Starting phenix.real_space_refine on Sun Sep 29 00:06:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u4t_26334/09_2024/7u4t_26334.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u4t_26334/09_2024/7u4t_26334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u4t_26334/09_2024/7u4t_26334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u4t_26334/09_2024/7u4t_26334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u4t_26334/09_2024/7u4t_26334.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u4t_26334/09_2024/7u4t_26334.cif" } resolution = 3.6 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= 0.002 sd= 0.085 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 380 5.16 5 C 45606 2.51 5 N 12205 2.21 5 O 13405 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 71598 Number of models: 1 Model: "" Number of chains: 40 Chain: "R" Number of atoms: 5876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 753, 5876 Classifications: {'peptide': 753} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 32, 'TRANS': 720} Chain breaks: 2 Unresolved non-hydrogen bonds: 283 Unresolved non-hydrogen angles: 360 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 7, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 178 Chain: "O" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 1817 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 328} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 355} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1202 Unresolved non-hydrogen angles: 1536 Unresolved non-hydrogen dihedrals: 1003 Unresolved non-hydrogen chiralities: 108 Planarities with less than four sites: {'GLN:plan1': 16, 'ARG:plan': 14, 'TYR:plan': 15, 'ASN:plan1': 24, 'TRP:plan': 6, 'HIS:plan': 6, 'PHE:plan': 14, 'GLU:plan': 25, 'ASP:plan': 24} Unresolved non-hydrogen planarities: 651 Chain: "J" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1774 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 219} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "M" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 889 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 1, 'TRANS': 112} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "I" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1661 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 5, 'TRANS': 215} Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 9, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 86 Chain: "L" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 748 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 1, 'TRANS': 111} Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 123 Chain: "H" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1611 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 5, 'TRANS': 214} Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 11, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 117 Chain: "K" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 735 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 1, 'TRANS': 112} Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 132 Chain: "S" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 631 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 6, 'TRANS': 70} Chain: "T" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 658 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain: "U" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1662 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "V" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 411 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} Chain: "0" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1498 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 5, 'TRANS': 198} Chain: "1" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "2" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "3" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "4" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "5" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "6" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "7" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "8" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "9" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "Q" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2844 Classifications: {'peptide': 351} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 337} Chain: "C" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 30, 'TRANS': 569} Chain: "A" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "B" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "D" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3666 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 440} Chain: "E" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3666 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 440} Chain: "Z" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2110 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 252} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 2136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2136 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 257} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2111 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 252} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "G" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1717 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 3, 'TRANS': 209} Chain: "N" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 875 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "P" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 2121 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 385} Link IDs: {'PTRANS': 9, 'TRANS': 417} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1457 Unresolved non-hydrogen angles: 1855 Unresolved non-hydrogen dihedrals: 1231 Unresolved non-hydrogen chiralities: 110 Planarities with less than four sites: {'GLN:plan1': 33, 'HIS:plan': 11, 'TYR:plan': 17, 'ASN:plan1': 21, 'TRP:plan': 8, 'ASP:plan': 18, 'PHE:plan': 17, 'GLU:plan': 38, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 859 Chain: "W" Number of atoms: 3023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3023 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 19, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 288 Unresolved non-hydrogen angles: 355 Unresolved non-hydrogen dihedrals: 234 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 11, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 149 Chain: "F" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3666 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 440} Chain: "R" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 32.14, per 1000 atoms: 0.45 Number of scatterers: 71598 At special positions: 0 Unit cell: (224.64, 267.84, 220.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 380 16.00 P 2 15.00 O 13405 8.00 N 12205 7.00 C 45606 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS U 371 " - pdb=" SG CYS U 418 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG R 901 " - " ASN R 488 " " NAG S 101 " - " ASN S 70 " " NAG U 501 " - " ASN U 350 " " NAG U 503 " - " ASN U 261 " " NAG U 506 " - " ASN U 273 " Time building additional restraints: 14.34 Conformation dependent library (CDL) restraints added in 7.7 seconds 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17872 Finding SS restraints... Secondary structure from input PDB file: 355 helices and 46 sheets defined 61.3% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.62 Creating SS restraints... Processing helix chain 'R' and resid 18 through 33 removed outlier: 4.000A pdb=" N CYS R 24 " --> pdb=" O GLU R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 49 removed outlier: 3.645A pdb=" N ARG R 49 " --> pdb=" O VAL R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 76 Processing helix chain 'R' and resid 93 through 134 removed outlier: 4.447A pdb=" N ALA R 117 " --> pdb=" O THR R 113 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS R 119 " --> pdb=" O GLN R 115 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU R 127 " --> pdb=" O LEU R 123 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU R 128 " --> pdb=" O GLU R 124 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU R 132 " --> pdb=" O LEU R 128 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 191 Processing helix chain 'R' and resid 226 through 240 Processing helix chain 'R' and resid 252 through 309 removed outlier: 3.566A pdb=" N GLU R 256 " --> pdb=" O GLN R 252 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN R 289 " --> pdb=" O ALA R 285 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ARG R 291 " --> pdb=" O ALA R 287 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL R 292 " --> pdb=" O LYS R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 329 through 344 Processing helix chain 'R' and resid 372 through 380 Processing helix chain 'R' and resid 391 through 396 Processing helix chain 'R' and resid 397 through 407 Processing helix chain 'R' and resid 409 through 426 Processing helix chain 'R' and resid 426 through 432 Processing helix chain 'R' and resid 437 through 445 removed outlier: 4.255A pdb=" N VAL R 443 " --> pdb=" O MET R 439 " (cutoff:3.500A) Processing helix chain 'R' and resid 446 through 464 Processing helix chain 'R' and resid 481 through 488 removed outlier: 3.781A pdb=" N PHE R 485 " --> pdb=" O VAL R 481 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR R 486 " --> pdb=" O ARG R 482 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR R 487 " --> pdb=" O PRO R 483 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN R 488 " --> pdb=" O MET R 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 481 through 488' Processing helix chain 'R' and resid 490 through 497 Processing helix chain 'R' and resid 519 through 525 Processing helix chain 'R' and resid 527 through 554 removed outlier: 3.809A pdb=" N PHE R 531 " --> pdb=" O ASN R 527 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ASN R 533 " --> pdb=" O LEU R 529 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL R 541 " --> pdb=" O MET R 537 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU R 554 " --> pdb=" O PHE R 550 " (cutoff:3.500A) Processing helix chain 'R' and resid 554 through 563 removed outlier: 3.634A pdb=" N ASN R 558 " --> pdb=" O LEU R 554 " (cutoff:3.500A) Processing helix chain 'R' and resid 565 through 570 Processing helix chain 'R' and resid 571 through 597 removed outlier: 4.423A pdb=" N TYR R 585 " --> pdb=" O SER R 581 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU R 586 " --> pdb=" O LEU R 582 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL R 587 " --> pdb=" O PHE R 583 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE R 588 " --> pdb=" O GLY R 584 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR R 597 " --> pdb=" O LYS R 593 " (cutoff:3.500A) Processing helix chain 'R' and resid 601 through 605 removed outlier: 3.523A pdb=" N ASN R 604 " --> pdb=" O THR R 601 " (cutoff:3.500A) Processing helix chain 'R' and resid 607 through 617 removed outlier: 3.740A pdb=" N HIS R 611 " --> pdb=" O SER R 607 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE R 612 " --> pdb=" O LEU R 608 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE R 616 " --> pdb=" O PHE R 612 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU R 617 " --> pdb=" O ILE R 613 " (cutoff:3.500A) Processing helix chain 'R' and resid 631 through 652 removed outlier: 3.743A pdb=" N VAL R 647 " --> pdb=" O ALA R 643 " (cutoff:3.500A) Proline residue: R 648 - end of helix Processing helix chain 'R' and resid 652 through 666 Processing helix chain 'R' and resid 712 through 738 removed outlier: 4.068A pdb=" N THR R 735 " --> pdb=" O CYS R 731 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA R 736 " --> pdb=" O ILE R 732 " (cutoff:3.500A) Processing helix chain 'R' and resid 739 through 758 Processing helix chain 'R' and resid 759 through 764 Processing helix chain 'R' and resid 767 through 789 removed outlier: 3.598A pdb=" N GLY R 772 " --> pdb=" O SER R 768 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU R 775 " --> pdb=" O GLY R 771 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE R 776 " --> pdb=" O GLY R 772 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE R 777 " --> pdb=" O LEU R 773 " (cutoff:3.500A) Processing helix chain 'R' and resid 792 through 809 removed outlier: 4.304A pdb=" N PHE R 799 " --> pdb=" O GLY R 795 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 23 removed outlier: 3.710A pdb=" N GLU O 20 " --> pdb=" O GLN O 16 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LYS O 21 " --> pdb=" O GLN O 17 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS O 23 " --> pdb=" O TRP O 19 " (cutoff:3.500A) Processing helix chain 'O' and resid 47 through 80 removed outlier: 3.971A pdb=" N ASP O 56 " --> pdb=" O VAL O 52 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU O 80 " --> pdb=" O MET O 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 97 through 104 Processing helix chain 'O' and resid 117 through 157 Processing helix chain 'O' and resid 171 through 175 Processing helix chain 'O' and resid 193 through 202 removed outlier: 4.111A pdb=" N GLU O 202 " --> pdb=" O ILE O 198 " (cutoff:3.500A) Processing helix chain 'O' and resid 233 through 243 Processing helix chain 'O' and resid 254 through 311 Proline residue: O 278 - end of helix removed outlier: 4.364A pdb=" N ARG O 281 " --> pdb=" O GLY O 277 " (cutoff:3.500A) Processing helix chain 'O' and resid 327 through 340 Processing helix chain 'J' and resid 6 through 107 removed outlier: 3.535A pdb=" N LYS J 10 " --> pdb=" O ALA J 6 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN J 11 " --> pdb=" O ASP J 7 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS J 13 " --> pdb=" O GLN J 9 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS J 14 " --> pdb=" O LYS J 10 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET J 15 " --> pdb=" O GLN J 11 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU J 36 " --> pdb=" O ALA J 32 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU J 37 " --> pdb=" O LYS J 33 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE J 38 " --> pdb=" O ALA J 34 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN J 39 " --> pdb=" O GLU J 35 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG J 44 " --> pdb=" O ILE J 40 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LEU J 51 " --> pdb=" O GLN J 47 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS J 107 " --> pdb=" O SER J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 128 Processing helix chain 'J' and resid 137 through 139 No H-bonds generated for 'chain 'J' and resid 137 through 139' Processing helix chain 'J' and resid 140 through 158 Proline residue: J 153 - end of helix Processing helix chain 'J' and resid 195 through 206 Processing helix chain 'J' and resid 207 through 217 Processing helix chain 'M' and resid 4 through 104 removed outlier: 3.830A pdb=" N GLN M 9 " --> pdb=" O SER M 5 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA M 19 " --> pdb=" O GLU M 15 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU M 24 " --> pdb=" O GLU M 20 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS M 37 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU M 38 " --> pdb=" O LYS M 34 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA M 40 " --> pdb=" O ALA M 36 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS M 53 " --> pdb=" O LEU M 49 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU M 54 " --> pdb=" O GLN M 50 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU M 59 " --> pdb=" O PHE M 55 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL M 73 " --> pdb=" O CYS M 69 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU M 79 " --> pdb=" O LYS M 75 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR M 82 " --> pdb=" O GLN M 78 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU M 84 " --> pdb=" O LYS M 80 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN M 90 " --> pdb=" O THR M 86 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN M 91 " --> pdb=" O TYR M 87 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG M 92 " --> pdb=" O PHE M 88 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP M 93 " --> pdb=" O ARG M 89 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU M 94 " --> pdb=" O GLN M 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 107 removed outlier: 3.791A pdb=" N LYS I 42 " --> pdb=" O PHE I 38 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS I 107 " --> pdb=" O SER I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 128 Processing helix chain 'I' and resid 140 through 158 Proline residue: I 153 - end of helix removed outlier: 3.990A pdb=" N ALA I 158 " --> pdb=" O MET I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 206 Processing helix chain 'I' and resid 207 through 217 Processing helix chain 'L' and resid 5 through 104 removed outlier: 3.848A pdb=" N GLU L 24 " --> pdb=" O GLU L 20 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA L 25 " --> pdb=" O LYS L 21 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU L 38 " --> pdb=" O LYS L 34 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU L 54 " --> pdb=" O GLN L 50 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU L 63 " --> pdb=" O GLU L 59 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ASP L 93 " --> pdb=" O ARG L 89 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N GLU L 94 " --> pdb=" O GLN L 90 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL L 95 " --> pdb=" O ASN L 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 105 removed outlier: 3.655A pdb=" N GLU H 22 " --> pdb=" O PHE H 18 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU H 90 " --> pdb=" O ALA H 86 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN H 100 " --> pdb=" O ASN H 96 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG H 101 " --> pdb=" O GLU H 97 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU H 102 " --> pdb=" O ALA H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 128 Processing helix chain 'H' and resid 140 through 158 Proline residue: H 153 - end of helix removed outlier: 3.868A pdb=" N ALA H 158 " --> pdb=" O MET H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 206 Processing helix chain 'H' and resid 207 through 216 Processing helix chain 'K' and resid 4 through 104 removed outlier: 4.253A pdb=" N GLN K 13 " --> pdb=" O GLN K 9 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA K 14 " --> pdb=" O GLN K 10 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU K 15 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS K 16 " --> pdb=" O LEU K 12 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU K 63 " --> pdb=" O GLU K 59 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU K 76 " --> pdb=" O GLU K 72 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ASP K 93 " --> pdb=" O ARG K 89 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N GLU K 94 " --> pdb=" O GLN K 90 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 23 removed outlier: 3.598A pdb=" N LEU S 10 " --> pdb=" O LEU S 6 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU S 23 " --> pdb=" O PHE S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 28 Processing helix chain 'S' and resid 33 through 59 removed outlier: 3.684A pdb=" N ALA S 58 " --> pdb=" O ILE S 54 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLN S 59 " --> pdb=" O ALA