start: 0.8285 (pttt) cc_final: 0.7962 (ptpp) REVERT: I 238 ASP cc_start: 0.8521 (p0) cc_final: 0.8114 (p0) REVERT: I 263 LYS cc_start: 0.6530 (mttt) cc_final: 0.5872 (mppt) REVERT: I 312 LYS cc_start: 0.8270 (mttt) cc_final: 0.7740 (mptm) REVERT: I 411 ASP cc_start: 0.7596 (m-30) cc_final: 0.6721 (p0) REVERT: J 201 MET cc_start: 0.4835 (mmt) cc_final: 0.4294 (mmt) REVERT: J 320 ASN cc_start: 0.5735 (OUTLIER) cc_final: 0.5528 (t0) REVERT: K 144 LEU cc_start: 0.5895 (mp) cc_final: 0.5600 (mt) REVERT: K 237 LYS cc_start: 0.5469 (ttmt) cc_final: 0.4988 (mtpt) REVERT: K 254 LEU cc_start: 0.5402 (mp) cc_final: 0.4660 (mt) REVERT: K 259 PHE cc_start: 0.4227 (m-80) cc_final: 0.3990 (m-10) REVERT: L 23 LYS cc_start: 0.7544 (ptmt) cc_final: 0.7113 (ttpp) REVERT: L 67 ARG cc_start: 0.7717 (ptm-80) cc_final: 0.7451 (ptm-80) REVERT: M 27 GLN cc_start: 0.7306 (tm-30) cc_final: 0.7000 (mt0) REVERT: M 83 LYS cc_start: 0.7973 (ttmt) cc_final: 0.7487 (tttm) REVERT: M 102 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.7631 (tmtp) REVERT: N 28 TRP cc_start: 0.7630 (t60) cc_final: 0.7322 (t-100) REVERT: N 31 ARG cc_start: 0.7383 (mtm110) cc_final: 0.7033 (mtt-85) REVERT: N 67 ARG cc_start: 0.7650 (mtp85) cc_final: 0.7197 (ttm-80) REVERT: N 127 TYR cc_start: 0.8288 (m-80) cc_final: 0.7905 (m-80) REVERT: O 73 PHE cc_start: 0.6969 (m-80) cc_final: 0.6253 (m-80) REVERT: O 170 LYS cc_start: 0.7845 (mtpt) cc_final: 0.7577 (mtpp) REVERT: P 23 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7976 (mtp-110) REVERT: Q 11 LYS cc_start: 0.7874 (tttt) cc_final: 0.7670 (tptm) REVERT: R 142 LYS cc_start: 0.8630 (ttpt) cc_final: 0.8226 (ttmt) REVERT: R 150 ARG cc_start: 0.8155 (tpt170) cc_final: 0.7558 (ttp80) REVERT: S 3 HIS cc_start: 0.6361 (OUTLIER) cc_final: 0.5681 (t-90) REVERT: S 8 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.8072 (tt0) REVERT: S 26 ARG cc_start: 0.6956 (mtt90) cc_final: 0.6708 (mtt90) REVERT: S 57 GLU cc_start: 0.7162 (tt0) cc_final: 0.6843 (pt0) REVERT: S 88 HIS cc_start: 0.7029 (m-70) cc_final: 0.6600 (m170) REVERT: S 119 ARG cc_start: 0.5976 (mtm110) cc_final: 0.5265 (mtm-85) REVERT: V 59 MET cc_start: 0.5766 (mmm) cc_final: 0.4977 (mmm) REVERT: V 83 LYS cc_start: 0.6624 (tttt) cc_final: 0.6084 (mppt) REVERT: W 8 LYS cc_start: 0.6018 (mmtt) cc_final: 0.5552 (tmtt) REVERT: W 152 GLU cc_start: 0.4155 (mp0) cc_final: 0.3740 (mp0) REVERT: W 162 GLU cc_start: 0.6077 (tp30) cc_final: 0.5358 (mm-30) REVERT: Y 38 GLU cc_start: 0.7550 (tt0) cc_final: 0.7171 (tm-30) REVERT: Y 69 LYS cc_start: 0.8279 (mttt) cc_final: 0.7921 (mtmm) REVERT: Y 115 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8194 (tpt-90) REVERT: Z 26 MET cc_start: 0.4338 (mtt) cc_final: 0.4008 (mtp) REVERT: Z 66 LYS cc_start: 0.3796 (mmpt) cc_final: 0.3061 (mtpt) REVERT: Z 67 LEU cc_start: 0.5345 (OUTLIER) cc_final: 0.4934 (tt) REVERT: Z 69 ASP cc_start: 0.2724 (OUTLIER) cc_final: 0.1917 (m-30) REVERT: Z 125 LYS cc_start: 0.2671 (mtpp) cc_final: 0.1803 (mptt) REVERT: Z 188 ARG cc_start: 0.4223 (OUTLIER) cc_final: 0.4013 (mtp180) REVERT: Z 204 ARG cc_start: 0.4466 (tpp-160) cc_final: 0.4056 (mtp-110) REVERT: a 102 LYS cc_start: 0.1757 (mmmt) cc_final: 0.1105 (mptt) REVERT: a 185 