S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 70 through 78 removed outlier: 3.684A pdb=" N LYS S 77 " --> pdb=" O ILE S 73 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR S 78 " --> pdb=" O TRP S 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 74 removed outlier: 3.941A pdb=" N ALA T 52 " --> pdb=" O PRO T 48 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS T 53 " --> pdb=" O LYS T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 97 through 129 Processing helix chain 'U' and resid 286 through 289 Processing helix chain 'U' and resid 423 through 449 removed outlier: 3.577A pdb=" N SER U 449 " --> pdb=" O HIS U 445 " (cutoff:3.500A) Processing helix chain 'V' and resid 302 through 330 Processing helix chain '0' and resid 2 through 28 Processing helix chain '0' and resid 31 through 35 Processing helix chain '0' and resid 36 through 44 removed outlier: 3.544A pdb=" N PHE 0 40 " --> pdb=" O ASP 0 36 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR 0 44 " --> pdb=" O PHE 0 40 " (cutoff:3.500A) Processing helix chain '0' and resid 46 through 80 removed outlier: 4.416A pdb=" N SER 0 75 " --> pdb=" O ILE 0 71 " (cutoff:3.500A) Processing helix chain '0' and resid 85 through 89 Processing helix chain '0' and resid 90 through 113 removed outlier: 4.461A pdb=" N ILE 0 94 " --> pdb=" O ASN 0 90 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA 0 101 " --> pdb=" O CYS 0 97 " (cutoff:3.500A) Processing helix chain '0' and resid 130 through 167 removed outlier: 3.877A pdb=" N ALA 0 167 " --> pdb=" O ALA 0 163 " (cutoff:3.500A) Processing helix chain '0' and resid 177 through 198 removed outlier: 4.018A pdb=" N ILE 0 186 " --> pdb=" O PHE 0 182 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY 0 187 " --> pdb=" O GLY 0 183 " (cutoff:3.500A) Processing helix chain '1' and resid 10 through 46 removed outlier: 4.456A pdb=" N PHE 1 14 " --> pdb=" O TYR 1 10 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA 1 15 " --> pdb=" O ALA 1 11 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA 1 21 " --> pdb=" O MET 1 17 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL 1 46 " --> pdb=" O ALA 1 42 " (cutoff:3.500A) Processing helix chain '1' and resid 48 through 55 removed outlier: 3.915A pdb=" N GLN 1 51 " --> pdb=" O ARG 1 48 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N MET 1 53 " --> pdb=" O GLU 1 50 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS 1 54 " --> pdb=" O GLN 1 51 " (cutoff:3.500A) Processing helix chain '1' and resid 56 through 79 removed outlier: 3.918A pdb=" N SER 1 79 " --> pdb=" O LEU 1 75 " (cutoff:3.500A) Processing helix chain '1' and resid 87 through 122 Processing helix chain '1' and resid 126 through 154 removed outlier: 4.739A pdb=" N GLY 1 130 " --> pdb=" O ARG 1 126 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY 1 142 " --> pdb=" O ALA 1 138 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU 1 143 " --> pdb=" O GLU 1 139 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL 1 148 " --> pdb=" O TYR 1 144 " (cutoff:3.500A) Processing helix chain '2' and resid 10 through 45 removed outlier: 4.292A pdb=" N PHE 2 14 " --> pdb=" O TYR 2 10 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA 2 15 " --> pdb=" O ALA 2 11 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA 2 21 " --> pdb=" O MET 2 17 " (cutoff:3.500A) Processing helix chain '2' and resid 48 through 55 removed outlier: 4.138A pdb=" N GLN 2 51 " --> pdb=" O ARG 2 48 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE 2 52 " --> pdb=" O PRO 2 49 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N MET 2 53 " --> pdb=" O GLU 2 50 " (cutoff:3.500A) Processing helix chain '2' and resid 56 through 79 removed outlier: 3.557A pdb=" N ILE 2 65 " --> pdb=" O MET 2 61 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA 2 66 " --> pdb=" O ALA 2 62 " (cutoff:3.500A) Processing helix chain '2' and resid 87 through 122 removed outlier: 3.550A pdb=" N ALA 2 122 " --> pdb=" O VAL 2 118 " (cutoff:3.500A) Processing helix chain '2' and resid 124 through 126 No H-bonds generated for 'chain '2' and resid 124 through 126' Processing helix chain '2' and resid 127 through 155 removed outlier: 3.600A pdb=" N LEU 2 141 " --> pdb=" O PHE 2 137 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY 2 142 " --> pdb=" O ALA 2 138 " (cutoff:3.500A) Processing helix chain '3' and resid 11 through 44 removed outlier: 4.071A pdb=" N ALA 3 15 " --> pdb=" O ALA 3 11 " (cutoff:3.500A) Processing helix chain '3' and resid 48 through 55 removed outlier: 4.363A pdb=" N GLN 3 51 " --> pdb=" O ARG 3 48 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N MET 3 53 " --> pdb=" O GLU 3 50 " (cutoff:3.500A) Processing helix chain '3' and resid 56 through 79 Processing helix chain '3' and resid 87 through 122 removed outlier: 3.900A pdb=" N ALA 3 122 " --> pdb=" O VAL 3 118 " (cutoff:3.500A) Processing helix chain '3' and resid 123 through 126 removed outlier: 7.057A pdb=" N ARG 3 126 " --> pdb=" O GLN 3 123 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 123 through 126' Processing helix chain '3' and resid 127 through 154 removed outlier: 3.504A pdb=" N ILE 3 134 " --> pdb=" O GLY 3 130 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY 3 142 " --> pdb=" O ALA 3 138 " (cutoff:3.500A) Processing helix chain '4' and resid 11 through 45 removed outlier: 3.963A pdb=" N ALA 4 15 " --> pdb=" O ALA 4 11 " (cutoff:3.500A) Processing helix chain '4' and resid 52 through 55 Processing helix chain '4' and resid 56 through 79 Processing helix chain '4' and resid 86 through 121 removed outlier: 3.604A pdb=" N PHE 4 90 " --> pdb=" O LEU 4 86 " (cutoff:3.500A) Processing helix chain '4' and resid 127 through 155 removed outlier: 3.583A pdb=" N LEU 4 141 " --> pdb=" O PHE 4 137 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY 4 142 " --> pdb=" O ALA 4 138 " (cutoff:3.500A) Processing helix chain '5' and resid 10 through 45 removed outlier: 4.191A pdb=" N PHE 5 14 " --> pdb=" O TYR 5 10 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA 5 15 " --> pdb=" O ALA 5 11 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA 5 21 " --> pdb=" O MET 5 17 " (cutoff:3.500A) Processing helix chain '5' and resid 48 through 55 removed outlier: 3.961A pdb=" N GLN 5 51 " --> pdb=" O ARG 5 48 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE 5 52 " --> pdb=" O PRO 5 49 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N MET 5 53 " --> pdb=" O GLU 5 50 " (cutoff:3.500A) Processing helix chain '5' and resid 56 through 79 removed outlier: 3.858A pdb=" N ALA 5 66 " --> pdb=" O ALA 5 62 " (cutoff:3.500A) Processing helix chain '5' and resid 87 through 122 removed outlier: 3.511A pdb=" N ALA 5 122 " --> pdb=" O VAL 5 118 " (cutoff:3.500A) Processing helix chain '5' and resid 123 through 126 removed outlier: 6.716A pdb=" N ARG 5 126 " --> pdb=" O GLN 5 123 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 123 through 126' Processing helix chain '5' and resid 127 through 154 removed outlier: 4.133A pdb=" N LEU 5 141 " --> pdb=" O PHE 5 137 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY 5 142 " --> pdb=" O ALA 5 138 " (cutoff:3.500A) Processing helix chain '6' and resid 11 through 45 removed outlier: 3.900A pdb=" N ALA 6 15 " --> pdb=" O ALA 6 11 " (cutoff:3.500A) Processing helix chain '6' and resid 52 through 55 Processing helix chain '6' and resid 56 through 79 removed outlier: 3.662A pdb=" N VAL 6 60 " --> pdb=" O ILE 6 56 " (cutoff:3.500A) Processing helix chain '6' and resid 87 through 121 Processing helix chain '6' and resid 122 through 123 No H-bonds generated for 'chain '6' and resid 122 through 123' Processing helix chain '6' and resid 124 through 126 No H-bonds generated for 'chain '6' and resid 124 through 126' Processing helix chain '6' and resid 127 through 154 removed outlier: 3.534A pdb=" N ILE 6 134 " --> pdb=" O GLY 6 130 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE 6 147 " --> pdb=" O LEU 6 143 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL 6 148 " --> pdb=" O TYR 6 144 " (cutoff:3.500A) Processing helix chain '7' and resid 10 through 45 removed outlier: 3.720A pdb=" N PHE 7 14 " --> pdb=" O TYR 7 10 " (cutoff:3.500A) Processing helix chain '7' and resid 48 through 55 removed outlier: 3.995A pdb=" N GLN 7 51 " --> pdb=" O ARG 7 48 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE 7 52 " --> pdb=" O PRO 7 49 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N MET 7 53 " --> pdb=" O GLU 7 50 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS 7 54 " --> pdb=" O GLN 7 51 " (cutoff:3.500A) Processing helix chain '7' and resid 56 through 79 removed outlier: 3.660A pdb=" N VAL 7 60 " --> pdb=" O ILE 7 56 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER 7 79 " --> pdb=" O LEU 7 75 " (cutoff:3.500A) Processing helix chain '7' and resid 87 through 122 removed outlier: 3.504A pdb=" N ALA 7 122 " --> pdb=" O VAL 7 118 " (cutoff:3.500A) Processing helix chain '7' and resid 123 through 126 removed outlier: 6.970A pdb=" N ARG 7 126 " --> pdb=" O GLN 7 123 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 123 through 126' Processing helix chain '7' and resid 127 through 155 removed outlier: 3.572A pdb=" N ILE 7 134 " --> pdb=" O GLY 7 130 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY 7 142 " --> pdb=" O ALA 7 138 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU 7 143 " --> pdb=" O GLU 7 139 " (cutoff:3.500A) Processing helix chain '8' and resid 10 through 46 removed outlier: 3.943A pdb=" N PHE 8 14 " --> pdb=" O TYR 8 10 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL 8 46 " --> pdb=" O ALA 8 42 " (cutoff:3.500A) Processing helix chain '8' and resid 48 through 50 No H-bonds generated for 'chain '8' and resid 48 through 50' Processing helix chain '8' and resid 51 through 56 Processing helix chain '8' and resid 56 through 80 removed outlier: 3.802A pdb=" N ILE 8 65 " --> pdb=" O MET 8 61 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA 8 66 " --> pdb=" O ALA 8 62 " (cutoff:3.500A) Processing helix chain '8' and resid 87 through 121 Processing helix chain '8' and resid 122 through 123 No H-bonds generated for 'chain '8' and resid 122 through 123' Processing helix chain '8' and resid 124 through 126 No H-bonds generated for 'chain '8' and resid 124 through 126' Processing helix chain '8' and resid 127 through 155 removed outlier: 3.901A pdb=" N LEU 8 141 " --> pdb=" O PHE 8 137 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY 8 142 " --> pdb=" O ALA 8 138 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS 8 155 " --> pdb=" O ILE 8 151 " (cutoff:3.500A) Processing helix chain '9' and resid 10 through 45 removed outlier: 3.666A pdb=" N PHE 9 14 " --> pdb=" O TYR 9 10 " (cutoff:3.500A) Processing helix chain '9' and resid 52 through 55 Processing helix chain '9' and resid 56 through 79 Processing helix chain '9' and resid 87 through 122 removed outlier: 3.500A pdb=" N LEU 9 91 " --> pdb=" O TYR 9 87 " (cutoff:3.500A) Processing helix chain '9' and resid 126 through 155 removed outlier: 4.845A pdb=" N GLY 9 130 " --> pdb=" O ARG 9 126 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE 9 134 " --> pdb=" O GLY 9 130 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU 9 135 " --> pdb=" O MET 9 131 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY 9 142 " --> pdb=" O ALA 9 138 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY 9 145 " --> pdb=" O LEU 9 141 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS 9 155 " --> pdb=" O ILE 9 151 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 25 removed outlier: 4.005A pdb=" N ASP Q 12 " --> pdb=" O TYR Q 8 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR Q 15 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU Q 16 " --> pdb=" O ASP Q 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 29 through 38 removed outlier: 4.028A pdb=" N GLN Q 38 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 50 Processing helix chain 'Q' and resid 66 through 87 removed outlier: 3.914A pdb=" N ILE Q 70 " --> pdb=" O THR Q 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 113 removed outlier: 4.093A pdb=" N PHE Q 96 " --> pdb=" O PRO Q 92 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER Q 103 " --> pdb=" O PHE Q 99 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR Q 104 " --> pdb=" O ILE Q 100 " (cutoff:3.500A) Processing helix chain 'Q' and resid 121 through 126 Processing helix chain 'Q' and resid 127 through 129 No H-bonds generated for 'chain 'Q' and resid 127 through 129' Processing helix chain 'Q' and resid 146 through 158 Processing helix chain 'Q' and resid 160 through 166 removed outlier: 4.751A pdb=" N ASP Q 166 " --> pdb=" O ALA Q 162 " (cutoff:3.500A) Processing helix chain 'Q' and resid 171 through 176 Processing helix chain 'Q' and resid 177 through 200 removed outlier: 3.518A pdb=" N LEU Q 200 " --> pdb=" O PHE Q 196 " (cutoff:3.500A) Processing helix chain 'Q' and resid 202 through 227 removed outlier: 3.504A pdb=" N ASP Q 206 " --> pdb=" O GLY Q 202 " (cutoff:3.500A) Proline residue: Q 210 - end of helix Processing helix chain 'Q' and resid 233 through 239 Processing helix chain 'Q' and resid 251 through 257 removed outlier: 3.879A pdb=" N ARG Q 257 " --> pdb=" O ALA Q 253 " (cutoff:3.500A) Processing helix chain 'Q' and resid 260 through 269 Processing helix chain 'Q' and resid 271 through 280 Processing helix chain 'Q' and resid 289 through 305 Processing helix chain 'Q' and resid 306 through 308 No H-bonds generated for 'chain 'Q' and resid 306 through 308' Processing helix chain 'Q' and resid 312 through 338 removed outlier: 4.327A pdb=" N TYR Q 316 " --> pdb=" O PHE Q 312 " (cutoff:3.500A) Processing helix chain 'Q' and resid 343 through 347 removed outlier: 3.588A pdb=" N TYR Q 347 " --> pdb=" O ILE Q 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 114 Processing helix chain 'C' and resid 255 through 266 removed outlier: 3.576A pdb=" N ILE C 259 " --> pdb=" O GLY C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 291 removed outlier: 3.719A pdb=" N SER C 285 " --> pdb=" O GLY C 281 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU C 286 " --> pdb=" O ASN C 282 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 340 removed outlier: 4.715A pdb=" N ILE C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N TYR C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 365 removed outlier: 3.652A pdb=" N TRP C 354 " --> pdb=" O SER C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.512A pdb=" N TYR C 374 " --> pdb=" O ASP C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 387 removed outlier: 3.769A pdb=" N ARG C 381 " --> pdb=" O TYR C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 429 Processing helix chain 'C' and resid 436 through 442 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 471 through 497 removed outlier: 4.031A pdb=" N LEU C 475 " --> pdb=" O GLU C 471 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ILE C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 519 Processing helix chain 'C' and resid 533 through 558 Processing helix chain 'C' and resid 566 through 574 removed outlier: 3.548A pdb=" N ILE C 570 " --> pdb=" O THR C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 584 Processing helix chain 'C' and resid 585 through 587 No H-bonds generated for 'chain 'C' and resid 585 through 587' Processing helix chain 'C' and resid 593 through 616 Processing helix chain 'A' and resid 105 through 114 Processing helix chain 'A' and resid 255 through 266 removed outlier: 3.583A pdb=" N ILE A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 294 removed outlier: 3.673A pdb=" N VAL A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 319 through 325 removed outlier: 3.781A pdb=" N ALA A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 340 removed outlier: 3.604A pdb=" N MET A 340 " --> pdb=" O TYR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 365 removed outlier: 3.711A pdb=" N TRP A 354 " --> pdb=" O SER A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 387 Processing helix chain 'A' and resid 419 through 429 Processing helix chain 'A' and resid 436 through 441 removed outlier: 3.579A pdb=" N ALA A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 471 through 497 removed outlier: 3.963A pdb=" N LEU A 475 " --> pdb=" O GLU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 519 Processing helix chain 'A' and resid 533 through 559 Processing helix chain 'A' and resid 566 through 574 removed outlier: 3.626A pdb=" N ILE A 570 " --> pdb=" O THR A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 582 Processing helix chain 'A' and resid 593 through 616 Processing helix chain 'B' and resid 105 through 114 Processing helix chain 'B' and resid 255 through 266 Processing helix chain 'B' and resid 280 through 291 removed outlier: 4.081A pdb=" N MET B 284 " --> pdb=" O ARG B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 340 removed outlier: 4.071A pdb=" N ALA B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET B 340 " --> pdb=" O TYR B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 366 removed outlier: 4.011A pdb=" N TRP B 354 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 387 removed outlier: 3.775A pdb=" N ARG B 381 " --> pdb=" O TYR B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 427 removed outlier: 3.610A pdb=" N GLY B 427 " --> pdb=" O SER B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 441 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 471 through 496 removed outlier: 4.171A pdb=" N LEU B 475 " --> pdb=" O GLU B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 519 Processing helix chain 'B' and resid 533 through 558 removed outlier: 3.998A pdb=" N THR B 558 " --> pdb=" O ALA B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 574 Processing helix chain 'B' and resid 574 through 584 Processing helix chain 'B' and resid 585 through 587 No H-bonds generated for 'chain 'B' and resid 585 through 587' Processing helix chain 'B' and resid 593 through 616 Processing helix chain 'D' and resid 124 through 128 removed outlier: 3.571A pdb=" N LEU D 128 " --> pdb=" O GLU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 198 through 210 removed outlier: 3.616A pdb=" N ILE D 202 " --> pdb=" O PRO D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 225 removed outlier: 4.257A pdb=" N TYR D 222 " --> pdb=" O ASP D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 250 Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 267 through 290 Proline residue: D 275 - end of helix Processing helix chain 'D' and resid 299 through 314 Processing helix chain 'D' and resid 319 through 323 Processing helix chain 'D' and resid 326 through 336 Processing helix chain 'D' and resid 357 through 360 Processing helix chain 'D' and resid 363 through 373 Processing helix chain 'D' and resid 380 through 385 removed outlier: 3.585A pdb=" N HIS D 384 " --> pdb=" O ASP D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 406 removed outlier: 3.604A pdb=" N ALA D 405 " --> pdb=" O LEU D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 440 Processing helix chain 'D' and resid 445 through 462 removed outlier: 3.541A pdb=" N LEU D 449 " --> pdb=" O THR D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 485 Processing helix chain 'D' and resid 496 through 504 Processing helix chain 'E' and resid 124 through 128 Processing helix chain 'E' and resid 159 through 161 No H-bonds generated for 'chain 'E' and resid 159 through 161' Processing helix chain 'E' and resid 174 through 178 removed outlier: 3.502A pdb=" N ILE E 177 " --> pdb=" O ILE E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 210 Processing helix chain 'E' and resid 218 through 226 removed outlier: 3.772A pdb=" N TYR E 222 " --> pdb=" O ASP E 218 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN E 226 " --> pdb=" O TYR E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 251 removed outlier: 3.518A pdb=" N ASN E 251 " --> pdb=" O ASP E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 290 removed outlier: 4.111A pdb=" N ILE E 273 " --> pdb=" O ILE E 269 " (cutoff:3.500A) Proline residue: E 275 - end of helix Processing helix chain 'E' and resid 299 through 315 removed outlier: 3.508A pdb=" N TYR E 303 " --> pdb=" O ASP E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 323 Processing helix chain 'E' and resid 326 through 336 Processing helix chain 'E' and resid 357 through 360 Processing helix chain 'E' and resid 363 through 373 Processing helix chain 'E' and resid 381 through 386 removed outlier: 3.844A pdb=" N ARG E 386 " --> pdb=" O GLN E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 406 Processing helix chain 'E' and resid 414 through 440 Processing helix chain 'E' and resid 441 through 444 Processing helix chain 'E' and resid 445 through 462 Processing helix chain 'E' and resid 472 through 485 Processing helix chain 'E' and resid 496 through 504 Processing helix chain 'Z' and resid 15 through 37 Processing helix chain 'Z' and resid 42 through 49 Processing helix chain 'Z' and resid 49 through 54 Processing helix chain 'Z' and resid 62 through 72 Processing helix chain 'Z' and resid 77 through 97 Processing helix chain 'Z' and resid 104 through 117 removed outlier: 3.521A pdb=" N GLN Z 117 " --> pdb=" O GLU Z 113 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 123 Processing helix chain 'Z' and resid 124 through 142 removed outlier: 3.902A pdb=" N VAL Z 128 " --> pdb=" O SER Z 124 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN Z 142 " --> pdb=" O ASP Z 138 " (cutoff:3.500A) Processing helix chain 'Z' and resid 146 through 166 Processing helix chain 'Z' and resid 173 through 187 Processing helix chain 'Z' and resid 193 through 206 Processing helix chain 'Z' and resid 218 through 234 removed outlier: 3.562A pdb=" N GLN Z 222 " --> pdb=" O PRO Z 218 " (cutoff:3.500A) Processing helix chain 'Z' and resid 239 through 250 Processing helix chain 'Z' and resid 256 through 273 removed outlier: 3.601A pdb=" N LYS Z 272 " --> pdb=" O LYS Z 268 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU Z 273 " --> pdb=" O GLU Z 269 " (cutoff:3.500A) Processing helix chain 'X' and resid 14 through 37 Processing helix chain 'X' and resid 42 through 49 Processing helix chain 'X' and resid 49 through 54 Processing helix chain 'X' and resid 63 through 72 Processing helix chain 'X' and resid 77 through 97 Processing helix chain 'X' and resid 104 through 117 removed outlier: 4.403A pdb=" N GLN X 117 " --> pdb=" O GLU X 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 120 through 123 Processing helix chain 'X' and resid 124 through 140 removed outlier: 3.902A pdb=" N VAL X 128 " --> pdb=" O SER X 124 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU X 140 " --> pdb=" O LEU X 136 " (cutoff:3.500A) Processing helix chain 'X' and resid 141 through 143 No H-bonds generated for 'chain 'X' and resid 141 through 143' Processing helix chain 'X' and resid 146 through 167 Processing helix chain 'X' and resid 173 through 187 removed outlier: 3.573A pdb=" N ALA X 187 " --> pdb=" O LEU X 183 " (cutoff:3.500A) Processing helix chain 'X' and resid 193 through 207 Processing helix chain 'X' and resid 218 through 234 removed outlier: 3.839A pdb=" N GLN X 222 " --> pdb=" O PRO X 218 " (cutoff:3.500A) Processing helix chain 'X' and resid 239 through 250 Processing helix chain 'X' and resid 256 through 272 Processing helix chain 'Y' and resid 15 through 37 Processing helix chain 'Y' and resid 42 through 47 Processing helix chain 'Y' and resid 49 through 54 Processing helix chain 'Y' and resid 62 through 71 Processing helix chain 'Y' and resid 77 through 97 Processing helix chain 'Y' and resid 104 through 117 removed outlier: 3.961A pdb=" N GLN Y 117 " --> pdb=" O GLU Y 113 " (cutoff:3.500A) Processing helix chain 'Y' and resid 124 through 140 removed outlier: 3.773A pdb=" N VAL Y 128 " --> pdb=" O SER Y 124 " (cutoff:3.500A) Processing helix chain 'Y' and resid 146 through 167 Processing helix chain 'Y' and resid 172 through 187 Processing helix chain 'Y' and resid 193 through 206 Processing helix chain 'Y' and resid 218 through 237 removed outlier: 3.692A pdb=" N GLN Y 222 " --> pdb=" O PRO Y 218 " (cutoff:3.500A) Proline residue: Y 235 - end of helix Processing helix chain 'Y' and resid 239 through 250 Processing helix chain 'Y' and resid 256 through 271 Processing helix chain 'Y' and resid 272 through 274 No H-bonds generated for 'chain 'Y' and resid 272 through 274' Processing helix chain 'G' and resid 12 through 76 removed outlier: 3.608A pdb=" N GLU G 60 " --> pdb=" O MET G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 85 Processing helix chain 'G' and resid 128 through 175 Processing helix chain 'G' and resid 175 through 215 removed outlier: 3.565A pdb=" N ARG G 179 " --> pdb=" O VAL G 175 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS G 215 " --> pdb=" O ILE G 211 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 24 Processing helix chain 'N' and resid 44 through 58 removed outlier: 3.861A pdb=" N ILE N 48 " --> pdb=" O THR N 44 " (cutoff:3.500A) Processing helix chain 'N' and resid 68 through 74 Processing helix chain 'N' and resid 74 through 81 removed outlier: 3.681A pdb=" N HIS N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 99 through 102 Processing helix chain 'N' and resid 103 through 109 removed outlier: 4.053A pdb=" N ARG N 108 " --> pdb=" O SER N 104 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA N 109 " --> pdb=" O ILE N 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 27 Processing helix chain 'P' and resid 33 through 37 removed outlier: 4.021A pdb=" N TYR P 36 " --> pdb=" O TRP P 33 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU P 37 " --> pdb=" O GLN P 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 33 through 37' Processing helix chain 'P' and resid 47 through 55 removed outlier: 3.777A pdb=" N ARG P 52 " --> pdb=" O GLU P 48 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE P 53 " --> pdb=" O PHE P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 69 Processing helix chain 'P' and resid 74 through 84 removed outlier: 4.144A pdb=" N ILE P 78 " --> pdb=" O ALA P 74 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN P 79 " --> pdb=" O LYS P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 88 through 104 removed outlier: 3.536A pdb=" N TYR P 92 " --> pdb=" O GLN P 88 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE P 93 " --> pdb=" O THR P 89 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP P 99 " --> pdb=" O THR P 95 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN P 104 " --> pdb=" O MET P 100 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 109 Processing helix chain 'P' and resid 111 through 115 removed outlier: 4.336A pdb=" N TYR P 114 " --> pdb=" O PHE P 111 " (cutoff:3.500A) Processing helix chain 'P' and resid 126 through 130 removed outlier: 3.621A pdb=" N LEU P 130 " --> pdb=" O LEU P 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 135 through 146 removed outlier: 4.184A pdb=" N HIS P 139 " --> pdb=" O PRO P 135 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 162 removed outlier: 4.209A pdb=" N LEU P 161 " --> pdb=" O GLU P 157 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN P 162 " --> pdb=" O GLY P 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 157 through 162' Processing helix chain 'P' and resid 168 through 173 removed outlier: 3.758A pdb=" N SER P 173 " --> pdb=" O THR P 170 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 209 removed outlier: 3.842A pdb=" N CYS P 200 " --> pdb=" O GLN P 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 221 Processing helix chain 'P' and resid 223 through 233 Processing helix chain 'P' and resid 236 through 251 Processing helix chain 'P' and resid 253 through 261 removed outlier: 3.530A pdb=" N HIS P 259 " --> pdb=" O GLN P 255 " (cutoff:3.500A) Processing helix chain 'P' and resid 265 through 275 Processing helix chain 'P' and resid 280 through 296 removed outlier: 4.256A pdb=" N SER P 296 " --> pdb=" O PHE P 292 " (cutoff:3.500A) Processing helix chain 'P' and resid 302 through 310 removed outlier: 3.890A pdb=" N ALA P 306 " --> pdb=" O ARG P 302 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU P 307 " --> pdb=" O GLN P 303 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET P 309 " --> pdb=" O TYR P 305 " (cutoff:3.500A) Processing helix chain 'P' and resid 314 through 324 Processing helix chain 'P' and resid 328 through 350 Processing helix chain 'P' and resid 351 through 362 removed outlier: 3.627A pdb=" N GLY P 362 " --> pdb=" O GLU P 358 " (cutoff:3.500A) Processing helix chain 'P' and resid 373 through 377 Processing helix chain 'P' and resid 379 through 383 Processing helix chain 'P' and resid 385 through 387 No H-bonds generated for 'chain 'P' and resid 385 through 387' Processing helix chain 'P' and resid 388 through 400 removed outlier: 3.951A pdb=" N LEU P 394 " --> pdb=" O LEU P 390 " (cutoff:3.500A) Processing helix chain 'P' and resid 403 through 420 removed outlier: 4.220A pdb=" N VAL P 409 " --> pdb=" O GLN P 405 " (cutoff:3.500A) Processing helix chain 'P' and resid 423 through 432 removed outlier: 3.979A pdb=" N VAL P 427 " --> pdb=" O ARG P 423 " (cutoff:3.500A) Processing helix chain 'P' and resid 432 through 442 removed outlier: 3.705A pdb=" N LEU P 436 " --> pdb=" O GLY P 432 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS P 442 " --> pdb=" O MET P 438 " (cutoff:3.500A) Processing helix chain 'P' and resid 445 through 461 removed outlier: 4.006A pdb=" N ASN P 451 " --> pdb=" O GLN P 447 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU P 454 " --> pdb=" O TYR P 450 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL P 461 " --> pdb=" O GLN P 457 " (cutoff:3.500A) Processing helix chain 'W' and resid 21 through 32 Processing helix chain 'W' and resid 46 through 55 removed outlier: 3.670A pdb=" N LEU W 50 " --> pdb=" O SER W 46 " (cutoff:3.500A) Processing helix chain 'W' and resid 56 through 58 No H-bonds generated for 'chain 'W' and resid 56 through 58' Processing helix chain 'W' and resid 59 through 72 Processing helix chain 'W' and resid 88 through 100 Processing helix chain 'W' and resid 102 through 115 Processing helix chain 'W' and resid 123 through 145 Processing helix chain 'W' and resid 159 through 171 Processing helix chain 'W' and resid 183 through 188 Processing helix chain 'W' and resid 192 through 203 Processing helix chain 'W' and resid 203 through 218 removed outlier: 4.404A pdb=" N ALA W 207 " --> pdb=" O VAL W 203 " (cutoff:3.500A) Processing helix chain 'W' and resid 247 through 257 removed outlier: 3.907A pdb=" N GLN W 257 " --> pdb=" O TYR W 253 " (cutoff:3.500A) Processing helix chain 'W' and resid 258 through 263 removed outlier: 6.096A pdb=" N GLU W 261 " --> pdb=" O LEU W 258 " (cutoff:3.500A) Processing helix chain 'W' and resid 272 through 276 Processing helix chain 'W' and resid 278 through 287 Processing helix chain 'W' and resid 430 through 441 Processing helix chain 'F' and resid 124 through 128 removed outlier: 3.500A pdb=" N LEU F 128 " --> pdb=" O GLU F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 163 removed outlier: 3.812A pdb=" N ARG F 163 " --> pdb=" O PRO F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 210 Processing helix chain 'F' and resid 218 through 225 removed outlier: 3.800A pdb=" N TYR F 222 " --> pdb=" O ASP F 218 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU F 224 " --> pdb=" O VAL F 220 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU F 225 " --> pdb=" O ASP F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 250 Processing helix chain 'F' and resid 269 through 272 Processing helix chain 'F' and resid 273 through 289 Processing helix chain 'F' and resid 299 through 314 removed outlier: 3.719A pdb=" N TYR F 303 " --> pdb=" O ASP F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 323 removed outlier: 3.829A pdb=" N GLY F 322 " --> pdb=" O GLY F 319 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE F 323 " --> pdb=" O ARG F 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 319 through 323' Processing helix chain 'F' and resid 326 through 336 Processing helix chain 'F' and resid 357 through 360 Processing helix chain 'F' and resid 363 through 373 removed outlier: 3.511A pdb=" N TYR F 371 " --> pdb=" O ASP F 367 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 385 removed outlier: 3.893A pdb=" N HIS F 384 " --> pdb=" O ASP F 380 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN F 385 " --> pdb=" O ARG F 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 380 through 385' Processing helix chain 'F' and resid 401 through 405 Processing helix chain 'F' and resid 414 through 440 removed outlier: 3.819A pdb=" N ALA F 437 " --> pdb=" O GLN F 433 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N VAL F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL F 439 " --> pdb=" O MET F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 462 Processing helix chain 'F' and resid 472 through 483 Processing helix chain 'F' and resid 488 through 492 Processing helix chain 'F' and resid 496 through 504 Processing sheet with id=AA1, first strand: chain 'R' and resid 10 through 17 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 10 through 17 current: chain 'R' and resid 319 through 326 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'R' and resid 197 through 202 Processing sheet with id=AA3, first strand: chain 'R' and resid 499 through 500 Processing sheet with id=AA4, first strand: chain 'O' and resid 34 through 37 Processing sheet with id=AA5, first strand: chain 'O' and resid 214 through 218 removed outlier: 3.887A pdb=" N ASN O 214 " --> pdb=" O ASN O 226 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN O 226 " --> pdb=" O ASN O 214 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU O 224 " --> pdb=" O LEU O 216 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N GLU O 218 " --> pdb=" O SER O 222 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N SER O 222 " --> pdb=" O GLU O 218 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR O 223 " --> pdb=" O VAL O 189 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL O 189 " --> pdb=" O TYR O 223 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS O 225 " --> pdb=" O VAL O 187 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU O 186 " --> pdb=" O ARG O 249 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 131 through 135 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 164 through 167 current: chain 'J' and resid 190 through 194 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 190 through 194 current: chain 'I' and resid 164 through 167 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 164 through 167 current: chain 'I' and resid 190 through 195 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 190 through 195 current: chain 'H' and resid 164 through 167 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 164 through 167 current: chain 'H' and resid 190 through 195 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 190 through 195 current: chain 'C' and resid 28 through 32 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 28 through 32 current: chain 'C' and resid 50 through 58 removed outlier: 6.522A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 61 through 66 current: chain 'B' and resid 28 through 32 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 28 through 32 current: chain 'B' and resid 50 through 58 removed outlier: 6.574A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 61 through 66 current: chain 'D' and resid 57 through 60 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 57 through 60 current: chain 'D' and resid 81 through 90 removed outlier: 6.613A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 93 through 98 current: chain 'E' and resid 57 through 60 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 57 through 60 current: chain 'E' and resid 81 through 90 removed outlier: 6.617A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 93 through 98 current: chain 'F' and resid 57 through 60 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 57 through 60 current: chain 'F' and resid 81 through 90 removed outlier: 6.321A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'U' and resid 258 through 260 removed outlier: 3.930A pdb=" N ILE U 267 " --> pdb=" O TYR U 260 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 267 through 270 current: chain 'U' and resid 283 through 284 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 283 through 284 current: chain 'U' and resid 394 through 403 Processing sheet with id=AA8, first strand: chain 'U' and resid 301 through 303 removed outlier: 3.618A pdb=" N PHE U 306 " --> pdb=" O ASN U 303 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG U 344 " --> pdb=" O ILE U 326 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA U 328 " --> pdb=" O MET U 342 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N MET U 342 " --> pdb=" O ALA U 328 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG U 330 " --> pdb=" O PHE U 340 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N PHE U 340 " --> pdb=" O ARG U 330 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TYR U 332 " --> pdb=" O HIS U 338 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N HIS U 338 " --> pdb=" O TYR U 332 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLU U 343 " --> pdb=" O ALA U 358 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA U 358 " --> pdb=" O GLU U 343 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 87 through 90 Processing sheet with id=AB1, first strand: chain 'C' and resid 98 through 99 removed outlier: 4.015A pdb=" N VAL C 271 " --> pdb=" O HIS C 343 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR C 246 " --> pdb=" O GLY C 408 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR C 245 " --> pdb=" O VAL C 431 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 164 through 167 removed outlier: 3.515A pdb=" N GLY C 154 " --> pdb=" O ILE C 166 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 146 through 147 removed outlier: 6.630A pdb=" N GLU C 193 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 295 through 297 Processing sheet with id=AB5, first strand: chain 'A' and resid 21 through 25 removed outlier: 6.729A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 64 through 66 removed outlier: 4.632A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR A 82 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 87 through 90 Processing sheet with id=AB8, first strand: chain 'A' and resid 98 through 99 removed outlier: 7.106A pdb=" N VAL A 271 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N MET A 347 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE A 273 " --> pdb=" O MET A 347 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ASP A 349 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL A 275 " --> pdb=" O ASP A 349 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 348 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 