MET cc_start: 0.2055 (ppp) cc_final: 0.1329 (pmt) REVERT: a 210 MET cc_start: 0.3261 (ttt) cc_final: 0.2552 (tpp) REVERT: b 15 ASN cc_start: 0.4964 (OUTLIER) cc_final: 0.4727 (p0) REVERT: b 41 ARG cc_start: 0.5461 (mtp85) cc_final: 0.4832 (mpt180) REVERT: b 111 ASP cc_start: 0.5520 (t0) cc_final: 0.5304 (t70) REVERT: b 166 ASN cc_start: 0.5656 (m-40) cc_final: 0.5292 (m110) REVERT: b 209 PHE cc_start: 0.6250 (p90) cc_final: 0.5812 (p90) REVERT: b 383 LYS cc_start: 0.5732 (ttpp) cc_final: 0.5338 (ptmt) REVERT: b 384 ASN cc_start: 0.3065 (p0) cc_final: 0.2758 (p0) REVERT: b 425 ASP cc_start: 0.4437 (OUTLIER) cc_final: 0.3954 (m-30) REVERT: f 21 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.6860 (mtt90) REVERT: f 54 ARG cc_start: 0.8267 (mtp180) cc_final: 0.7756 (mtt-85) REVERT: h 61 GLN cc_start: 0.8131 (mt0) cc_final: 0.7830 (mt0) REVERT: i 56 ARG cc_start: 0.6901 (ttm-80) cc_final: 0.6542 (ttt180) REVERT: i 62 ARG cc_start: 0.6001 (mtm180) cc_final: 0.5573 (mtt180) REVERT: i 68 ARG cc_start: 0.7240 (mmm-85) cc_final: 0.6978 (mmm160) REVERT: i 71 LYS cc_start: 0.7945 (mtpp) cc_final: 0.7690 (mttp) REVERT: i 79 SER cc_start: 0.8462 (OUTLIER) cc_final: 0.8111 (t) REVERT: i 81 THR cc_start: 0.8490 (p) cc_final: 0.7912 (m) REVERT: i 86 LYS cc_start: 0.8319 (tppt) cc_final: 0.7978 (tppt) REVERT: i 89 GLU cc_start: 0.7848 (tt0) cc_final: 0.7565 (tt0) REVERT: i 90 MET cc_start: 0.8238 (mmp) cc_final: 0.7941 (mmm) REVERT: j 25 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8388 (tmm-80) REVERT: l 1 MET cc_start: 0.1502 (mpp) cc_final: 0.1066 (mtt) REVERT: l 136 MET cc_start: 0.2018 (mpt) cc_final: 0.1278 (ptt) REVERT: m 292 LYS cc_start: 0.5821 (OUTLIER) cc_final: 0.5538 (ptpt) REVERT: n 42 TYR cc_start: 0.3157 (OUTLIER) cc_final: 0.2841 (m-80) REVERT: o 178 LYS cc_start: 0.6976 (OUTLIER) cc_final: 0.6596 (mttt) REVERT: o 193 VAL cc_start: 0.4358 (OUTLIER) cc_final: 0.4052 (m) REVERT: o 194 LYS cc_start: 0.4266 (pptt) cc_final: 0.3659 (ttmt) REVERT: q 261 PHE cc_start: 0.2025 (t80) cc_final: 0.1669 (t80) REVERT: q 291 ASN cc_start: 0.5010 (m-40) cc_final: 0.4714 (m-40) REVERT: q 346 ASN cc_start: 0.3842 (OUTLIER) cc_final: 0.3029 (p0) REVERT: r 13 GLN cc_start: 0.6940 (mm-40) cc_final: 0.6714 (mt0) REVERT: r 133 MET cc_start: 0.2488 (ttt) cc_final: 0.2264 (tpt) REVERT: r 208 MET cc_start: 0.4832 (OUTLIER) cc_final: 0.4552 (tpt) REVERT: r 222 GLU cc_start: 0.2965 (tp30) cc_final: 0.2490 (tp30) REVERT: u 48 LYS cc_start: 0.5387 (mtmt) cc_final: 0.4919 (mmtp) REVERT: u 49 LEU cc_start: 0.6784 (mm) cc_final: 0.6499 (mp) REVERT: v 24 LYS cc_start: 0.8037 (mmtt) cc_final: 0.7605 (mttt) REVERT: v 26 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7366 (tpp-160) REVERT: v 197 LYS cc_start: 0.7396 (ttmt) cc_final: 0.6707 (ttpp) REVERT: v 203 LYS cc_start: 0.7861 (ptpt) cc_final: 0.6969 (mttt) REVERT: v 221 ARG cc_start: 0.7506 (mtt180) cc_final: 0.7216 (ttm-80) REVERT: w 4 SER cc_start: 0.7828 (t) cc_final: 0.7520 (m) REVERT: w 8 LYS cc_start: 0.8075 (mttt) cc_final: 0.7700 (mtmt) REVERT: w 22 LEU cc_start: 0.8806 (tp) cc_final: 0.8537 (tt) REVERT: w 37 ASN cc_start: 0.8066 (OUTLIER) cc_final: 0.7784 (m110) REVERT: w 38 LYS cc_start: 0.8026 (mttt) cc_final: 0.7741 (mtmm) REVERT: w 78 ASP cc_start: 0.6698 (t0) cc_final: 0.6224 (t0) REVERT: w 204 LYS cc_start: 0.6867 (OUTLIER) cc_final: 0.6643 (tmtt) REVERT: w 228 TYR cc_start: 0.7262 (m-80) cc_final: 0.6875 (m-10) REVERT: x 19 PHE cc_start: 0.8137 (m-80) cc_final: 0.6688 (t80) REVERT: x 48 ARG cc_start: 0.7291 (ttt-90) cc_final: 0.6683 (ttt-90) REVERT: x 50 GLN cc_start: 0.6390 (tp40) cc_final: 0.6057 (mm110) REVERT: x 62 ASN cc_start: 0.7462 (m-40) cc_final: 0.7059 (m110) REVERT: x 71 ASN cc_start: 0.7453 (m-40) cc_final: 0.7051 (m110) REVERT: x 79 ASP cc_start: 0.7613 (m-30) cc_final: 0.7372 (m-30) REVERT: x 142 ARG cc_start: 0.8073 (mtt180) cc_final: 0.7670 (mtt180) REVERT: x 189 ARG cc_start: 0.7811 (mmt180) cc_final: 0.7383 (mmt90) REVERT: x 277 GLU cc_start: 0.8132 (pm20) cc_final: 0.7857 (pm20) REVERT: y 8 GLU cc_start: 0.6265 (mm-30) cc_final: 0.5853 (mp0) REVERT: y 206 THR cc_start: 0.7935 (OUTLIER) cc_final: 0.7553 (t) outliers start: 147 outliers final: 73 residues processed: 1166 average time/residue: 2.0425 time to fit residues: 3301.0953 Evaluate side-chains 1148 residues out of total 8126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1044 time to evaluate : 7.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 609 LEU Chi-restraints excluded: chain 3 residue 628 MET Chi-restraints excluded: chain 3 residue 633 LEU Chi-restraints excluded: chain 3 residue 646 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 15 GLU Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain K residue 70 ASP Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 131 ASP Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 243 THR Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 190 THR Chi-restraints excluded: chain P residue 23 ARG Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain S residue 3 HIS Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain W residue 102 LEU Chi-restraints excluded: chain W residue 196 ASP Chi-restraints excluded: chain W residue 197 VAL Chi-restraints excluded: chain W residue 216 LYS Chi-restraints excluded: chain W residue 228 VAL Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 115 ARG Chi-restraints excluded: chain Z residue 67 LEU Chi-restraints excluded: chain Z residue 69 ASP Chi-restraints excluded: chain Z residue 124 LEU Chi-restraints excluded: chain Z residue 188 ARG Chi-restraints excluded: chain Z residue 342 ILE Chi-restraints excluded: chain a residue 147 LYS Chi-restraints excluded: chain a residue 163 LEU Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain b residue 15 ASN Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 287 ILE Chi-restraints excluded: chain b residue 309 VAL Chi-restraints excluded: chain b residue 425 ASP Chi-restraints excluded: chain e residue 80 LYS Chi-restraints excluded: chain f residue 21 ARG Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 25 ARG Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain l residue 9 THR Chi-restraints excluded: chain m residue 156 THR Chi-restraints excluded: chain m residue 292 LYS Chi-restraints excluded: chain m residue 384 ILE Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 42 TYR Chi-restraints excluded: chain n residue 162 ILE Chi-restraints excluded: chain n residue 255 ILE Chi-restraints excluded: chain n residue 453 LEU Chi-restraints excluded: chain o residue 162 LEU Chi-restraints excluded: chain o residue 178 LYS Chi-restraints excluded: chain o residue 185 VAL Chi-restraints excluded: chain o residue 193 VAL Chi-restraints excluded: chain o residue 197 LYS Chi-restraints excluded: chain q residue 346 ASN Chi-restraints excluded: chain r residue 59 VAL Chi-restraints excluded: chain r residue 208 MET Chi-restraints excluded: chain r residue 223 VAL Chi-restraints excluded: chain t residue 104 THR Chi-restraints excluded: chain t residue 214 ILE Chi-restraints excluded: chain t residue 286 LEU Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain v residue 21 ASN Chi-restraints excluded: chain v residue 26 ARG Chi-restraints excluded: chain w residue 37 ASN Chi-restraints excluded: chain w residue 204 LYS Chi-restraints excluded: chain w residue 205 ILE Chi-restraints excluded: chain x residue 56 VAL Chi-restraints excluded: chain x residue 65 VAL Chi-restraints excluded: chain x residue 87 SER Chi-restraints excluded: chain y residue 52 THR Chi-restraints excluded: chain y residue 186 VAL Chi-restraints excluded: chain y residue 206 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1127 random chunks: chunk 710 optimal weight: 20.0000 chunk 952 optimal weight: 0.0570 chunk 273 optimal weight: 20.0000 chunk 824 optimal weight: 3.9990 chunk 132 optimal weight: 30.0000 chunk 248 optimal weight: 30.0000 chunk 895 optimal weight: 5.9990 chunk 374 optimal weight: 10.0000 chunk 919 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 164 optimal weight: 20.0000 overall best weight: 6.0108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN A 165 ASN C 58 HIS D 141 HIS H 51 GLN H 59 ASN H 163 GLN I 63 ASN J 284 HIS J 320 ASN K 104 HIS N 23 GLN O 55 HIS ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 132 ASN Y 98 ASN a 12 HIS a 127 GLN h 16 GLN h 104 GLN ** m 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 163 GLN q 344 HIS v 10 ASN ** v 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 210 GLN w 5 ASN ** x 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 90 ASN y 6 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.224775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.181111 restraints weight = 112730.801| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.43 r_work: 0.3542 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 128121 Z= 0.324 Angle : 0.688 18.281 183401 Z= 0.349 Chirality : 0.043 0.339 22273 Planarity : 0.006 0.077 15165 Dihedral : 21.601 178.606 43817 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.24 % Allowed : 19.85 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.09), residues: 9119 helix: 1.43 (0.08), residues: 3813 sheet: 0.12 (0.14), residues: 1356 loop : -0.52 (0.09), residues: 3950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 230 HIS 0.011 0.002 HIS b 75 PHE 0.047 0.003 PHE D 96 TYR 0.031 0.002 TYR C 194 ARG 0.022 0.001 ARG a 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 48186.62 seconds wall clock time: 829 minutes 13.15 seconds (49753.15 seconds total)