164 through 167 removed outlier: 3.601A pdb=" N GLY A 154 " --> pdb=" O ILE A 166 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 146 through 147 removed outlier: 6.628A pdb=" N GLU A 193 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 295 through 298 Processing sheet with id=AC3, first strand: chain 'B' and resid 87 through 90 Processing sheet with id=AC4, first strand: chain 'B' and resid 98 through 100 removed outlier: 6.845A pdb=" N VAL B 271 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N MET B 347 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ILE B 273 " --> pdb=" O MET B 347 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ASP B 349 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL B 275 " --> pdb=" O ASP B 349 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL B 344 " --> pdb=" O SER B 405 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N VAL B 407 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N MET B 346 " --> pdb=" O VAL B 407 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR B 246 " --> pdb=" O GLY B 408 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 164 through 167 removed outlier: 3.839A pdb=" N GLY B 154 " --> pdb=" O ILE B 166 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 146 through 147 removed outlier: 6.388A pdb=" N GLU B 193 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 295 through 297 Processing sheet with id=AC8, first strand: chain 'B' and resid 431 through 432 Processing sheet with id=AC9, first strand: chain 'D' and resid 120 through 123 Processing sheet with id=AD1, first strand: chain 'D' and resid 131 through 133 removed outlier: 8.763A pdb=" N CYS D 258 " --> pdb=" O PHE D 227 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE D 229 " --> pdb=" O CYS D 258 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N PHE D 260 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N PHE D 231 " --> pdb=" O PHE D 260 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ASN D 262 " --> pdb=" O PHE D 231 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA D 233 " --> pdb=" O ASN D 262 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA D 228 " --> pdb=" O LEU D 294 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ILE D 296 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL D 230 " --> pdb=" O ILE D 296 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N THR D 298 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA D 232 " --> pdb=" O THR D 298 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 163 through 164 removed outlier: 4.474A pdb=" N ARG D 340 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 191 through 193 removed outlier: 6.398A pdb=" N ILE D 191 " --> pdb=" O LEU D 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'E' and resid 120 through 123 Processing sheet with id=AD5, first strand: chain 'E' and resid 131 through 133 removed outlier: 6.718A pdb=" N VAL E 230 " --> pdb=" O ILE E 296 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N THR E 298 " --> pdb=" O VAL E 230 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ALA E 232 " --> pdb=" O THR E 298 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 163 through 164 removed outlier: 3.605A pdb=" N ILE E 164 " --> pdb=" O ARG E 340 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ARG E 340 " --> pdb=" O ILE E 164 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'E' and resid 183 through 184 removed outlier: 4.386A pdb=" N ILE E 183 " --> pdb=" O ILE E 170 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 191 through 193 removed outlier: 6.313A pdb=" N ILE E 191 " --> pdb=" O LEU E 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'E' and resid 375 through 376 Processing sheet with id=AE1, first strand: chain 'G' and resid 92 through 101 Processing sheet with id=AE2, first strand: chain 'N' and resid 36 through 39 removed outlier: 6.668A pdb=" N ALA N 9 " --> pdb=" O LEU N 65 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N ASN N 67 " --> pdb=" O ALA N 9 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ILE N 11 " --> pdb=" O ASN N 67 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE N 64 " --> pdb=" O LEU N 89 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ILE N 91 " --> pdb=" O ILE N 64 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE N 66 " --> pdb=" O ILE N 91 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'W' and resid 44 through 45 Processing sheet with id=AE4, first strand: chain 'W' and resid 121 through 122 removed outlier: 3.646A pdb=" N VAL W 121 " --> pdb=" O CYS W 191 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N CYS W 191 " --> pdb=" O VAL W 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'W' and resid 233 through 235 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 265 through 271 current: chain 'W' and resid 303 through 308 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 303 through 308 current: chain 'W' and resid 334 through 336 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 334 through 336 current: chain 'W' and resid 358 through 361 removed outlier: 5.713A pdb=" N LYS W 378 " --> pdb=" O ASP W 373 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 120 through 123 Processing sheet with id=AE7, first strand: chain 'F' and resid 131 through 133 Processing sheet with id=AE8, first strand: chain 'F' and resid 169 through 170 removed outlier: 4.580A pdb=" N ILE F 183 " --> pdb=" O ILE F 170 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 191 through 193 removed outlier: 6.578A pdb=" N ILE F 191 " --> pdb=" O LEU F 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'F' and resid 375 through 376 4462 hydrogen bonds defined for protein. 13068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 32.30 Time building geometry restraints manager: 17.09 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: 18192 1.33 - 1.45: 14528 1.45 - 1.58: 39462 1.58 - 1.70: 15 1.70 - 1.82: 662 Bond restraints: 72859 Sorted by residual: bond pdb=" C ARG F 120 " pdb=" N THR F 121 " ideal model delta sigma weight residual 1.331 1.274 0.057 2.07e-02 2.33e+03 7.65e+00 bond pdb=" CB PRO O 313 " pdb=" CG PRO O 313 " ideal model delta sigma weight residual 1.506 1.614 -0.108 3.90e-02 6.57e+02 7.60e+00 bond pdb=" CB PRO W 38 " pdb=" CG PRO W 38 " ideal model delta sigma weight residual 1.492 1.611 -0.119 5.00e-02 4.00e+02 5.62e+00 bond pdb=" CB CYS S 47 " pdb=" SG CYS S 47 " ideal model delta sigma weight residual 1.808 1.730 0.078 3.30e-02 9.18e+02 5.52e+00 bond pdb=" CB PRO R 248 " pdb=" CG PRO R 248 " ideal model delta sigma weight residual 1.492 1.604 -0.112 5.00e-02 4.00e+02 5.01e+00 ... (remaining 72854 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 96913 2.36 - 4.72: 1661 4.72 - 7.09: 211 7.09 - 9.45: 39 9.45 - 11.81: 3 Bond angle restraints: 98827 Sorted by residual: angle pdb=" CA PRO F 496 " pdb=" N PRO F 496 " pdb=" CD PRO F 496 " ideal model delta sigma weight residual 112.00 103.59 8.41 1.40e+00 5.10e-01 3.61e+01 angle pdb=" N ILE T 97 " pdb=" CA ILE T 97 " pdb=" C ILE T 97 " ideal model delta sigma weight residual 112.96 107.14 5.82 1.00e+00 1.00e+00 3.38e+01 angle pdb=" CA PRO U 390 " pdb=" N PRO U 390 " pdb=" CD PRO U 390 " ideal model delta sigma weight residual 112.00 104.40 7.60 1.40e+00 5.10e-01 2.95e+01 angle pdb=" N LYS O 111 " pdb=" CA LYS O 111 " pdb=" C LYS O 111 " ideal model delta sigma weight residual 114.04 107.58 6.46 1.24e+00 6.50e-01 2.72e+01 angle pdb=" CA PRO R 181 " pdb=" N PRO R 181 " pdb=" CD PRO R 181 " ideal model delta sigma weight residual 112.00 105.40 6.60 1.40e+00 5.10e-01 2.23e+01 ... (remaining 98822 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.32: 42591 30.32 - 60.63: 1269 60.63 - 90.95: 119 90.95 - 121.27: 0 121.27 - 151.58: 1 Dihedral angle restraints: 43980 sinusoidal: 16221 harmonic: 27759 Sorted by residual: dihedral pdb=" O2A ADP B 701 " pdb=" O3A ADP B 701 " pdb=" PA ADP B 701 " pdb=" PB ADP B 701 " ideal model delta sinusoidal sigma weight residual 300.00 148.42 151.58 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" CA PHE I 224 " pdb=" C PHE I 224 " pdb=" N LEU I 225 " pdb=" CA LEU I 225 " ideal model delta harmonic sigma weight residual -180.00 -148.40 -31.60 0 5.00e+00 4.00e-02 3.99e+01 dihedral pdb=" CA THR A 295 " pdb=" C THR A 295 " pdb=" N MET A 296 " pdb=" CA MET A 296 " ideal model delta harmonic sigma weight residual 180.00 148.53 31.47 0 5.00e+00 4.00e-02 3.96e+01 ... (remaining 43977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 10255 0.075 - 0.150: 1178 0.150 - 0.225: 39 0.225 - 0.300: 3 0.300 - 0.375: 1 Chirality restraints: 11476 Sorted by residual: chirality pdb=" C1 NAG U 501 " pdb=" ND2 ASN U 350 " pdb=" C2 NAG U 501 " pdb=" O5 NAG U 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CB VAL A 75 " pdb=" CA VAL A 75 " pdb=" CG1 VAL A 75 " pdb=" CG2 VAL A 75 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB ILE A 118 " pdb=" CA ILE A 118 " pdb=" CG1 ILE A 118 " pdb=" CG2 ILE A 118 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 11473 not shown) Planarity restraints: 12785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE F 495 " 0.095 5.00e-02 4.00e+02 1.38e-01 3.03e+01 pdb=" N PRO F 496 " -0.238 5.00e-02 4.00e+02 pdb=" CA PRO F 496 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO F 496 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO W 59 " -0.073 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO W 60 " 0.184 5.00e-02 4.00e+02 pdb=" CA PRO W 60 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO W 60 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER W 37 " -0.072 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO W 38 " 0.183 5.00e-02 4.00e+02 pdb=" CA PRO W 38 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO W 38 " -0.058 5.00e-02 4.00e+02 ... (remaining 12782 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 408 2.52 - 3.11: 58107 3.11 - 3.71: 110499 3.71 - 4.30: 148422 4.30 - 4.90: 250869 Nonbonded interactions: 568305 Sorted by model distance: nonbonded pdb=" O TYR J 155 " pdb=" O ALA J 158 " model vdw 1.919 3.040 nonbonded pdb=" OH TYR F 426 " pdb=" OE2 GLU F 459 " model vdw 2.090 3.040 nonbonded pdb=" O SER A 71 " pdb=" NH1 ARG A 120 " model vdw 2.099 3.120 nonbonded pdb=" O THR U 298 " pdb=" OG SER U 310 " model vdw 2.115 3.040 nonbonded pdb=" OG SER C 316 " pdb=" OE2 GLU F 336 " model vdw 2.116 3.040 ... (remaining 568300 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' } ncs_group { reference = chain 'A' selection = (chain 'B' and resid 17 through 616) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = (chain 'I' and ((resid 7 through 58 and (name N or name CA or name C or name O o \ r name CB )) or resid 59 through 226)) selection = (chain 'J' and ((resid 7 through 42 and (name N or name CA or name C or name O o \ r name CB )) or resid 43 or (resid 44 through 58 and (name N or name CA or name \ C or name O or name CB )) or resid 59 through 226)) } ncs_group { reference = (chain 'K' and resid 4 through 116) selection = (chain 'L' and ((resid 4 through 63 and (name N or name CA or name C or name O o \ r name CB )) or resid 64 or (resid 65 through 66 and (name N or name CA or name \ C or name O or name CB )) or resid 67 through 116)) selection = (chain 'M' and ((resid 4 through 63 and (name N or name CA or name C or name O o \ r name CB )) or resid 64 or (resid 65 through 66 and (name N or name CA or name \ C or name O or name CB )) or resid 67 through 116)) } ncs_group { reference = (chain 'X' and (resid 14 through 235 or (resid 236 and (name CA or name C or nam \ e O or name CB or name CG or name CD or name CE or name NZ )) or resid 237 throu \ gh 275)) selection = (chain 'Y' and (resid 14 through 219 or (resid 220 and (name N or name CA or nam \ e C or name O or name CB )) or resid 221 through 222 or (resid 223 and (name N o \ r name CA or name C or name O or name CB )) or resid 224 through 235 or (resid 2 \ 36 and (name CA or name C or name O or name CB or name CG or name CD or name CE \ or name NZ )) or resid 237 through 275)) selection = (chain 'Z' and (resid 14 through 219 or (resid 220 and (name N or name CA or nam \ e C or name O or name CB )) or resid 221 through 222 or (resid 223 and (name N o \ r name CA or name C or name O or name CB )) or resid 224 through 275)) } 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 group one per residue 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: 53.950 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: 0.050 Extract box with map and model: 2.360 Check model and map are aligned: 0.410 Set scattering table: 0.520 Process input model: 132.400 Find NCS groups from input model: 2.580 Set up NCS constraints: 0.560 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: 0.020 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 195.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 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 : 0.006 0.119 72859 Z= 0.427 Angle : 0.762 11.810 98827 Z= 0.408 Chirality : 0.047 0.375 11476 Planarity : 0.006 0.138 12780 Dihedral : 14.147 151.583 26105 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.33 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.29 (0.09), residues: 9526 helix: 1.01 (0.07), residues: 5422 sheet: -0.90 (0.18), residues: 801 loop : -2.06 (0.10), residues: 3303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 450 HIS 0.017 0.001 HIS R 801 PHE 0.063 0.002 PHE S 16 TYR 0.042 0.002 TYR 0 70 ARG 0.016 0.001 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1622 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1622 time to evaluate : 7.824 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: 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: R 9 GLU cc_start: 0.2056 (tm-30) cc_final: 0.1267 (mm-30) REVERT: R 35 VAL cc_start: 0.7372 (t) cc_final: 0.7022 (t) REVERT: R 80 MET cc_start: 0.5882 (mpp) cc_final: 0.5444 (mtt) REVERT: R 294 PHE cc_start: 0.7444 (t80) cc_final: 0.7211 (t80) REVERT: R 358 ASN cc_start: 0.5258 (p0) cc_final: 0.4807 (m110) REVERT: R 383 ILE cc_start: 0.6147 (mp) cc_final: 0.5935 (mt) REVERT: R 421 VAL cc_start: 0.6799 (t) cc_final: 0.6536 (p) REVERT: R 439 MET cc_start: 0.3992 (ppp) cc_final: 0.2135 (tpp) REVERT: R 479 TRP cc_start: 0.5311 (m100) cc_final: 0.4666 (m100) REVERT: R 492 GLU cc_start: 0.7486 (tp30) cc_final: 0.7015 (pp20) REVERT: R 808 VAL cc_start: 0.6799 (t) cc_final: 0.6370 (t) REVERT: O 313 PRO cc_start: 0.6480 (Cg_endo) cc_final: 0.6087 (Cg_exo) REVERT: J 53 ILE cc_start: 0.1408 (pt) cc_final: 0.0432 (pt) REVERT: J 65 GLU cc_start: 0.7898 (tt0) cc_final: 0.7371 (mm-30) REVERT: J 72 MET cc_start: 0.6768 (mmp) cc_final: 0.5744 (tmm) REVERT: J 182 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8096 (mt-10) REVERT: M 56 LYS cc_start: 0.6790 (mptt) cc_final: 0.6589 (ttmt) REVERT: M 63 LEU cc_start: 0.6670 (mp) cc_final: 0.6366 (mt) REVERT: M 86 THR cc_start: 0.5151 (p) cc_final: 0.4931 (p) REVERT: M 105 ASP cc_start: 0.6502 (t0) cc_final: 0.5876 (p0) REVERT: I 52 LYS cc_start: 0.8316 (tttp) cc_final: 0.8110 (tmtt) REVERT: I 59 LYS cc_start: 0.8188 (ttpt) cc_final: 0.7848 (tmmt) REVERT: I 77 ASN cc_start: 0.7800 (t0) cc_final: 0.7430 (t0) REVERT: I 172 TYR cc_start: 0.6786 (m-80) cc_final: 0.6477 (m-10) REVERT: L 58 LYS cc_start: 0.7829 (mptt) cc_final: 0.7371 (mttt) REVERT: L 63 LEU cc_start: 0.5936 (mp) cc_final: 0.5704 (tt) REVERT: L 78 GLN cc_start: 0.7451 (tp-100) cc_final: 0.7134 (mm-40) REVERT: L 85 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7652 (mp10) REVERT: H 66 GLN cc_start: 0.7855 (mm-40) cc_final: 0.7564 (mm-40) REVERT: H 117 ASP cc_start: 0.7532 (t0) cc_final: 0.7079 (m-30) REVERT: H 168 ASP cc_start: 0.7481 (m-30) cc_final: 0.6614 (t70) REVERT: H 184 TYR cc_start: 0.7033 (m-10) cc_final: 0.6730 (m-80) REVERT: K 83 ILE cc_start: 0.8262 (tt) cc_final: 0.7971 (mm) REVERT: S 40 MET cc_start: 0.8269 (ptp) cc_final: 0.7384 (ppp) REVERT: U 342 MET cc_start: 0.5374 (ttm) cc_final: 0.5086 (tpp) REVERT: U 401 GLN cc_start: 0.5386 (tp40) cc_final: 0.5080 (mt0) REVERT: U 408 MET cc_start: 0.6537 (mpp) cc_final: 0.6006 (mtt) REVERT: 1 124 GLN cc_start: 0.5350 (tm-30) cc_final: 0.4982 (tt0) REVERT: 1 146 LEU cc_start: 0.7407 (tt) cc_final: 0.7103 (mm) REVERT: 2 61 MET cc_start: 0.5460 (mtp) cc_final: 0.5006 (mtp) REVERT: 3 53 MET cc_start: 0.1733 (mmp) cc_final: 0.1139 (ptm) REVERT: 6 47 MET cc_start: 0.6122 (mpp) cc_final: 0.4340 (tmm) REVERT: 6 53 MET cc_start: 0.6538 (mmm) cc_final: 0.5831 (mtp) REVERT: 7 76 ILE cc_start: 0.7125 (mm) cc_final: 0.6917 (mt) REVERT: 9 14 PHE cc_start: 0.6759 (m-80) cc_final: 0.6262 (m-80) REVERT: 9 70 LEU cc_start: 0.7445 (tp) cc_final: 0.7171 (tp) REVERT: Q 3 PHE cc_start: 0.5466 (t80) cc_final: 0.5027 (m-10) REVERT: Q 208 MET cc_start: 0.7045 (mmm) cc_final: 0.6835 (mmp) REVERT: C 438 LYS cc_start: 0.7403 (tmtt) cc_final: 0.7155 (tptm) REVERT: C 478 LYS cc_start: 0.8259 (mmmm) cc_final: 0.7993 (tppt) REVERT: C 498 LYS cc_start: 0.7163 (tttt) cc_final: 0.6850 (tmmt) REVERT: C 591 LYS cc_start: 0.7116 (mmtt) cc_final: 0.6327 (ptpp) REVERT: C 608 MET cc_start: 0.4403 (ptm) cc_final: 0.4126 (ptm) REVERT: A 39 MET cc_start: 0.8473 (mpp) cc_final: 0.8255 (mpp) REVERT: A 296 MET cc_start: 0.4979 (mpp) cc_final: 0.3813 (ptm) REVERT: A 349 ASP cc_start: 0.7994 (t70) cc_final: 0.7666 (t0) REVERT: A 353 ARG cc_start: 0.7198 (mmt-90) cc_final: 0.6792 (mmp80) REVERT: A 367 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7644 (mt-10) REVERT: A 443 LYS cc_start: 0.8376 (tttm) cc_final: 0.8083 (mmtm) REVERT: A 600 ASP cc_start: 0.6681 (m-30) cc_final: 0.6384 (m-30) REVERT: B 193 GLU cc_start: 0.7550 (tp30) cc_final: 0.7230 (tp30) REVERT: B 299 ASP cc_start: 0.6896 (p0) cc_final: 0.6480 (p0) REVERT: B 436 ASP cc_start: 0.8276 (t70) cc_final: 0.8017 (t0) REVERT: B 550 MET cc_start: 0.6842 (mtm) cc_final: 0.6589 (mtt) REVERT: D 141 ARG cc_start: 0.7536 (tpt170) cc_final: 0.7121 (tpt90) REVERT: D 214 LYS cc_start: 0.8310 (pptt) cc_final: 0.7244 (ptpp) REVERT: D 247 ASP cc_start: 0.8551 (t0) cc_final: 0.8095 (t0) REVERT: D 309 GLU cc_start: 0.7240 (tt0) cc_final: 0.6913 (mt-10) REVERT: D 456 GLN cc_start: 0.7552 (tp40) cc_final: 0.6980 (tt0) REVERT: E 141 ARG cc_start: 0.8091 (ttp80) cc_final: 0.7891 (ttp80) REVERT: E 456 GLN cc_start: 0.7599 (tm-30) cc_final: 0.7314 (tp-100) REVERT: Z 54 ILE cc_start: 0.8495 (tp) cc_final: 0.8279 (tp) REVERT: Z 59 ASN cc_start: 0.7225 (m-40) cc_final: 0.6467 (p0) REVERT: Z 74 CYS cc_start: 0.7975 (p) cc_final: 0.7638 (p) REVERT: Z 184 HIS cc_start: 0.7720 (t70) cc_final: 0.7416 (t70) REVERT: X 139 TYR cc_start: 0.7610 (t80) cc_final: 0.7245 (t80) REVERT: X 180 LYS cc_start: 0.7994 (ttpp) cc_final: 0.7491 (tppt) REVERT: X 251 SER cc_start: 0.7572 (t) cc_final: 0.7330 (p) REVERT: Y 39 GLU cc_start: 0.7298 (pt0) cc_final: 0.6969 (pm20) REVERT: Y 125 ASP cc_start: 0.6994 (p0) cc_final: 0.6153 (m-30) REVERT: Y 137 THR cc_start: 0.6788 (t) cc_final: 0.6399 (p) REVERT: Y 196 GLN cc_start: 0.3594 (mt0) cc_final: 0.3343 (tt0) REVERT: G 45 ARG cc_start: 0.7733 (ttm170) cc_final: 0.7495 (mmm-85) REVERT: G 58 MET cc_start: 0.4982 (tmm) cc_final: 0.4623 (ttp) REVERT: G 85 GLN cc_start: 0.7934 (pp30) cc_final: 0.7191 (pp30) REVERT: N 33 HIS cc_start: 0.7302 (m170) cc_final: 0.7033 (m-70) REVERT: N 69 TYR cc_start: 0.8071 (p90) cc_final: 0.6900 (p90) REVERT: N 72 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6916 (mm-30) REVERT: N 93 SER cc_start: 0.5906 (p) cc_final: 0.3652 (t) REVERT: N 102 LYS cc_start: 0.6474 (ttmm) cc_final: 0.5603 (tppt) REVERT: N 107 ARG cc_start: 0.7021 (mtt180) cc_final: 0.6208 (mtt180) REVERT: N 110 ARG cc_start: 0.5619 (mpt180) cc_final: 0.4810 (ttm170) REVERT: W 333 MET cc_start: 0.6331 (mmt) cc_final: 0.5975 (mmm) REVERT: W 336 TYR cc_start: 0.6872 (m-80) cc_final: 0.6422 (m-80) REVERT: W 345 TYR cc_start: 0.7451 (m-80) cc_final: 0.6918 (m-10) REVERT: W 378 LYS cc_start: 0.8563 (mtpp) cc_final: 0.8293 (mmtm) REVERT: F 239 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7458 (tm-30) REVERT: F 423 TYR cc_start: 0.7309 (t80) cc_final: 0.6967 (t80) REVERT: F 435 MET cc_start: 0.7132 (mmm) cc_final: 0.5944 (mmm) outliers start: 0 outliers final: 0 residues processed: 1622 average time/residue: 0.6998 time to fit residues: 1929.5116 Evaluate side-chains 1035 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1035 time to evaluate : 6.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 803 optimal weight: 0.8980 chunk 720 optimal weight: 9.9990 chunk 399 optimal weight: 6.9990 chunk 246 optimal weight: 5.9990 chunk 486 optimal weight: 10.0000 chunk 385 optimal weight: 20.0000 chunk 745 optimal weight: 8.9990 chunk 288 optimal weight: 5.9990 chunk 453 optimal weight: 2.9990 chunk 554 optimal weight: 4.9990 chunk 863 optimal weight: 50.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 719 HIS ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 30 ASN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 GLN I 71 GLN H 139 GLN ** U 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 348 HIS ** V 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 81 ASN 1 92 GLN 2 78 ASN 3 92 GLN 4 92 GLN ** 5 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 10 ASN Q 137 GLN ** Q 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 ASN C 430 GLN A 317 ASN A 449 ASN B 261 GLN D 265 ASN ** Z 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 162 GLN ** X 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 118 HIS ** Y 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 160 GLN N 33 HIS N 46 ASN ** W 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 72859 Z= 0.434 Angle : 0.753 13.008 98827 Z= 0.393 Chirality : 0.048 0.341 11476 Planarity : 0.006 0.084 12780 Dihedral : 5.764 150.865 10472 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.27 % Favored : 94.71 % Rotamer: Outliers : 2.19 % Allowed : 10.49 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.06 (0.09), residues: 9526 helix: 1.27 (0.07), residues: 5445 sheet: -1.07 (0.18), residues: 818 loop : -2.05 (0.10), residues: 3263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP S 52 HIS 0.015 0.002 HIS R 801 PHE 0.048 0.002 PHE S 16 TYR 0.056 0.003 TYR D 68 ARG 0.012 0.001 ARG 7 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1283 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1128 time to evaluate : 6.480 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: R 59 GLU cc_start: 0.7793 (mm-30) cc_final: 0.6940 (pp20) REVERT: R 80 MET cc_start: 0.5972 (mpp) cc_final: 0.5625 (mmt) REVERT: R 358 ASN cc_start: 0.5114 (p0) cc_final: 0.4635 (m-40) REVERT: R 439 MET cc_start: 0.4173 (ppp) cc_final: 0.2263 (tpp) REVERT: R 479 TRP cc_start: 0.5362 (m100) cc_final: 0.4720 (m100) REVERT: R 492 GLU cc_start: 0.7239 (tp30) cc_final: 0.6795 (tm-30) REVERT: R 539 MET cc_start: 0.8374 (tmm) cc_final: 0.8096 (tmm) REVERT: R 572 PHE cc_start: 0.3856 (t80) cc_final: 0.2632 (t80) REVERT: R 573 ILE cc_start: 0.6913 (mt) cc_final: 0.6652 (mp) REVERT: R 615 MET cc_start: 0.7660 (tmm) cc_final: 0.6888 (tmm) REVERT: J 72 MET cc_start: 0.7245 (mmp) cc_final: 0.5995 (tmm) REVERT: J 76 MET cc_start: 0.8243 (mmt) cc_final: 0.7983 (mmt) REVERT: M 30 ASN cc_start: 0.7150 (t0) cc_final: 0.6913 (m-40) REVERT: M 63 LEU cc_start: 0.6537 (mp) cc_final: 0.6242 (mt) REVERT: M 87 TYR cc_start: 0.6664 (m-80) cc_final: 0.6398 (m-80) REVERT: I 52 LYS cc_start: 0.8362 (tttp) cc_final: 0.8149 (tmtt) REVERT: I 210 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.8048 (pm20) REVERT: L 58 LYS cc_start: 0.7818 (mptt) cc_final: 0.7349 (mttt) REVERT: L 63 LEU cc_start: 0.6334 (mp) cc_final: 0.5915 (tt) REVERT: L 75 LYS cc_start: 0.9140 (tptt) cc_final: 0.8574 (pttp) REVERT: L 76 GLU cc_start: 0.7909 (tt0) cc_final: 0.7688 (tt0) REVERT: L 94 GLU cc_start: 0.7038 (pm20) cc_final: 0.6692 (pm20) REVERT: H 139 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8243 (pp30) REVERT: K 75 LYS cc_start: 0.8015 (ttpp) cc_final: 0.7588 (ttpp) REVERT: K 83 ILE cc_start: 0.8468 (tt) cc_final: 0.8112 (mt) REVERT: K 94 GLU cc_start: 0.8337 (pm20) cc_final: 0.8045 (pm20) REVERT: S 40 MET cc_start: 0.8126 (ptp) cc_final: 0.7449 (ppp) REVERT: T 50 LEU cc_start: 0.3190 (tp) cc_final: 0.2871 (mt) REVERT: T 67 MET cc_start: 0.7217 (mtt) cc_final: 0.6547 (tpt) REVERT: T 71 PHE cc_start: 0.5958 (OUTLIER) cc_final: 0.5614 (t80) REVERT: U 395 MET cc_start: 0.2874 (tpp) cc_final: 0.2276 (tpt) REVERT: U 453 MET cc_start: 0.2184 (mmm) cc_final: 0.1511 (mmt) REVERT: 1 23 MET cc_start: 0.7126 (tpp) cc_final: 0.6882 (tpt) REVERT: 1 47 MET cc_start: 0.5840 (ppp) cc_final: 0.5475 (mmt) REVERT: 1 146 LEU cc_start: 0.7475 (tt) cc_final: 0.6913 (mm) REVERT: 2 61 MET cc_start: 0.6028 (mtp) cc_final: 0.5820 (mtp) REVERT: 2 128 PHE cc_start: 0.5545 (t80) cc_final: 0.5118 (m-80) REVERT: 3 28 LEU cc_start: 0.7227 (mm) cc_final: 0.6993 (tp) REVERT: 3 53 MET cc_start: 0.1761 (mmp) cc_final: 0.1093 (ptm) REVERT: 3 134 ILE cc_start: 0.6131 (mp) cc_final: 0.5929 (mm) REVERT: 5 10 TYR cc_start: 0.5345 (p90) cc_final: 0.4083 (m-80) REVERT: 5 44 MET cc_start: 0.6106 (ppp) cc_final: 0.5894 (ttp) REVERT: 6 53 MET cc_start: 0.6650 (mmm) cc_final: 0.5734 (mtt) REVERT: 9 14 PHE cc_start: 0.6897 (m-80) cc_final: 0.6437 (m-80) REVERT: 9 93 LEU cc_start: 0.4001 (tt) cc_final: 0.3703 (tt) REVERT: Q 208 MET cc_start: 0.6897 (mmm) cc_final: 0.6462 (mmp) REVERT: C 142 ARG cc_start: 0.8107 (mtm110) cc_final: 0.7828 (mtm-85) REVERT: C 266 TYR cc_start: 0.7155 (m-10) cc_final: 0.6648 (m-10) REVERT: C 438 LYS cc_start: 0.7314 (tmtt) cc_final: 0.7054 (tptm) REVERT: C 586 PHE cc_start: 0.7553 (m-80) cc_final: 0.7343 (m-80) REVERT: A 39 MET cc_start: 0.8368 (mpp) cc_final: 0.8138 (mtp) REVERT: A 81 ARG cc_start: 0.6008 (mtm-85) cc_final: 0.4792 (ptp-170) REVERT: A 296 MET cc_start: 0.5169 (mpp) cc_final: 0.4437 (mtm) REVERT: A 314 ASN cc_start: 0.8114 (t0) cc_final: 0.7702 (t0) REVERT: A 349 ASP cc_start: 0.7979 (t70) cc_final: 0.7716 (t0) REVERT: A 353 ARG cc_start: 0.7228 (mmt-90) cc_final: 0.6892 (mmp80) REVERT: A 367 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7661 (mt-10) REVERT: A 443 LYS cc_start: 0.8354 (tttm) cc_final: 0.8087 (mmtm) REVERT: A 518 ASP cc_start: 0.8160 (t0) cc_final: 0.7896 (t0) REVERT: A 570 ILE cc_start: 0.5324 (mm) cc_final: 0.5085 (mm) REVERT: A 600 ASP cc_start: 0.6956 (m-30) cc_final: 0.6701 (m-30) REVERT: B 203 PHE cc_start: 0.6841 (t80) cc_final: 0.5904 (t80) REVERT: B 299 ASP cc_start: 0.6989 (p0) cc_final: 0.6648 (p0) REVERT: B 550 MET cc_start: 0.6861 (mtm) cc_final: 0.6525 (mtt) REVERT: B 594 GLU cc_start: 0.6292 (tm-30) cc_final: 0.5815 (tm-30) REVERT: D 141 ARG cc_start: 0.7625 (tpt170) cc_final: 0.7222 (tpt90) REVERT: D 154 MET cc_start: 0.7910 (ptm) cc_final: 0.7667 (ptp) REVERT: D 214 LYS cc_start: 0.8355 (pptt) cc_final: 0.7376 (ptpp) REVERT: D 309 GLU cc_start: 0.7183 (tt0) cc_final: 0.6889 (mt-10) REVERT: D 456 GLN cc_start: 0.7617 (tp40) cc_final: 0.7078 (tt0) REVERT: E 80 THR cc_start: 0.9067 (m) cc_final: 0.8641 (p) REVERT: E 456 GLN cc_start: 0.7603 (tm-30) cc_final: 0.7223 (tp-100) REVERT: Z 59 ASN cc_start: 0.7089 (m-40) cc_final: 0.6326 (p0) REVERT: Z 74 CYS cc_start: 0.8255 (p) cc_final: 0.7890 (p) REVERT: Z 170 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.6143 (pm20) REVERT: Z 184 HIS cc_start: 0.7689 (t70) cc_final: 0.7468 (t70) REVERT: Z 271 GLU cc_start: 0.3853 (OUTLIER) cc_final: 0.3332 (mm-30) REVERT: X 161 MET cc_start: 0.7806 (tpt) cc_final: 0.7487 (tpt) REVERT: X 180 LYS cc_start: 0.8046 (ttpp) cc_final: 0.7510 (tppt) REVERT: Y 213 PHE cc_start: 0.7579 (m-80) cc_final: 0.7355 (m-80) REVERT: G 45 ARG cc_start: 0.7848 (ttm170) cc_final: 0.7490 (mmm-85) REVERT: G 58 MET cc_start: 0.4768 (tmm) cc_final: 0.4385 (ttp) REVERT: G 85 GLN cc_start: 0.8082 (pp30) cc_final: 0.7507 (pp30) REVERT: N 93 SER cc_start: 0.6505 (p) cc_final: 0.3990 (t) REVERT: N 96 HIS cc_start: 0.5046 (m90) cc_final: 0.4457 (m90) REVERT: N 110 ARG cc_start: 0.6193 (mpt180) cc_final: 0.5342 (ttm170) REVERT: W 333 MET cc_start: 0.6425 (mmt) cc_final: 0.6189 (mmm) REVERT: W 345 TYR cc_start: 0.7501 (m-80) cc_final: 0.7146 (m-10) REVERT: W 378 LYS cc_start: 0.8626 (mtpp) cc_final: 0.8421 (mmtt) REVERT: F 88 GLU cc_start: 0.7845 (tp30) cc_final: 0.7459 (tp30) REVERT: F 239 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7405 (tm-30) REVERT: F 299 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.7886 (t0) REVERT: F 387 GLN cc_start: 0.7368 (mm110) cc_final: 0.7106 (mt0) REVERT: F 402 MET cc_start: 0.5037 (ptm) cc_final: 0.4802 (pmm) REVERT: F 435 MET cc_start: 0.7224 (mmm) cc_final: 0.6382 (mmm) outliers start: 155 outliers final: 88 residues processed: 1218 average time/residue: 0.6859 time to fit residues: 1430.4740 Evaluate side-chains 1056 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 962 time to evaluate : 6.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 333 ILE Chi-restraints excluded: chain R residue 394 TYR Chi-restraints excluded: chain R residue 418 LEU Chi-restraints excluded: chain R residue 535 PHE Chi-restraints excluded: chain R residue 617 LEU Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain I residue 56 TYR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 210 GLU Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain H residue 139 GLN Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain T residue 71 PHE Chi-restraints excluded: chain 0 residue 76 ILE Chi-restraints excluded: chain 0 residue 149 LEU Chi-restraints excluded: chain 0 residue 178 ILE Chi-restraints excluded: chain 1 residue 64 ILE Chi-restraints excluded: chain 1 residue 81 ASN Chi-restraints excluded: chain 1 residue 113 VAL Chi-restraints excluded: chain 4 residue 46 VAL Chi-restraints excluded: chain 4 residue 47 MET Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 5 residue 59 VAL Chi-restraints excluded: chain 5 residue 70 LEU Chi-restraints excluded: chain 5 residue 150 LEU Chi-restraints excluded: chain 6 residue 39 THR Chi-restraints excluded: chain 6 residue 57 ILE Chi-restraints excluded: chain 7 residue 57 ILE Chi-restraints excluded: chain 7 residue 82 ASP Chi-restraints excluded: chain 7 residue 140 VAL Chi-restraints excluded: chain 8 residue 39 THR Chi-restraints excluded: chain 8 residue 47 MET Chi-restraints excluded: chain 8 residue 143 LEU Chi-restraints excluded: chain 9 residue 34 THR Chi-restraints excluded: chain Q residue 12 ASP Chi-restraints excluded: chain Q residue 24 LYS Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain Q residue 150 LEU Chi-restraints excluded: chain Q residue 197 CYS Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain Z residue 146 THR Chi-restraints excluded: chain Z residue 170 GLU Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 271 GLU Chi-restraints excluded: chain X residue 10 MET Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain X residue 177 GLN Chi-restraints excluded: chain X residue 241 VAL Chi-restraints excluded: chain Y residue 169 THR Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain W residue 228 THR Chi-restraints excluded: chain W residue 280 SER Chi-restraints excluded: chain W residue 282 LEU Chi-restraints excluded: chain W residue 373 ASP Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 345 ASN Chi-restraints excluded: chain F residue 359 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 479 optimal weight: 0.8980 chunk 268 optimal weight: 20.0000 chunk 718 optimal weight: 3.9990 chunk 588 optimal weight: 3.9990 chunk 238 optimal weight: 30.0000 chunk 865 optimal weight: 50.0000 chunk 934 optimal weight: 1.9990 chunk 770 optimal weight: 0.8980 chunk 857 optimal weight: 6.9990 chunk 294 optimal weight: 20.0000 chunk 694 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 106 ASN R 316 GLN R 523 ASN R 533 ASN ** R 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 811 GLN ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 GLN S 61 ASN U 338 HIS U 348 HIS 0 51 ASN 2 78 ASN ** 5 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN Z 41 ASN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 160 GLN ** W 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 72859 Z= 0.234 Angle : 0.617 12.629 98827 Z= 0.322 Chirality : 0.043 0.358 11476 Planarity : 0.004 0.066 12780 Dihedral : 5.320 149.074 10472 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.42 % Allowed : 13.12 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.35 (0.09), residues: 9526 helix: 1.61 (0.07), residues: 5471 sheet: -0.87 (0.18), residues: 816 loop : -1.95 (0.10), residues: 3239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP 0 49 HIS 0.008 0.001 HIS R 801 PHE 0.039 0.002 PHE 0 189 TYR 0.048 0.002 TYR 8 144 ARG 0.007 0.001 ARG 9 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1263 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1092 time to evaluate : 6.317 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: R 59 GLU cc_start: 0.7774 (mm-30) cc_final: 0.6801 (pp20) REVERT: R 80 MET cc_start: 0.5829 (mpp) cc_final: 0.5448 (mmt) REVERT: R 358 ASN cc_start: 0.5088 (p0) cc_final: 0.4570 (m-40) REVERT: R 406 MET cc_start: 0.4087 (mtt) cc_final: 0.3683 (mtm) REVERT: R 439 MET cc_start: 0.4050 (ppp) cc_final: 0.1925 (tpp) REVERT: R 479 TRP cc_start: 0.5025 (m100) cc_final: 0.4410 (m100) REVERT: R 492 GLU cc_start: 0.7372 (tp30) cc_final: 0.6975 (tm-30) REVERT: R 572 PHE cc_start: 0.3719 (t80) cc_final: 0.2403 (t80) REVERT: R 615 MET cc_start: 0.7666 (tmm) cc_final: 0.6908 (tmm) REVERT: J 72 MET cc_start: 0.7315 (mmp) cc_final: 0.5909 (tmm) REVERT: J 76 MET cc_start: 0.8199 (mmt) cc_final: 0.7954 (mmt) REVERT: J 111 ARG cc_start: 0.8169 (mtm180) cc_final: 0.7863 (mtm180) REVERT: J 131 ARG cc_start: 0.7661 (mtp-110) cc_final: 0.7390 (mtp85) REVERT: J 207 MET cc_start: 0.8857 (mmm) cc_final: 0.8508 (tpp) REVERT: M 30 ASN cc_start: 0.6988 (t0) cc_final: 0.6782 (m-40) REVERT: M 81 MET cc_start: 0.6478 (mtt) cc_final: 0.6147 (tmm) REVERT: M 98 ASN cc_start: 0.6413 (t0) cc_final: 0.6206 (m-40) REVERT: I 52 LYS cc_start: 0.8428 (tttp) cc_final: 0.8209 (tmtt) REVERT: I 74 ASN cc_start: 0.8076 (t0) cc_final: 0.7787 (m-40) REVERT: I 172 TYR cc_start: 0.6890 (m-80) cc_final: 0.6638 (m-10) REVERT: I 210 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7959 (pm20) REVERT: L 58 LYS cc_start: 0.7809 (mptt) cc_final: 0.7363 (mttt) REVERT: L 63 LEU cc_start: 0.6330 (mp) cc_final: 0.5936 (tt) REVERT: L 75 LYS cc_start: 0.9065 (tptt) cc_final: 0.8509 (pttp) REVERT: L 76 GLU cc_start: 0.7851 (tt0) cc_final: 0.7636 (tt0) REVERT: L 85 GLN cc_start: 0.8317 (mm-40) cc_final: 0.8070 (mt0) REVERT: H 117 ASP cc_start: 0.8058 (t0) cc_final: 0.7139 (m-30) REVERT: K 74 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7392 (tm-30) REVERT: K 83 ILE cc_start: 0.8409 (tt) cc_final: 0.8079 (mt) REVERT: S 40 MET cc_start: 0.8228 (ptp) cc_final: 0.7575 (ppp) REVERT: T 67 MET cc_start: 0.7340 (mtt) cc_final: 0.6650 (tpt) REVERT: T 71 PHE cc_start: 0.5951 (OUTLIER) cc_final: 0.5505 (t80) REVERT: U 395 MET cc_start: 0.2968 (tpp) cc_final: 0.2363 (tpt) REVERT: U 408 MET cc_start: 0.7624 (mpp) cc_final: 0.6984 (mtt) REVERT: U 428 MET cc_start: 0.3370 (mtt) cc_final: 0.3162 (mtm) REVERT: U 453 MET cc_start: 0.2170 (mmm) cc_final: 0.1620 (mmt) REVERT: V 299 TYR cc_start: 0.1070 (OUTLIER) cc_final: -0.0181 (t80) REVERT: 1 44 MET cc_start: 0.6870 (tmm) cc_final: 0.5838 (tmm) REVERT: 1 146 LEU cc_start: 0.7474 (tt) cc_final: 0.6846 (mm) REVERT: 3 53 MET cc_start: 0.1944 (mmp) cc_final: 0.1142 (ptm) REVERT: 4 131 MET cc_start: 0.6529 (mtm) cc_final: 0.6165 (mtm) REVERT: 5 10 TYR cc_start: 0.5481 (p90) cc_final: 0.4228 (m-80) REVERT: 5 78 ASN cc_start: 0.5963 (OUTLIER) cc_final: 0.5715 (t0) REVERT: 6 53 MET cc_start: 0.6817 (mmm) cc_final: 0.5842 (mtt) REVERT: 6 124 GLN cc_start: 0.5957 (tm-30) cc_final: 0.5754 (tt0) REVERT: 6 155 LYS cc_start: 0.5076 (OUTLIER) cc_final: 0.3173 (mmtm) REVERT: 7 82 ASP cc_start: 0.5977 (OUTLIER) cc_final: 0.5637 (t0) REVERT: 9 14 PHE cc_start: 0.6711 (m-80) cc_final: 0.6312 (m-80) REVERT: Q 208 MET cc_start: 0.6686 (mmm) cc_final: 0.6395 (mmp) REVERT: Q 306 PHE cc_start: 0.6228 (m-80) cc_final: 0.6011 (t80) REVERT: C 142 ARG cc_start: 0.8108 (mtm110) cc_final: 0.7842 (mtm-85) REVERT: C 203 PHE cc_start: 0.6198 (t80) cc_final: 0.5807 (t80) REVERT: C 306 MET cc_start: 0.8538 (mmt) cc_final: 0.8330 (tpt) REVERT: C 438 LYS cc_start: 0.7345 (tmtt) cc_final: 0.7080 (tptm) REVERT: C 586 PHE cc_start: 0.7511 (m-80) cc_final: 0.7238 (m-80) REVERT: A 53 GLU cc_start: 0.5704 (OUTLIER) cc_final: 0.5173 (pm20) REVERT: A 81 ARG cc_start: 0.5758 (mtm-85) cc_final: 0.4833 (ptp-170) REVERT: A 314 ASN cc_start: 0.7906 (t0) cc_final: 0.7478 (t0) REVERT: A 349 ASP cc_start: 0.8007 (t70) cc_final: 0.7796 (t0) REVERT: A 353 ARG cc_start: 0.7080 (mmt-90) cc_final: 0.6748 (mmp80) REVERT: A 399 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7504 (mp0) REVERT: A 443 LYS cc_start: 0.8350 (tttm) cc_final: 0.8039 (mmtm) REVERT: A 518 ASP cc_start: 0.7994 (t0) cc_final: 0.7769 (t0) REVERT: A 570 ILE cc_start: 0.5518 (mm) cc_final: 0.5216 (mm) REVERT: A 600 ASP cc_start: 0.6948 (m-30) cc_final: 0.6630 (m-30) REVERT: B 136 THR cc_start: 0.7687 (OUTLIER) cc_final: 0.7435 (t) REVERT: B 142 ARG cc_start: 0.8508 (mtm-85) cc_final: 0.8022 (mtm110) REVERT: B 203 PHE cc_start: 0.6708 (t80) cc_final: 0.5996 (t80) REVERT: B 299 ASP cc_start: 0.6703 (p0) cc_final: 0.6435 (p0) REVERT: B 485 GLU cc_start: 0.7956 (mp0) cc_final: 0.7742 (mp0) REVERT: B 577 ILE cc_start: 0.7627 (OUTLIER) cc_final: 0.7240 (tt) REVERT: D 141 ARG cc_start: 0.7622 (tpt170) cc_final: 0.7176 (mmm160) REVERT: D 154 MET cc_start: 0.7877 (ptm) cc_final: 0.7608 (ptp) REVERT: D 164 ILE cc_start: 0.8516 (mm) cc_final: 0.8235 (mp) REVERT: D 214 LYS cc_start: 0.8252 (pptt) cc_final: 0.7246 (ptpp) REVERT: D 309 GLU cc_start: 0.7146 (tt0) cc_final: 0.6868 (mt-10) REVERT: D 435 MET cc_start: 0.7029 (tmm) cc_final: 0.6727 (tmm) REVERT: D 456 GLN cc_start: 0.7581 (tp40) cc_final: 0.7053 (tt0) REVERT: E 80 THR cc_start: 0.9093 (m) cc_final: 0.8639 (p) REVERT: E 403 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8138 (mtmm) REVERT: E 456 GLN cc_start: 0.7579 (tm-30) cc_final: 0.7171 (tp-100) REVERT: Z 59 ASN cc_start: 0.7143 (m-40) cc_final: 0.6368 (p0) REVERT: Z 74 CYS cc_start: 0.8055 (p) cc_final: 0.7836 (p) REVERT: Z 271 GLU cc_start: 0.3790 (OUTLIER) cc_final: 0.3226 (mm-30) REVERT: X 139 TYR cc_start: 0.8102 (t80) cc_final: 0.7770 (t80) REVERT: X 161 MET cc_start: 0.7861 (tpt) cc_final: 0.7424 (tpt) REVERT: X 180 LYS cc_start: 0.7826 (ttpp) cc_final: 0.7244 (tppt) REVERT: X 243 GLN cc_start: 0.7482 (mt0) cc_final: 0.7112 (mm-40) REVERT: X 251 SER cc_start: 0.7558 (t) cc_final: 0.7299 (p) REVERT: Y 139 TYR cc_start: 0.7267 (t80) cc_final: 0.6929 (t80) REVERT: G 45 ARG cc_start: 0.7806 (ttm170) cc_final: 0.7507 (mmm-85) REVERT: G 58 MET cc_start: 0.4668 (tmm) cc_final: 0.4265 (ttp) REVERT: N 69 TYR cc_start: 0.7172 (p90) cc_final: 0.6403 (p90) REVERT: N 96 HIS cc_start: 0.5210 (m90) cc_final: 0.4920 (m90) REVERT: W 333 MET cc_start: 0.6463 (mmt) cc_final: 0.6200 (mmm) REVERT: W 378 LYS cc_start: 0.8652 (mtpp) cc_final: 0.8422 (mmtt) REVERT: F 239 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7405 (tm-30) REVERT: F 299 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7798 (t0) REVERT: F 387 GLN cc_start: 0.7378 (mm110) cc_final: 0.7097 (mt0) REVERT: F 402 MET cc_start: 0.5064 (ptm) cc_final: 0.4812 (pmm) REVERT: F 435 MET cc_start: 0.7108 (mmm) cc_final: 0.6524 (mmm) REVERT: F 462 PHE cc_start: 0.8124 (t80) cc_final: 0.7612 (t80) REVERT: F 475 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7355 (pm20) outliers start: 171 outliers final: 88 residues processed: 1196 average time/residue: 0.7159 time to fit residues: 1484.5259 Evaluate side-chains 1057 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 955 time to evaluate : 6.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 333 ILE Chi-restraints excluded: chain R residue 535 PHE Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain M residue 27 LYS Chi-restraints excluded: chain I residue 56 TYR Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 149 GLN Chi-restraints excluded: chain I residue 210 GLU Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain T residue 71 PHE Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain U residue 407 VAL Chi-restraints excluded: chain V residue 299 TYR Chi-restraints excluded: chain 0 residue 76 ILE Chi-restraints excluded: chain 1 residue 64 ILE Chi-restraints excluded: chain 1 residue 113 VAL Chi-restraints excluded: chain 1 residue 143 LEU Chi-restraints excluded: chain 2 residue 135 LEU Chi-restraints excluded: chain 4 residue 10 TYR Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 4 residue 136 ILE Chi-restraints excluded: chain 5 residue 70 LEU Chi-restraints excluded: chain 5 residue 78 ASN Chi-restraints excluded: chain 6 residue 39 THR Chi-restraints excluded: chain 6 residue 57 ILE Chi-restraints excluded: chain 6 residue 155 LYS Chi-restraints excluded: chain 7 residue 57 ILE Chi-restraints excluded: chain 7 residue 82 ASP Chi-restraints excluded: chain 7 residue 143 LEU Chi-restraints excluded: chain 8 residue 39 THR Chi-restraints excluded: chain 8 residue 47 MET Chi-restraints excluded: chain 8 residue 60 VAL Chi-restraints excluded: chain 8 residue 104 LEU Chi-restraints excluded: chain 8 residue 143 LEU Chi-restraints excluded: chain 9 residue 65 ILE Chi-restraints excluded: chain Q residue 12 ASP Chi-restraints excluded: chain Q residue 24 LYS Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 107 ASP Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain Q residue 197 CYS Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 403 LYS Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain Z residue 146 THR Chi-restraints excluded: chain Z residue 271 GLU Chi-restraints excluded: chain X residue 177 GLN Chi-restraints excluded: chain X residue 241 VAL Chi-restraints excluded: chain Y residue 62 PHE Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Y residue 169 THR Chi-restraints excluded: chain Y residue 179 PHE Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain W residue 174 LYS Chi-restraints excluded: chain W residue 280 SER Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 475 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 854 optimal weight: 50.0000 chunk 650 optimal weight: 1.9990 chunk 449 optimal weight: 4.9990 chunk 95 optimal weight: 50.0000 chunk 412 optimal weight: 20.0000 chunk 580 optimal weight: 0.0670 chunk 868 optimal weight: 40.0000 chunk 919 optimal weight: 3.9990 chunk 453 optimal weight: 2.9990 chunk 822 optimal weight: 30.0000 chunk 247 optimal weight: 8.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 49 GLN ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 30 ASN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 348 HIS U 411 GLN 2 78 ASN ** 5 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 92 GLN ** 7 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 137 GLN ** Q 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 ASN B 317 ASN ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 HIS ** W 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 72859 Z= 0.310 Angle : 0.641 13.144 98827 Z= 0.333 Chirality : 0.044 0.445 11476 Planarity : 0.005 0.066 12780 Dihedral : 5.315 147.559 10472 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.90 % Allowed : 15.05 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.36 (0.09), residues: 9526 helix: 1.65 (0.07), residues: 5466 sheet: -0.83 (0.19), residues: 766 loop : -1.99 (0.10), residues: 3294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 756 HIS 0.008 0.001 HIS R 801 PHE 0.029 0.002 PHE J 224 TYR 0.055 0.002 TYR 8 144 ARG 0.006 0.001 ARG C 530 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1227 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1022 time to evaluate : 6.309 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: R 80 MET cc_start: 0.5751 (mpp) cc_final: 0.5388 (mmt) REVERT: R 358 ASN cc_start: 0.5051 (p0) cc_final: 0.4526 (m-40) REVERT: R 423 MET cc_start: 0.4750 (tpp) cc_final: 0.3990 (tpp) REVERT: R 439 MET cc_start: 0.4010 (ppp) cc_final: 0.1943 (tpp) REVERT: R 459 TYR cc_start: 0.6133 (t80) cc_final: 0.5589 (t80) REVERT: R 479 TRP cc_start: 0.5104 (m100) cc_final: 0.4485 (m100) REVERT: R 484 MET cc_start: 0.4827 (mmm) cc_final: 0.4120 (tpt) REVERT: R 492 GLU cc_start: 0.7280 (tp30) cc_final: 0.6870 (tm-30) REVERT: R 539 MET cc_start: 0.8301 (tmm) cc_final: 0.7333 (tmm) REVERT: R 615 MET cc_start: 0.7704 (tmm) cc_final: 0.6848 (tmm) REVERT: J 72 MET cc_start: 0.7365 (mmp) cc_final: 0.5870 (tmm) REVERT: J 131 ARG cc_start: 0.7638 (mtp-110) cc_final: 0.7403 (mtp85) REVERT: M 30 ASN cc_start: 0.6929 (t0) cc_final: 0.6680 (m-40) REVERT: M 81 MET cc_start: 0.6863 (mtt) cc_final: 0.6551 (mtt) REVERT: I 74 ASN cc_start: 0.8141 (t0) cc_final: 0.7812 (m-40) REVERT: I 92 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8540 (p) REVERT: I 149 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7338 (mp10) REVERT: I 172 TYR cc_start: 0.6901 (m-80) cc_final: 0.6347 (m-10) REVERT: I 193 SER cc_start: 0.8305 (p) cc_final: 0.7993 (p) REVERT: L 58 LYS cc_start: 0.7810 (mptt) cc_final: 0.7351 (mttt) REVERT: L 63 LEU cc_start: 0.6167 (mp) cc_final: 0.5758 (tt) REVERT: L 75 LYS cc_start: 0.9078 (tptt) cc_final: 0.8521 (pttp) REVERT: L 76 GLU cc_start: 0.7872 (tt0) cc_final: 0.7655 (tt0) REVERT: L 85 GLN cc_start: 0.8351 (mm-40) cc_final: 0.8079 (mt0) REVERT: H 63 GLN cc_start: 0.8021 (tm-30) cc_final: 0.7720 (tm-30) REVERT: H 117 ASP cc_start: 0.8065 (t0) cc_final: 0.7157 (m-30) REVERT: K 74 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7381 (tp30) REVERT: K 75 LYS cc_start: 0.7806 (ttpp) cc_final: 0.7550 (ptmm) REVERT: K 83 ILE cc_start: 0.8374 (tt) cc_final: 0.8026 (mt) REVERT: K 94 GLU cc_start: 0.8230 (pm20) cc_final: 0.7897 (pm20) REVERT: S 40 MET cc_start: 0.8236 (ptp) cc_final: 0.7599 (ppp) REVERT: T 67 MET cc_start: 0.7487 (mtt) cc_final: 0.6811 (tpt) REVERT: U 395 MET cc_start: 0.3030 (tpp) cc_final: 0.2327 (tpt) REVERT: U 428 MET cc_start: 0.3129 (mtt) cc_final: 0.2785 (mtm) REVERT: U 453 MET cc_start: 0.2432 (mmm) cc_final: 0.1909 (mmt) REVERT: V 299 TYR cc_start: 0.0627 (OUTLIER) cc_final: -0.0400 (t80) REVERT: 0 71 ILE cc_start: 0.6679 (OUTLIER) cc_final: 0.6455 (tt) REVERT: 1 23 MET cc_start: 0.7147 (tpt) cc_final: 0.6942 (tpt) REVERT: 1 44 MET cc_start: 0.6420 (tmm) cc_final: 0.5407 (tmm) REVERT: 1 47 MET cc_start: 0.6536 (ppp) cc_final: 0.5625 (mmt) REVERT: 1 54 LYS cc_start: 0.3937 (tptt) cc_final: 0.3706 (tptt) REVERT: 2 128 PHE cc_start: 0.5311 (t80) cc_final: 0.4928 (m-80) REVERT: 3 53 MET cc_start: 0.2460 (mmp) cc_final: 0.1358 (ptm) REVERT: 3 82 ASP cc_start: 0.3861 (t0) cc_final: 0.3588 (t0) REVERT: 4 131 MET cc_start: 0.6481 (mtm) cc_final: 0.5976 (mtm) REVERT: 5 10 TYR cc_start: 0.5608 (p90) cc_final: 0.4296 (m-80) REVERT: 7 17 MET cc_start: 0.7885 (ttt) cc_final: 0.7618 (ttt) REVERT: Q 208 MET cc_start: 0.6571 (mmm) cc_final: 0.6226 (mmp) REVERT: C 203 PHE cc_start: 0.6305 (t80) cc_final: 0.5766 (t80) REVERT: C 266 TYR cc_start: 0.7020 (m-10) cc_final: 0.6632 (m-10) REVERT: C 438 LYS cc_start: 0.7325 (tmtt) cc_final: 0.7005 (tttm) REVERT: C 586 PHE cc_start: 0.7520 (m-80) cc_final: 0.7238 (m-80) REVERT: C 608 MET cc_start: 0.3969 (ptt) cc_final: 0.3754 (ptm) REVERT: A 39 MET cc_start: 0.8985 (mmm) cc_final: 0.8347 (mmm) REVERT: A 81 ARG cc_start: 0.6123 (mtm-85) cc_final: 0.5067 (ptp-170) REVERT: A 314 ASN cc_start: 0.8074 (t0) cc_final: 0.7684 (t0) REVERT: A 349 ASP cc_start: 0.8051 (t70) cc_final: 0.7832 (t0) REVERT: A 353 ARG cc_start: 0.7171 (mmt-90) cc_final: 0.6889 (mmp80) REVERT: A 399 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7441 (mp0) REVERT: A 443 LYS cc_start: 0.8349 (tttm) cc_final: 0.8045 (mmtm) REVERT: A 463 GLU cc_start: 0.7918 (mp0) cc_final: 0.7637 (tp30) REVERT: A 518 ASP cc_start: 0.7890 (t0) cc_final: 0.7588 (t0) REVERT: A 570 ILE cc_start: 0.5753 (mm) cc_final: 0.5499 (mm) REVERT: A 600 ASP cc_start: 0.6918 (m-30) cc_final: 0.6577 (m-30) REVERT: B 20 TYR cc_start: 0.8013 (m-80) cc_final: 0.7775 (m-80) REVERT: B 136 THR cc_start: 0.7746 (OUTLIER) cc_final: 0.7463 (t) REVERT: B 142 ARG cc_start: 0.8548 (mtm-85) cc_final: 0.8126 (mtm110) REVERT: B 299 ASP cc_start: 0.6625 (p0) cc_final: 0.6372 (p0) REVERT: B 577 ILE cc_start: 0.7749 (OUTLIER) cc_final: 0.7434 (tt) REVERT: B 588 ASP cc_start: 0.8156 (t0) cc_final: 0.7946 (t0) REVERT: B 594 GLU cc_start: 0.6340 (tm-30) cc_final: 0.5842 (tm-30) REVERT: D 141 ARG cc_start: 0.7620 (tpt170) cc_final: 0.7186 (mmm160) REVERT: D 154 MET cc_start: 0.7970 (ptm) cc_final: 0.7726 (ptp) REVERT: D 214 LYS cc_start: 0.8175 (pptt) cc_final: 0.7150 (ptpp) REVERT: D 309 GLU cc_start: 0.7165 (tt0) cc_final: 0.6914 (mt-10) REVERT: D 435 MET cc_start: 0.7239 (tmm) cc_final: 0.6822 (tmm) REVERT: D 456 GLN cc_start: 0.7626 (tp40) cc_final: 0.7025 (tt0) REVERT: E 80 THR cc_start: 0.9157 (m) cc_final: 0.8716 (p) REVERT: E 154 MET cc_start: 0.8638 (mmm) cc_final: 0.8300 (mmt) REVERT: E 403 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8045 (mtmm) REVERT: E 456 GLN cc_start: 0.7602 (tm-30) cc_final: 0.7385 (tp40) REVERT: Z 59 ASN cc_start: 0.7047 (m-40) cc_final: 0.6288 (p0) REVERT: Z 74 CYS cc_start: 0.8005 (p) cc_final: 0.7696 (p) REVERT: Z 184 HIS cc_start: 0.7672 (t70) cc_final: 0.7385 (t-90) REVERT: Z 271 GLU cc_start: 0.3746 (OUTLIER) cc_final: 0.3153 (mm-30) REVERT: X 139 TYR cc_start: 0.8137 (t80) cc_final: 0.7880 (t80) REVERT: X 161 MET cc_start: 0.7753 (tpt) cc_final: 0.7357 (tpt) REVERT: X 166 TYR cc_start: 0.7619 (m-10) cc_final: 0.7327 (m-10) REVERT: X 180 LYS cc_start: 0.7882 (ttpp) cc_final: 0.7334 (tppt) REVERT: X 243 GLN cc_start: 0.7496 (mt0) cc_final: 0.7126 (mm-40) REVERT: X 251 SER cc_start: 0.7354 (t) cc_final: 0.7111 (p) REVERT: G 45 ARG cc_start: 0.7835 (ttm170) cc_final: 0.7510 (mmm-85) REVERT: G 58 MET cc_start: 0.4731 (tmm) cc_final: 0.4304 (ttp) REVERT: N 73 MET cc_start: 0.6575 (OUTLIER) cc_final: 0.6267 (tmm) REVERT: N 93 SER cc_start: 0.4598 (p) cc_final: 0.4214 (t) REVERT: W 333 MET cc_start: 0.6606 (mmt) cc_final: 0.5721 (mmt) REVERT: W 378 LYS cc_start: 0.8634 (mtpp) cc_final: 0.8410 (mmtt) REVERT: W 406 MET cc_start: 0.7250 (ttm) cc_final: 0.6940 (ttm) REVERT: F 239 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7384 (tm-30) REVERT: F 297 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8355 (mt) REVERT: F 299 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7939 (t0) REVERT: F 387 GLN cc_start: 0.7494 (mm110) cc_final: 0.7245 (mt0) REVERT: F 402 MET cc_start: 0.5051 (ptm) cc_final: 0.4689 (pmm) REVERT: F 435 MET cc_start: 0.6725 (mmm) cc_final: 0.6341 (tpt) REVERT: F 456 GLN cc_start: 0.7437 (mm-40) cc_final: 0.7084 (mp-120) REVERT: F 475 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7360 (pm20) outliers start: 205 outliers final: 128 residues processed: 1152 average time/residue: 0.6710 time to fit residues: 1329.2844 Evaluate side-chains 1084 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 943 time to evaluate : 6.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 333 ILE Chi-restraints excluded: chain R residue 418 LEU Chi-restraints excluded: chain R residue 535 PHE Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain M residue 27 LYS Chi-restraints excluded: chain I residue 56 TYR Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 149 GLN Chi-restraints excluded: chain I residue 210 GLU Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 102 PHE Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain T residue 101 TYR Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain U residue 407 VAL Chi-restraints excluded: chain V residue 299 TYR Chi-restraints excluded: chain 0 residue 71 ILE Chi-restraints excluded: chain 0 residue 76 ILE Chi-restraints excluded: chain 1 residue 64 ILE Chi-restraints excluded: chain 2 residue 57 ILE Chi-restraints excluded: chain 2 residue 135 LEU Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 4 residue 136 ILE Chi-restraints excluded: chain 5 residue 70 LEU Chi-restraints excluded: chain 5 residue 150 LEU Chi-restraints excluded: chain 6 residue 39 THR Chi-restraints excluded: chain 6 residue 57 ILE Chi-restraints excluded: chain 7 residue 57 ILE Chi-restraints excluded: chain 8 residue 39 THR Chi-restraints excluded: chain 8 residue 47 MET Chi-restraints excluded: chain 8 residue 60 VAL Chi-restraints excluded: chain 8 residue 104 LEU Chi-restraints excluded: chain 8 residue 143 LEU Chi-restraints excluded: chain 8 residue 148 VAL Chi-restraints excluded: chain 9 residue 65 ILE Chi-restraints excluded: chain 9 residue 93 LEU Chi-restraints excluded: chain 9 residue 150 LEU Chi-restraints excluded: chain Q residue 24 LYS Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 107 ASP Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain Q residue 150 LEU Chi-restraints excluded: chain Q residue 197 CYS Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 358 ASN Chi-restraints excluded: chain E residue 403 LYS Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain Z residue 146 THR Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 221 ASP Chi-restraints excluded: chain Z residue 271 GLU Chi-restraints excluded: chain X residue 10 MET Chi-restraints excluded: chain X residue 168 ILE Chi-restraints excluded: chain X residue 177 GLN Chi-restraints excluded: chain X residue 241 VAL Chi-restraints excluded: chain Y residue 62 PHE Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Y residue 169 THR Chi-restraints excluded: chain Y residue 179 PHE Chi-restraints excluded: chain Y residue 256 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain N residue 73 MET Chi-restraints excluded: chain W residue 206 VAL Chi-restraints excluded: chain W residue 229 THR Chi-restraints excluded: chain W residue 280 SER Chi-restraints excluded: chain W residue 373 ASP Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 359 ASP Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 475 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 765 optimal weight: 8.9990 chunk 521 optimal weight: 3.9990 chunk 13 optimal weight: 30.0000 chunk 684 optimal weight: 0.9980 chunk 379 optimal weight: 0.9990 chunk 784 optimal weight: 3.9990 chunk 635 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 469 optimal weight: 1.9990 chunk 825 optimal weight: 50.0000 chunk 231 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 811 GLN ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 107 ASN U 348 HIS 0 128 HIS 2 78 ASN ** Q 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 ASN B 65 GLN B 317 ASN B 449 ASN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 165 GLN Z 207 GLN ** X 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 96 HIS ** W 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 72859 Z= 0.243 Angle : 0.612 12.733 98827 Z= 0.316 Chirality : 0.043 0.475 11476 Planarity : 0.004 0.058 12780 Dihedral : 5.149 146.212 10472 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.93 % Allowed : 16.43 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.45 (0.09), residues: 9526 helix: 1.71 (0.07), residues: 5518 sheet: -0.81 (0.19), residues: 732 loop : -2.00 (0.10), residues: 3276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 0 39 HIS 0.010 0.001 HIS N 96 PHE 0.029 0.002 PHE 1 137 TYR 0.051 0.002 TYR 8 144 ARG 0.009 0.000 ARG 8 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1215 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1008 time to evaluate : 6.445 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: R 80 MET cc_start: 0.5699 (mpp) cc_final: 0.5302 (mmt) REVERT: R 358 ASN cc_start: 0.5079 (p0) cc_final: 0.4532 (m-40) REVERT: R 439 MET cc_start: 0.3977 (ppp) cc_final: 0.1887 (tpp) REVERT: R 479 TRP cc_start: 0.5063 (m100) cc_final: 0.4466 (m100) REVERT: R 484 MET cc_start: 0.4960 (mmm) cc_final: 0.4427 (mmt) REVERT: R 492 GLU cc_start: 0.7301 (tp30) cc_final: 0.6888 (tm-30) REVERT: R 539 MET cc_start: 0.8220 (tmm) cc_final: 0.7230 (tmm) REVERT: R 615 MET cc_start: 0.7616 (tmm) cc_final: 0.6716 (tmm) REVERT: R 793 MET cc_start: 0.5484 (tpp) cc_final: 0.5163 (tpp) REVERT: O 313 PRO cc_start: 0.7167 (Cg_endo) cc_final: 0.6850 (Cg_exo) REVERT: J 72 MET cc_start: 0.7461 (mmp) cc_final: 0.5997 (tmm) REVERT: J 111 ARG cc_start: 0.8228 (mtm180) cc_final: 0.7919 (mtm180) REVERT: J 131 ARG cc_start: 0.7571 (mtp-110) cc_final: 0.7353 (mtp85) REVERT: M 81 MET cc_start: 0.6639 (mtt) cc_final: 0.6052 (tmm) REVERT: M 105 ASP cc_start: 0.6110 (t0) cc_final: 0.5585 (p0) REVERT: I 52 LYS cc_start: 0.7850 (tmtt) cc_final: 0.7189 (pttm) REVERT: I 74 ASN cc_start: 0.8088 (t0) cc_final: 0.7783 (m-40) REVERT: I 172 TYR cc_start: 0.6865 (m-80) cc_final: 0.6381 (m-10) REVERT: I 193 SER cc_start: 0.8297 (p) cc_final: 0.7956 (p) REVERT: L 58 LYS cc_start: 0.7795 (mptt) cc_final: 0.7336 (mttt) REVERT: L 63 LEU cc_start: 0.6218 (mp) cc_final: 0.5900 (tt) REVERT: L 75 LYS cc_start: 0.9075 (tptt) cc_final: 0.8520 (pttp) REVERT: L 76 GLU cc_start: 0.7855 (tt0) cc_final: 0.7635 (tt0) REVERT: L 85 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7858 (mt0) REVERT: L 112 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7935 (pp20) REVERT: H 63 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7775 (tm-30) REVERT: H 117 ASP cc_start: 0.8010 (t0) cc_final: 0.7153 (m-30) REVERT: K 74 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7455 (tp30) REVERT: K 75 LYS cc_start: 0.7780 (ttpp) cc_final: 0.7135 (ttpp) REVERT: K 83 ILE cc_start: 0.8380 (tt) cc_final: 0.8034 (mt) REVERT: K 94 GLU cc_start: 0.8209 (pm20) cc_final: 0.7942 (pm20) REVERT: S 40 MET cc_start: 0.8184 (ptp) cc_final: 0.7510 (ppp) REVERT: T 67 MET cc_start: 0.7170 (mtt) cc_final: 0.6645 (tpt) REVERT: U 262 ASP cc_start: 0.5521 (OUTLIER) cc_final: 0.4903 (p0) REVERT: U 395 MET cc_start: 0.3152 (tpp) cc_final: 0.2490 (tpt) REVERT: U 428 MET cc_start: 0.3422 (mtt) cc_final: 0.3086 (mtm) REVERT: U 453 MET cc_start: 0.2405 (mmm) cc_final: 0.1981 (mmt) REVERT: V 299 TYR cc_start: 0.0520 (OUTLIER) cc_final: -0.0400 (t80) REVERT: 0 71 ILE cc_start: 0.6757 (OUTLIER) cc_final: 0.6542 (tt) REVERT: 0 107 MET cc_start: 0.5110 (mmm) cc_final: 0.4502 (mtm) REVERT: 1 44 MET cc_start: 0.6509 (tmm) cc_final: 0.5785 (tmm) REVERT: 1 47 MET cc_start: 0.6629 (ppp) cc_final: 0.5681 (mmt) REVERT: 1 146 LEU cc_start: 0.7575 (tt) cc_final: 0.6968 (mm) REVERT: 2 128 PHE cc_start: 0.5131 (t80) cc_final: 0.4790 (m-80) REVERT: 3 53 MET cc_start: 0.2645 (mmp) cc_final: 0.1446 (ptm) REVERT: 3 82 ASP cc_start: 0.4020 (t0) cc_final: 0.3761 (t0) REVERT: 4 131 MET cc_start: 0.6644 (mtm) cc_final: 0.6409 (mtm) REVERT: 5 10 TYR cc_start: 0.5664 (p90) cc_final: 0.4266 (m-80) REVERT: 7 137 PHE cc_start: 0.8014 (m-80) cc_final: 0.7724 (m-10) REVERT: 8 23 MET cc_start: 0.5946 (tpt) cc_final: 0.5713 (tpt) REVERT: 9 28 LEU cc_start: 0.7307 (tp) cc_final: 0.7103 (tt) REVERT: Q 105 MET cc_start: 0.6094 (ttm) cc_final: 0.5877 (ttm) REVERT: Q 176 MET cc_start: 0.4958 (ptp) cc_final: 0.4609 (ptp) REVERT: Q 208 MET cc_start: 0.6463 (mmm) cc_final: 0.6191 (mmp) REVERT: C 203 PHE cc_start: 0.6245 (t80) cc_final: 0.5809 (t80) REVERT: C 283 GLU cc_start: 0.8261 (mt-10) cc_final: 0.8016 (tt0) REVERT: C 438 LYS cc_start: 0.7417 (tmtt) cc_final: 0.7115 (tttm) REVERT: C 586 PHE cc_start: 0.7544 (m-80) cc_final: 0.7276 (m-80) REVERT: C 608 MET cc_start: 0.4108 (ptt) cc_final: 0.3831 (ptm) REVERT: A 81 ARG cc_start: 0.6156 (mtm-85) cc_final: 0.5191 (ptp-170) REVERT: A 314 ASN cc_start: 0.7954 (t0) cc_final: 0.7566 (t0) REVERT: A 353 ARG cc_start: 0.7143 (mmt-90) cc_final: 0.6869 (mmp80) REVERT: A 399 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7367 (mp0) REVERT: A 443 LYS cc_start: 0.8343 (tttm) cc_final: 0.8017 (mmtm) REVERT: A 463 GLU cc_start: 0.7970 (mp0) cc_final: 0.7707 (tm-30) REVERT: A 518 ASP cc_start: 0.7978 (t0) cc_final: 0.7674 (t0) REVERT: A 600 ASP cc_start: 0.6832 (m-30) cc_final: 0.6515 (m-30) REVERT: B 20 TYR cc_start: 0.8001 (m-80) cc_final: 0.7775 (m-80) REVERT: B 136 THR cc_start: 0.7739 (OUTLIER) cc_final: 0.7452 (t) REVERT: B 142 ARG cc_start: 0.8544 (mtm-85) cc_final: 0.8137 (mtm110) REVERT: B 203 PHE cc_start: 0.6655 (t80) cc_final: 0.5904 (t80) REVERT: B 577 ILE cc_start: 0.7449 (OUTLIER) cc_final: 0.7247 (tt) REVERT: B 588 ASP cc_start: 0.8172 (t0) cc_final: 0.7942 (t0) REVERT: B 594 GLU cc_start: 0.6316 (tm-30) cc_final: 0.5826 (tm-30) REVERT: B 608 MET cc_start: 0.7213 (mtp) cc_final: 0.6939 (mtm) REVERT: D 141 ARG cc_start: 0.7640 (tpt170) cc_final: 0.7192 (mmm160) REVERT: D 154 MET cc_start: 0.8027 (ptm) cc_final: 0.7826 (ptp) REVERT: D 214 LYS cc_start: 0.8132 (pptt) cc_final: 0.7130 (ptpp) REVERT: D 309 GLU cc_start: 0.7142 (tt0) cc_final: 0.6875 (mt-10) REVERT: D 435 MET cc_start: 0.7243 (tmm) cc_final: 0.6766 (tmm) REVERT: D 456 GLN cc_start: 0.7612 (tp40) cc_final: 0.7030 (tt0) REVERT: E 44 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7305 (mtt90) REVERT: E 80 THR cc_start: 0.9160 (m) cc_final: 0.8714 (p) REVERT: E 154 MET cc_start: 0.8586 (mmm) cc_final: 0.8287 (mmt) REVERT: E 403 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8070 (mtmm) REVERT: E 456 GLN cc_start: 0.7506 (tm-30) cc_final: 0.7291 (tp40) REVERT: Z 59 ASN cc_start: 0.7029 (m-40) cc_final: 0.6309 (p0) REVERT: Z 74 CYS cc_start: 0.7907 (p) cc_final: 0.7613 (p) REVERT: Z 170 GLU cc_start: 0.6444 (OUTLIER) cc_final: 0.6152 (pt0) REVERT: Z 271 GLU cc_start: 0.3889 (OUTLIER) cc_final: 0.3285 (mm-30) REVERT: X 115 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7519 (ttp) REVERT: X 161 MET cc_start: 0.7757 (tpt) cc_final: 0.7372 (tpt) REVERT: X 166 TYR cc_start: 0.7616 (m-10) cc_final: 0.7376 (m-10) REVERT: X 180 LYS cc_start: 0.7824 (ttpp) cc_final: 0.7242 (tppt) REVERT: X 243 GLN cc_start: 0.7520 (mt0) cc_final: 0.7078 (mm-40) REVERT: X 251 SER cc_start: 0.7357 (t) cc_final: 0.7111 (p) REVERT: G 45 ARG cc_start: 0.7832 (ttm170) cc_final: 0.7508 (mmm-85) REVERT: G 56 MET cc_start: 0.4940 (mmp) cc_final: 0.3222 (ptm) REVERT: G 58 MET cc_start: 0.4678 (tmm) cc_final: 0.4282 (ttp) REVERT: N 69 TYR cc_start: 0.8060 (p90) cc_final: 0.7529 (p90) REVERT: N 73 MET cc_start: 0.6726 (OUTLIER) cc_final: 0.6454 (tmm) REVERT: N 93 SER cc_start: 0.5458 (p) cc_final: 0.4175 (t) REVERT: N 102 LYS cc_start: 0.6712 (ttmm) cc_final: 0.5910 (tppt) REVERT: N 107 ARG cc_start: 0.7184 (mtt180) cc_final: 0.6921 (mtm-85) REVERT: W 252 MET cc_start: 0.6538 (mpp) cc_final: 0.6268 (mpp) REVERT: W 333 MET cc_start: 0.6603 (mmt) cc_final: 0.5723 (mmt) REVERT: W 378 LYS cc_start: 0.8647 (mtpp) cc_final: 0.8421 (mmtt) REVERT: F 239 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7393 (tm-30) REVERT: F 297 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8402 (mt) REVERT: F 299 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.7880 (t0) REVERT: F 387 GLN cc_start: 0.7461 (mm110) cc_final: 0.7214 (mt0) REVERT: F 402 MET cc_start: 0.4923 (ptm) cc_final: 0.4637 (pmm) REVERT: F 456 GLN cc_start: 0.7428 (mm-40) cc_final: 0.7046 (mp-120) REVERT: F 475 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7330 (pm20) outliers start: 207 outliers final: 137 residues processed: 1154 average time/residue: 0.6639 time to fit residues: 1326.2116 Evaluate side-chains 1109 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 956 time to evaluate : 6.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 333 ILE Chi-restraints excluded: chain R residue 418 LEU Chi-restraints excluded: chain R residue 535 PHE Chi-restraints excluded: chain R residue 735 THR Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain M residue 109 GLU Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 149 GLN Chi-restraints excluded: chain I residue 210 GLU Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 102 PHE Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain T residue 101 TYR Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain U residue 262 ASP Chi-restraints excluded: chain U residue 383 LEU Chi-restraints excluded: chain U residue 407 VAL Chi-restraints excluded: chain V residue 299 TYR Chi-restraints excluded: chain 0 residue 71 ILE Chi-restraints excluded: chain 0 residue 72 THR Chi-restraints excluded: chain 0 residue 76 ILE Chi-restraints excluded: chain 1 residue 59 VAL Chi-restraints excluded: chain 1 residue 64 ILE Chi-restraints excluded: chain 1 residue 129 VAL Chi-restraints excluded: chain 2 residue 57 ILE Chi-restraints excluded: chain 2 residue 135 LEU Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 148 VAL Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 4 residue 136 ILE Chi-restraints excluded: chain 5 residue 57 ILE Chi-restraints excluded: chain 5 residue 59 VAL Chi-restraints excluded: chain 5 residue 70 LEU Chi-restraints excluded: chain 5 residue 150 LEU Chi-restraints excluded: chain 6 residue 39 THR Chi-restraints excluded: chain 6 residue 57 ILE Chi-restraints excluded: chain 7 residue 57 ILE Chi-restraints excluded: chain 8 residue 39 THR Chi-restraints excluded: chain 8 residue 47 MET Chi-restraints excluded: chain 8 residue 53 MET Chi-restraints excluded: chain 8 residue 60 VAL Chi-restraints excluded: chain 8 residue 104 LEU Chi-restraints excluded: chain 8 residue 143 LEU Chi-restraints excluded: chain 8 residue 148 VAL Chi-restraints excluded: chain 9 residue 56 ILE Chi-restraints excluded: chain 9 residue 65 ILE Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 107 ASP Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain Q residue 150 LEU Chi-restraints excluded: chain Q residue 197 CYS Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 358 ASN Chi-restraints excluded: chain E residue 403 LYS Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain Z residue 146 THR Chi-restraints excluded: chain Z residue 170 GLU Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 271 GLU Chi-restraints excluded: chain X residue 10 MET Chi-restraints excluded: chain X residue 115 MET Chi-restraints excluded: chain X residue 168 ILE Chi-restraints excluded: chain X residue 177 GLN Chi-restraints excluded: chain X residue 241 VAL Chi-restraints excluded: chain Y residue 62 PHE Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Y residue 169 THR Chi-restraints excluded: chain Y residue 179 PHE Chi-restraints excluded: chain Y residue 256 THR Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain N residue 73 MET Chi-restraints excluded: chain W residue 280 SER Chi-restraints excluded: chain W residue 373 ASP Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 359 ASP Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 475 GLU Chi-restraints excluded: chain F residue 498 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 309 optimal weight: 5.9990 chunk 827 optimal weight: 50.0000 chunk 181 optimal weight: 6.9990 chunk 539 optimal weight: 0.0070 chunk 226 optimal weight: 6.9990 chunk 920 optimal weight: 2.9990 chunk 763 optimal weight: 7.9990 chunk 426 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 304 optimal weight: 5.9990 chunk 483 optimal weight: 5.9990 overall best weight: 3.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 59 GLN ** T 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 348 HIS ** 5 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 ASN B 65 GLN B 449 ASN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 165 GLN ** X 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 72859 Z= 0.331 Angle : 0.650 13.100 98827 Z= 0.335 Chirality : 0.045 0.432 11476 Planarity : 0.005 0.058 12780 Dihedral : 5.213 145.716 10472 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.38 % Allowed : 17.18 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.33 (0.09), residues: 9526 helix: 1.64 (0.07), residues: 5541 sheet: -0.99 (0.19), residues: 752 loop : -2.09 (0.10), residues: 3233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP S 52 HIS 0.010 0.001 HIS U 370 PHE 0.028 0.002 PHE J 224 TYR 0.050 0.002 TYR 8 144 ARG 0.010 0.001 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1232 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 993 time to evaluate : 6.339 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: R 17 LEU cc_start: 0.3988 (OUTLIER) cc_final: 0.3584 (mp) REVERT: R 80 MET cc_start: 0.5725 (mpp) cc_final: 0.5360 (mmt) REVERT: R 358 ASN cc_start: 0.4959 (p0) cc_final: 0.4513 (m-40) REVERT: R 439 MET cc_start: 0.4016 (ppp) cc_final: 0.2027 (tpp) REVERT: R 479 TRP cc_start: 0.5181 (m100) cc_final: 0.4574 (m100) REVERT: R 484 MET cc_start: 0.5093 (mmm) cc_final: 0.4555 (mmt) REVERT: R 492 GLU cc_start: 0.7244 (tp30) cc_final: 0.6788 (tm-30) REVERT: R 539 MET cc_start: 0.8044 (tmm) cc_final: 0.7153 (tmm) REVERT: R 588 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8361 (tp) REVERT: R 615 MET cc_start: 0.7597 (tmm) cc_final: 0.6716 (tmm) REVERT: O 313 PRO cc_start: 0.7229 (Cg_endo) cc_final: 0.6895 (Cg_exo) REVERT: J 72 MET cc_start: 0.7686 (mmp) cc_final: 0.6348 (tmm) REVERT: J 73 SER cc_start: 0.7540 (t) cc_final: 0.6892 (p) REVERT: J 111 ARG cc_start: 0.8322 (mtm180) cc_final: 0.8001 (mtm180) REVERT: J 131 ARG cc_start: 0.7653 (mtp-110) cc_final: 0.7419 (mtp85) REVERT: M 53 LYS cc_start: 0.8107 (pttt) cc_final: 0.7641 (tttt) REVERT: M 75 LYS cc_start: 0.8506 (mmmm) cc_final: 0.8044 (mmmm) REVERT: M 79 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7677 (pm20) REVERT: M 105 ASP cc_start: 0.6161 (t0) cc_final: 0.5580 (p0) REVERT: I 74 ASN cc_start: 0.8268 (t0) cc_final: 0.7919 (m-40) REVERT: I 92 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8680 (p) REVERT: I 149 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7364 (mp10) REVERT: I 172 TYR cc_start: 0.6899 (m-80) cc_final: 0.6516 (m-10) REVERT: I 193 SER cc_start: 0.8296 (p) cc_final: 0.7939 (p) REVERT: L 58 LYS cc_start: 0.7794 (mptt) cc_final: 0.7319 (mttt) REVERT: L 63 LEU cc_start: 0.6212 (mp) cc_final: 0.5891 (tt) REVERT: L 85 GLN cc_start: 0.8363 (mm-40) cc_final: 0.8056 (mt0) REVERT: L 92 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7059 (ttp80) REVERT: L 112 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7869 (pp20) REVERT: H 63 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7795 (tm-30) REVERT: H 117 ASP cc_start: 0.7997 (t0) cc_final: 0.7155 (m-30) REVERT: K 74 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7209 (tp30) REVERT: K 94 GLU cc_start: 0.8252 (pm20) cc_final: 0.7793 (pm20) REVERT: S 40 MET cc_start: 0.8172 (ptp) cc_final: 0.7563 (ppp) REVERT: T 64 MET cc_start: 0.4494 (mmp) cc_final: 0.3424 (mtp) REVERT: T 67 MET cc_start: 0.7101 (mtt) cc_final: 0.6613 (tpt) REVERT: U 262 ASP cc_start: 0.5568 (OUTLIER) cc_final: 0.4861 (p0) REVERT: U 395 MET cc_start: 0.3149 (tpp) cc_final: 0.2441 (tpt) REVERT: U 428 MET cc_start: 0.3631 (mtt) cc_final: 0.3226 (mtm) REVERT: U 453 MET cc_start: 0.2426 (mmm) cc_final: 0.2114 (mmt) REVERT: V 299 TYR cc_start: 0.0637 (OUTLIER) cc_final: -0.0298 (t80) REVERT: 1 44 MET cc_start: 0.6189 (tmm) cc_final: 0.5517 (tmm) REVERT: 1 47 MET cc_start: 0.6874 (ppp) cc_final: 0.5883 (mmt) REVERT: 2 128 PHE cc_start: 0.5124 (t80) cc_final: 0.4717 (m-80) REVERT: 3 53 MET cc_start: 0.2807 (mmp) cc_final: 0.1450 (ptm) REVERT: 5 10 TYR cc_start: 0.5372 (p90) cc_final: 0.4303 (m-80) REVERT: 5 44 MET cc_start: 0.5474 (ttt) cc_final: 0.4616 (tmm) REVERT: 6 47 MET cc_start: 0.6520 (mpp) cc_final: 0.6218 (mpp) REVERT: 9 126 ARG cc_start: 0.6356 (ptt-90) cc_final: 0.5875 (ttp-170) REVERT: Q 105 MET cc_start: 0.6114 (ttm) cc_final: 0.5798 (ttm) REVERT: Q 176 MET cc_start: 0.5073 (ptp) cc_final: 0.4683 (ptp) REVERT: Q 208 MET cc_start: 0.6470 (mmm) cc_final: 0.6216 (mmp) REVERT: C 203 PHE cc_start: 0.6379 (t80) cc_final: 0.5887 (t80) REVERT: C 266 TYR cc_start: 0.6997 (m-10) cc_final: 0.6678 (m-10) REVERT: C 438 LYS cc_start: 0.7363 (tmtt) cc_final: 0.7095 (tttm) REVERT: A 81 ARG cc_start: 0.6282 (mtm-85) cc_final: 0.5177 (ptp-170) REVERT: A 353 ARG cc_start: 0.7283 (mmt-90) cc_final: 0.6986 (mmp80) REVERT: A 399 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: A 443 LYS cc_start: 0.8330 (tttm) cc_final: 0.8043 (mmtm) REVERT: A 518 ASP cc_start: 0.7975 (t0) cc_final: 0.7724 (t0) REVERT: A 596 LYS cc_start: 0.7730 (tptp) cc_final: 0.6955 (tmtt) REVERT: A 600 ASP cc_start: 0.6756 (m-30) cc_final: 0.6437 (m-30) REVERT: B 20 TYR cc_start: 0.8056 (m-80) cc_final: 0.7820 (m-80) REVERT: B 61 MET cc_start: 0.8446 (tpp) cc_final: 0.7427 (mmm) REVERT: B 136 THR cc_start: 0.7806 (OUTLIER) cc_final: 0.7533 (t) REVERT: B 142 ARG cc_start: 0.8552 (mtm-85) cc_final: 0.8150 (mtm110) REVERT: B 203 PHE cc_start: 0.6737 (t80) cc_final: 0.5944 (t80) REVERT: B 213 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.7927 (mt0) REVERT: B 459 ARG cc_start: 0.8496 (tpp-160) cc_final: 0.8042 (mmm-85) REVERT: B 577 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.7152 (tt) REVERT: B 588 ASP cc_start: 0.8231 (t0) cc_final: 0.7989 (t0) REVERT: B 594 GLU cc_start: 0.6374 (tm-30) cc_final: 0.5887 (tm-30) REVERT: B 608 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6924 (mtm) REVERT: D 141 ARG cc_start: 0.7660 (tpt170) cc_final: 0.7227 (mmm160) REVERT: D 154 MET cc_start: 0.7995 (ptm) cc_final: 0.7774 (ptp) REVERT: D 214 LYS cc_start: 0.8152 (pptt) cc_final: 0.7154 (ptpp) REVERT: D 309 GLU cc_start: 0.7152 (tt0) cc_final: 0.6915 (mt-10) REVERT: D 362 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8653 (p) REVERT: D 435 MET cc_start: 0.7324 (tmm) cc_final: 0.6867 (tmm) REVERT: D 456 GLN cc_start: 0.7662 (tp40) cc_final: 0.7054 (tt0) REVERT: E 44 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7380 (mtt90) REVERT: E 80 THR cc_start: 0.9170 (m) cc_final: 0.8739 (p) REVERT: E 141 ARG cc_start: 0.8551 (ttt180) cc_final: 0.8291 (ttp80) REVERT: E 403 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8091 (mtmm) REVERT: E 456 GLN cc_start: 0.7535 (tm-30) cc_final: 0.7310 (tp40) REVERT: Z 74 CYS cc_start: 0.7780 (p) cc_final: 0.7528 (p) REVERT: Z 170 GLU cc_start: 0.6503 (OUTLIER) cc_final: 0.6189 (pt0) REVERT: Z 271 GLU cc_start: 0.3865 (OUTLIER) cc_final: 0.3214 (mm-30) REVERT: X 161 MET cc_start: 0.7817 (tpt) cc_final: 0.7449 (tpt) REVERT: X 166 TYR cc_start: 0.7656 (m-10) cc_final: 0.7373 (m-80) REVERT: X 180 LYS cc_start: 0.7862 (ttpp) cc_final: 0.7331 (tppt) REVERT: X 243 GLN cc_start: 0.7519 (mt0) cc_final: 0.7098 (mm-40) REVERT: G 45 ARG cc_start: 0.7838 (ttm170) cc_final: 0.7502 (mmm-85) REVERT: G 56 MET cc_start: 0.4878 (mmp) cc_final: 0.3111 (ptm) REVERT: G 58 MET cc_start: 0.4736 (tmm) cc_final: 0.4312 (ttp) REVERT: N 73 MET cc_start: 0.6808 (OUTLIER) cc_final: 0.6595 (tmm) REVERT: N 93 SER cc_start: 0.5518 (p) cc_final: 0.5232 (t) REVERT: W 174 LYS cc_start: 0.4063 (OUTLIER) cc_final: 0.3860 (mtmm) REVERT: W 333 MET cc_start: 0.6632 (mmt) cc_final: 0.5772 (mmt) REVERT: W 378 LYS cc_start: 0.8739 (mtpp) cc_final: 0.8509 (mmtt) REVERT: F 239 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7449 (tm-30) REVERT: F 297 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8372 (mt) REVERT: F 299 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.7983 (t0) REVERT: F 321 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8068 (tpp80) REVERT: F 435 MET cc_start: 0.6108 (mmm) cc_final: 0.5477 (tpt) REVERT: F 456 GLN cc_start: 0.7448 (mm-40) cc_final: 0.6989 (mp-120) REVERT: F 462 PHE cc_start: 0.8115 (t80) cc_final: 0.7651 (t80) REVERT: F 475 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7362 (pm20) outliers start: 239 outliers final: 156 residues processed: 1160 average time/residue: 0.6942 time to fit residues: 1403.0283 Evaluate side-chains 1117 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 936 time to evaluate : 6.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 333 ILE Chi-restraints excluded: chain R residue 418 LEU Chi-restraints excluded: chain R residue 535 PHE Chi-restraints excluded: chain R residue 588 ILE Chi-restraints excluded: chain R residue 735 THR Chi-restraints excluded: chain R residue 751 LEU Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain M residue 27 LYS Chi-restraints excluded: chain M residue 79 GLU Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 149 GLN Chi-restraints excluded: chain L residue 92 ARG Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 102 PHE Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain T residue 101 TYR Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain U residue 262 ASP Chi-restraints excluded: chain U residue 374 VAL Chi-restraints excluded: chain U residue 383 LEU Chi-restraints excluded: chain U residue 407 VAL Chi-restraints excluded: chain V residue 299 TYR Chi-restraints excluded: chain V residue 335 TYR Chi-restraints excluded: chain 0 residue 72 THR Chi-restraints excluded: chain 0 residue 76 ILE Chi-restraints excluded: chain 1 residue 59 VAL Chi-restraints excluded: chain 1 residue 64 ILE Chi-restraints excluded: chain 1 residue 71 VAL Chi-restraints excluded: chain 1 residue 129 VAL Chi-restraints excluded: chain 2 residue 57 ILE Chi-restraints excluded: chain 2 residue 135 LEU Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 140 VAL Chi-restraints excluded: chain 3 residue 148 VAL Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 4 residue 136 ILE Chi-restraints excluded: chain 5 residue 59 VAL Chi-restraints excluded: chain 5 residue 70 LEU Chi-restraints excluded: chain 6 residue 57 ILE Chi-restraints excluded: chain 6 residue 59 VAL Chi-restraints excluded: chain 7 residue 57 ILE Chi-restraints excluded: chain 8 residue 39 THR Chi-restraints excluded: chain 8 residue 56 ILE Chi-restraints excluded: chain 8 residue 60 VAL Chi-restraints excluded: chain 8 residue 104 LEU Chi-restraints excluded: chain 9 residue 56 ILE Chi-restraints excluded: chain 9 residue 65 ILE Chi-restraints excluded: chain 9 residue 93 LEU Chi-restraints excluded: chain 9 residue 108 PHE Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain Q residue 150 LEU Chi-restraints excluded: chain Q residue 197 CYS Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 358 ASN Chi-restraints excluded: chain E residue 403 LYS Chi-restraints excluded: chain Z residue 54 ILE Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain Z residue 146 THR Chi-restraints excluded: chain Z residue 170 GLU Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 221 ASP Chi-restraints excluded: chain Z residue 225 LEU Chi-restraints excluded: chain Z residue 271 GLU Chi-restraints excluded: chain X residue 10 MET Chi-restraints excluded: chain X residue 95 VAL Chi-restraints excluded: chain X residue 168 ILE Chi-restraints excluded: chain X residue 177 GLN Chi-restraints excluded: chain X residue 241 VAL Chi-restraints excluded: chain Y residue 62 PHE Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Y residue 169 THR Chi-restraints excluded: chain Y residue 179 PHE Chi-restraints excluded: chain Y residue 256 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain N residue 73 MET Chi-restraints excluded: chain W residue 174 LYS Chi-restraints excluded: chain W residue 206 VAL Chi-restraints excluded: chain W residue 245 ILE Chi-restraints excluded: chain W residue 280 SER Chi-restraints excluded: chain W residue 292 CYS Chi-restraints excluded: chain W residue 373 ASP Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 321 ARG Chi-restraints excluded: chain F residue 359 ASP Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 475 GLU Chi-restraints excluded: chain F residue 498 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 887 optimal weight: 5.9990 chunk 103 optimal weight: 50.0000 chunk 524 optimal weight: 0.8980 chunk 671 optimal weight: 0.9990 chunk 520 optimal weight: 0.5980 chunk 774 optimal weight: 0.8980 chunk 513 optimal weight: 0.9990 chunk 916 optimal weight: 0.7980 chunk 573 optimal weight: 1.9990 chunk 558 optimal weight: 7.9990 chunk 423 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 811 GLN ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 255 HIS U 272 GLN U 348 HIS ** 5 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 ASN B 261 GLN B 449 ASN D 187 GLN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 270 ASN ** Y 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 281 GLN ** W 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 72859 Z= 0.180 Angle : 0.599 14.555 98827 Z= 0.305 Chirality : 0.042 0.415 11476 Planarity : 0.004 0.059 12780 Dihedral : 4.907 142.788 10472 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.46 % Allowed : 18.90 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.65 (0.09), residues: 9526 helix: 1.91 (0.07), residues: 5489 sheet: -0.91 (0.19), residues: 769 loop : -1.89 (0.11), residues: 3268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP 0 49 HIS 0.009 0.001 HIS R 801 PHE 0.035 0.001 PHE 1 137 TYR 0.049 0.001 TYR 8 144 ARG 0.013 0.000 ARG 8 119 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1203 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1029 time to evaluate : 6.346 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: R 17 LEU cc_start: 0.3969 (OUTLIER) cc_final: 0.3577 (mp) REVERT: R 80 MET cc_start: 0.5627 (mpp) cc_final: 0.5236 (mmt) REVERT: R 358 ASN cc_start: 0.5068 (p0) cc_final: 0.4578 (m-40) REVERT: R 423 MET cc_start: 0.4999 (tpp) cc_final: 0.4096 (tpp) REVERT: R 439 MET cc_start: 0.4246 (ppp) cc_final: 0.2129 (tpp) REVERT: R 479 TRP cc_start: 0.4936 (m100) cc_final: 0.4252 (m100) REVERT: R 484 MET cc_start: 0.5186 (mmm) cc_final: 0.4695 (mmt) REVERT: R 492 GLU cc_start: 0.7162 (tp30) cc_final: 0.6694 (tm-30) REVERT: R 539 MET cc_start: 0.8220 (tmm) cc_final: 0.7694 (ttt) REVERT: R 615 MET cc_start: 0.7436 (tmm) cc_final: 0.6566 (tmm) REVERT: O 313 PRO cc_start: 0.7212 (Cg_endo) cc_final: 0.6874 (Cg_exo) REVERT: J 72 MET cc_start: 0.7572 (mmp) cc_final: 0.6416 (tmm) REVERT: J 73 SER cc_start: 0.7552 (t) cc_final: 0.6949 (p) REVERT: J 111 ARG cc_start: 0.8243 (mtm180) cc_final: 0.7932 (mtm180) REVERT: M 53 LYS cc_start: 0.8129 (pttt) cc_final: 0.7661 (tttt) REVERT: M 75 LYS cc_start: 0.8618 (mmmm) cc_final: 0.8205 (mmmm) REVERT: M 79 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7643 (pm20) REVERT: M 81 MET cc_start: 0.6525 (OUTLIER) cc_final: 0.6051 (tmm) REVERT: M 86 THR cc_start: 0.6495 (p) cc_final: 0.6212 (t) REVERT: M 105 ASP cc_start: 0.6045 (t0) cc_final: 0.5533 (p0) REVERT: I 52 LYS cc_start: 0.7829 (tmtt) cc_final: 0.7254 (pttm) REVERT: I 74 ASN cc_start: 0.7988 (t0) cc_final: 0.7671 (m-40) REVERT: I 117 ASP cc_start: 0.7628 (t0) cc_final: 0.7368 (t0) REVERT: I 132 MET cc_start: 0.8472 (mmt) cc_final: 0.7821 (mmt) REVERT: I 172 TYR cc_start: 0.6877 (m-80) cc_final: 0.6500 (m-10) REVERT: L 63 LEU cc_start: 0.6162 (mp) cc_final: 0.5904 (tt) REVERT: L 75 LYS cc_start: 0.9037 (tptt) cc_final: 0.8558 (pttp) REVERT: L 85 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7774 (mt0) REVERT: L 112 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7873 (pp20) REVERT: H 63 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7752 (tm-30) REVERT: H 117 ASP cc_start: 0.7819 (t0) cc_final: 0.7003 (m-30) REVERT: K 74 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7440 (tp30) REVERT: K 83 ILE cc_start: 0.8462 (tt) cc_final: 0.8104 (mt) REVERT: K 94 GLU cc_start: 0.8240 (pm20) cc_final: 0.7747 (pm20) REVERT: S 40 MET cc_start: 0.8155 (ptp) cc_final: 0.7558 (ppp) REVERT: T 64 MET cc_start: 0.4476 (mmp) cc_final: 0.3693 (mtp) REVERT: T 67 MET cc_start: 0.7486 (mtt) cc_final: 0.6819 (tpt) REVERT: U 262 ASP cc_start: 0.6061 (OUTLIER) cc_final: 0.5292 (p0) REVERT: U 428 MET cc_start: 0.3360 (mtt) cc_final: 0.3016 (mtm) REVERT: U 453 MET cc_start: 0.2500 (mmm) cc_final: 0.2239 (mmt) REVERT: V 299 TYR cc_start: 0.0668 (OUTLIER) cc_final: -0.0263 (t80) REVERT: 1 44 MET cc_start: 0.6062 (tmm) cc_final: 0.5478 (tmm) REVERT: 1 47 MET cc_start: 0.6980 (ppp) cc_final: 0.5886 (mmt) REVERT: 1 59 VAL cc_start: 0.1750 (OUTLIER) cc_final: 0.1344 (m) REVERT: 2 137 PHE cc_start: 0.6127 (m-80) cc_final: 0.5202 (m-10) REVERT: 3 17 MET cc_start: 0.4867 (mmt) cc_final: 0.4657 (mmp) REVERT: 3 53 MET cc_start: 0.2857 (mmp) cc_final: 0.1426 (ptm) REVERT: 6 47 MET cc_start: 0.6466 (mpp) cc_final: 0.6162 (mpp) REVERT: 7 82 ASP cc_start: 0.6057 (OUTLIER) cc_final: 0.5686 (t0) REVERT: 7 126 ARG cc_start: 0.6841 (OUTLIER) cc_final: 0.4884 (ptp90) REVERT: 9 126 ARG cc_start: 0.6385 (ptt-90) cc_final: 0.5902 (ttp-170) REVERT: Q 105 MET cc_start: 0.6100 (ttm) cc_final: 0.5862 (ttm) REVERT: Q 176 MET cc_start: 0.4880 (ptp) cc_final: 0.4510 (ptp) REVERT: C 192 LEU cc_start: 0.8455 (tp) cc_final: 0.8187 (tp) REVERT: C 203 PHE cc_start: 0.6191 (t80) cc_final: 0.5786 (t80) REVERT: C 232 ARG cc_start: 0.6650 (mtm180) cc_final: 0.6381 (mtm180) REVERT: C 283 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7908 (tt0) REVERT: C 438 LYS cc_start: 0.7458 (tmtt) cc_final: 0.7113 (tttm) REVERT: C 586 PHE cc_start: 0.7538 (m-80) cc_final: 0.7235 (m-80) REVERT: C 608 MET cc_start: 0.4185 (ptt) cc_final: 0.3872 (ptm) REVERT: A 53 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7021 (pt0) REVERT: A 61 MET cc_start: 0.4869 (ptm) cc_final: 0.4577 (ptt) REVERT: A 81 ARG cc_start: 0.6236 (mtm-85) cc_final: 0.5336 (ptp-170) REVERT: A 399 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7273 (mp0) REVERT: A 443 LYS cc_start: 0.8307 (tttm) cc_final: 0.8044 (mmtm) REVERT: A 518 ASP cc_start: 0.8119 (t0) cc_final: 0.7846 (t0) REVERT: A 596 LYS cc_start: 0.7750 (tptp) cc_final: 0.7036 (tmtt) REVERT: A 600 ASP cc_start: 0.6782 (m-30) cc_final: 0.6513 (m-30) REVERT: B 20 TYR cc_start: 0.7977 (m-80) cc_final: 0.7707 (m-80) REVERT: B 61 MET cc_start: 0.8400 (tpp) cc_final: 0.8047 (mmm) REVERT: B 136 THR cc_start: 0.7640 (OUTLIER) cc_final: 0.7387 (t) REVERT: B 142 ARG cc_start: 0.8530 (mtm-85) cc_final: 0.8136 (mtm110) REVERT: B 203 PHE cc_start: 0.6756 (t80) cc_final: 0.6093 (t80) REVERT: B 213 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.7889 (mt0) REVERT: B 299 ASP cc_start: 0.6340 (p0) cc_final: 0.6088 (p0) REVERT: B 459 ARG cc_start: 0.8534 (tpp-160) cc_final: 0.8041 (mmm-85) REVERT: B 588 ASP cc_start: 0.8211 (t0) cc_final: 0.7958 (t0) REVERT: B 594 GLU cc_start: 0.6255 (tm-30) cc_final: 0.5728 (tm-30) REVERT: D 124 SER cc_start: 0.8651 (t) cc_final: 0.8217 (m) REVERT: D 141 ARG cc_start: 0.7641 (tpt170) cc_final: 0.7192 (tpt90) REVERT: D 214 LYS cc_start: 0.8024 (pptt) cc_final: 0.7073 (ptpp) REVERT: D 309 GLU cc_start: 0.7095 (tt0) cc_final: 0.6818 (mt-10) REVERT: D 362 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8673 (p) REVERT: D 435 MET cc_start: 0.7333 (tmm) cc_final: 0.6805 (tmm) REVERT: D 456 GLN cc_start: 0.7560 (tp40) cc_final: 0.6988 (tt0) REVERT: E 44 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7334 (mtt90) REVERT: E 80 THR cc_start: 0.9162 (m) cc_final: 0.8731 (p) REVERT: E 154 MET cc_start: 0.8546 (mmm) cc_final: 0.8285 (mmt) REVERT: E 330 ASP cc_start: 0.8231 (t0) cc_final: 0.7937 (t0) REVERT: E 403 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8030 (mtmm) REVERT: E 456 GLN cc_start: 0.7488 (tm-30) cc_final: 0.7249 (tp40) REVERT: Z 59 ASN cc_start: 0.6985 (m-40) cc_final: 0.6342 (p0) REVERT: Z 188 MET cc_start: 0.6336 (tpp) cc_final: 0.6125 (mmp) REVERT: Z 271 GLU cc_start: 0.3484 (OUTLIER) cc_final: 0.3123 (mm-30) REVERT: X 115 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7598 (ttp) REVERT: X 161 MET cc_start: 0.7911 (tpt) cc_final: 0.7642 (tpt) REVERT: X 166 TYR cc_start: 0.7637 (m-10) cc_final: 0.7395 (m-80) REVERT: X 180 LYS cc_start: 0.7794 (ttpp) cc_final: 0.7200 (tppt) REVERT: X 243 GLN cc_start: 0.7516 (mt0) cc_final: 0.7102 (mm-40) REVERT: X 251 SER cc_start: 0.7413 (t) cc_final: 0.7204 (p) REVERT: G 45 ARG cc_start: 0.7845 (ttm170) cc_final: 0.7504 (mmm-85) REVERT: G 56 MET cc_start: 0.4866 (mmp) cc_final: 0.3263 (ptm) REVERT: G 58 MET cc_start: 0.4680 (tmm) cc_final: 0.4294 (ttp) REVERT: N 73 MET cc_start: 0.6726 (OUTLIER) cc_final: 0.6443 (tmm) REVERT: W 174 LYS cc_start: 0.4090 (mtpt) cc_final: 0.3829 (mtmm) REVERT: W 333 MET cc_start: 0.6587 (mmt) cc_final: 0.5797 (mmt) REVERT: W 378 LYS cc_start: 0.8740 (mtpp) cc_final: 0.8507 (mmtt) REVERT: F 39 TYR cc_start: 0.6330 (m-10) cc_final: 0.6058 (m-10) REVERT: F 299 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7593 (t0) REVERT: F 435 MET cc_start: 0.6025 (mmm) cc_final: 0.5393 (tpt) REVERT: F 456 GLN cc_start: 0.7462 (mm-40) cc_final: 0.6993 (mp-120) REVERT: F 462 PHE cc_start: 0.7977 (t80) cc_final: 0.7509 (t80) REVERT: F 475 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7303 (pm20) outliers start: 174 outliers final: 107 residues processed: 1146 average time/residue: 0.6594 time to fit residues: 1303.1126 Evaluate side-chains 1078 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 950 time to evaluate : 6.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 333 ILE Chi-restraints excluded: chain R residue 418 LEU Chi-restraints excluded: chain R residue 535 PHE Chi-restraints excluded: chain R residue 717 MET Chi-restraints excluded: chain R residue 801 HIS Chi-restraints excluded: chain J residue 66 GLN Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain M residue 27 LYS Chi-restraints excluded: chain M residue 79 GLU Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 102 PHE Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain T residue 101 TYR Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain U residue 262 ASP Chi-restraints excluded: chain U residue 374 VAL Chi-restraints excluded: chain U residue 407 VAL Chi-restraints excluded: chain V residue 299 TYR Chi-restraints excluded: chain 0 residue 72 THR Chi-restraints excluded: chain 0 residue 76 ILE Chi-restraints excluded: chain 1 residue 59 VAL Chi-restraints excluded: chain 1 residue 64 ILE Chi-restraints excluded: chain 1 residue 129 VAL Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 140 VAL Chi-restraints excluded: chain 3 residue 148 VAL Chi-restraints excluded: chain 4 residue 136 ILE Chi-restraints excluded: chain 5 residue 70 LEU Chi-restraints excluded: chain 6 residue 57 ILE Chi-restraints excluded: chain 7 residue 57 ILE Chi-restraints excluded: chain 7 residue 82 ASP Chi-restraints excluded: chain 7 residue 126 ARG Chi-restraints excluded: chain 8 residue 39 THR Chi-restraints excluded: chain 8 residue 52 ILE Chi-restraints excluded: chain 8 residue 56 ILE Chi-restraints excluded: chain 8 residue 60 VAL Chi-restraints excluded: chain 8 residue 104 LEU Chi-restraints excluded: chain 9 residue 56 ILE Chi-restraints excluded: chain 9 residue 93 LEU Chi-restraints excluded: chain 9 residue 108 PHE Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 150 LEU Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 403 LYS Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain Z residue 146 THR Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 271 GLU Chi-restraints excluded: chain X residue 10 MET Chi-restraints excluded: chain X residue 115 MET Chi-restraints excluded: chain X residue 168 ILE Chi-restraints excluded: chain X residue 177 GLN Chi-restraints excluded: chain X residue 241 VAL Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Y residue 169 THR Chi-restraints excluded: chain Y residue 179 PHE Chi-restraints excluded: chain Y residue 256 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain N residue 15 ASP Chi-restraints excluded: chain N residue 73 MET Chi-restraints excluded: chain W residue 206 VAL Chi-restraints excluded: chain W residue 280 SER Chi-restraints excluded: chain W residue 292 CYS Chi-restraints excluded: chain W residue 373 ASP Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 475 GLU Chi-restraints excluded: chain F residue 498 SER Chi-restraints excluded: chain F residue 499 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 567 optimal weight: 3.9990 chunk 366 optimal weight: 6.9990 chunk 547 optimal weight: 9.9990 chunk 276 optimal weight: 30.0000 chunk 180 optimal weight: 40.0000 chunk 177 optimal weight: 2.9990 chunk 582 optimal weight: 3.9990 chunk 624 optimal weight: 0.0000 chunk 453 optimal weight: 1.9990 chunk 85 optimal weight: 50.0000 chunk 720 optimal weight: 9.9990 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 50 GLN M 90 GLN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 272 GLN U 348 HIS ** 5 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 ASN B 449 ASN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN F 265 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 72859 Z= 0.289 Angle : 0.644 14.319 98827 Z= 0.329 Chirality : 0.044 0.392 11476 Planarity : 0.004 0.057 12780 Dihedral : 5.060 142.659 10472 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.21 % Favored : 94.78 % Rotamer: Outliers : 2.65 % Allowed : 19.21 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.50 (0.09), residues: 9526 helix: 1.79 (0.07), residues: 5533 sheet: -0.98 (0.19), residues: 752 loop : -2.02 (0.10), residues: 3241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP 0 49 HIS 0.009 0.001 HIS R 801 PHE 0.039 0.002 PHE 1 137 TYR 0.057 0.002 TYR 2 144 ARG 0.012 0.000 ARG 1 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1142 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 955 time to evaluate : 6.350 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: R 9 GLU cc_start: 0.2903 (tm-30) cc_final: 0.1847 (pm20) REVERT: R 17 LEU cc_start: 0.4028 (OUTLIER) cc_final: 0.3626 (mp) REVERT: R 80 MET cc_start: 0.5661 (mpp) cc_final: 0.5274 (mmt) REVERT: R 280 GLN cc_start: 0.6085 (mp10) cc_final: 0.5673 (mp10) REVERT: R 358 ASN cc_start: 0.4803 (p0) cc_final: 0.4371 (m-40) REVERT: R 439 MET cc_start: 0.4168 (ppp) cc_final: 0.2187 (tpp) REVERT: R 479 TRP cc_start: 0.4927 (m100) cc_final: 0.4288 (m100) REVERT: R 484 MET cc_start: 0.5149 (mmm) cc_final: 0.4889 (mmt) REVERT: R 539 MET cc_start: 0.8167 (tmm) cc_final: 0.7689 (ttt) REVERT: R 588 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8314 (tp) REVERT: R 615 MET cc_start: 0.7553 (tmm) cc_final: 0.7325 (tmm) REVERT: R 801 HIS cc_start: 0.5566 (OUTLIER) cc_final: 0.5258 (m-70) REVERT: O 313 PRO cc_start: 0.7376 (Cg_endo) cc_final: 0.7041 (Cg_exo) REVERT: J 65 GLU cc_start: 0.8051 (tt0) cc_final: 0.7327 (tp30) REVERT: J 111 ARG cc_start: 0.8300 (mtm180) cc_final: 0.7978 (mtm180) REVERT: M 53 LYS cc_start: 0.8097 (pttt) cc_final: 0.7644 (tttt) REVERT: M 75 LYS cc_start: 0.8656 (mmmm) cc_final: 0.8238 (mmmm) REVERT: M 79 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7698 (pm20) REVERT: M 105 ASP cc_start: 0.6068 (t0) cc_final: 0.5564 (p0) REVERT: I 74 ASN cc_start: 0.8237 (t0) cc_final: 0.7909 (m-40) REVERT: I 132 MET cc_start: 0.8535 (mmt) cc_final: 0.7818 (mmt) REVERT: I 172 TYR cc_start: 0.6834 (m-80) cc_final: 0.6493 (m-10) REVERT: L 58 LYS cc_start: 0.7816 (mptt) cc_final: 0.7339 (mttt) REVERT: L 63 LEU cc_start: 0.5916 (mp) cc_final: 0.5674 (tt) REVERT: L 75 LYS cc_start: 0.9061 (tptt) cc_final: 0.8468 (pttp) REVERT: L 85 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7817 (mt0) REVERT: L 112 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7898 (pp20) REVERT: H 63 GLN cc_start: 0.8053 (tm-30) cc_final: 0.7738 (tm-30) REVERT: H 117 ASP cc_start: 0.7890 (t0) cc_final: 0.7080 (m-30) REVERT: K 74 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7477 (tp30) REVERT: K 94 GLU cc_start: 0.8243 (pm20) cc_final: 0.7739 (pm20) REVERT: S 40 MET cc_start: 0.8163 (ptp) cc_final: 0.7617 (ppp) REVERT: T 64 MET cc_start: 0.4536 (mmp) cc_final: 0.3852 (mtp) REVERT: T 67 MET cc_start: 0.7443 (mtt) cc_final: 0.6823 (tpt) REVERT: U 262 ASP cc_start: 0.6070 (OUTLIER) cc_final: 0.5363 (p0) REVERT: U 453 MET cc_start: 0.2451 (mmm) cc_final: 0.2132 (mmt) REVERT: V 299 TYR cc_start: 0.0886 (OUTLIER) cc_final: -0.0099 (t80) REVERT: 1 44 MET cc_start: 0.6210 (tmm) cc_final: 0.5540 (tmm) REVERT: 1 47 MET cc_start: 0.7094 (ppp) cc_final: 0.5897 (mmt) REVERT: 1 59 VAL cc_start: 0.1241 (OUTLIER) cc_final: 0.0825 (m) REVERT: 2 128 PHE cc_start: 0.5091 (t80) cc_final: 0.4777 (m-80) REVERT: 2 137 PHE cc_start: 0.6147 (m-80) cc_final: 0.5234 (m-10) REVERT: 3 53 MET cc_start: 0.3064 (mmp) cc_final: 0.1445 (ptm) REVERT: 6 47 MET cc_start: 0.6559 (mpp) cc_final: 0.6297 (mpp) REVERT: 7 44 MET cc_start: 0.7810 (tpp) cc_final: 0.6932 (tmm) REVERT: 7 53 MET cc_start: 0.6917 (tmm) cc_final: 0.5991 (mmm) REVERT: 7 126 ARG cc_start: 0.6816 (OUTLIER) cc_final: 0.5160 (ptp90) REVERT: 9 13 PHE cc_start: 0.7007 (t80) cc_final: 0.6776 (t80) REVERT: 9 126 ARG cc_start: 0.6406 (ptt-90) cc_final: 0.5923 (ttp-170) REVERT: C 203 PHE cc_start: 0.6335 (t80) cc_final: 0.5835 (t80) REVERT: C 266 TYR cc_start: 0.7084 (m-10) cc_final: 0.6725 (m-10) REVERT: C 283 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8071 (tt0) REVERT: C 438 LYS cc_start: 0.7421 (tmtt) cc_final: 0.7168 (tttm) REVERT: C 586 PHE cc_start: 0.7555 (m-80) cc_final: 0.7248 (m-80) REVERT: A 61 MET cc_start: 0.4537 (ptm) cc_final: 0.4305 (ptt) REVERT: A 353 ARG cc_start: 0.7315 (mmt-90) cc_final: 0.7003 (mmp80) REVERT: A 367 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7559 (mt-10) REVERT: A 399 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: A 443 LYS cc_start: 0.8302 (tttm) cc_final: 0.8045 (mmtm) REVERT: A 596 LYS cc_start: 0.7736 (tptp) cc_final: 0.6942 (tmtt) REVERT: A 600 ASP cc_start: 0.6942 (m-30) cc_final: 0.6565 (m-30) REVERT: B 20 TYR cc_start: 0.8019 (m-80) cc_final: 0.7816 (m-80) REVERT: B 61 MET cc_start: 0.8504 (tpp) cc_final: 0.7450 (mmm) REVERT: B 136 THR cc_start: 0.7781 (OUTLIER) cc_final: 0.7503 (t) REVERT: B 142 ARG cc_start: 0.8569 (mtm-85) cc_final: 0.8168 (mtm110) REVERT: B 213 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.7920 (mt0) REVERT: B 299 ASP cc_start: 0.6514 (p0) cc_final: 0.6296 (p0) REVERT: B 459 ARG cc_start: 0.8516 (tpp-160) cc_final: 0.8055 (mmm-85) REVERT: B 588 ASP cc_start: 0.8260 (t0) cc_final: 0.7994 (t0) REVERT: B 594 GLU cc_start: 0.6330 (tm-30) cc_final: 0.5811 (tm-30) REVERT: D 141 ARG cc_start: 0.7669 (tpt170) cc_final: 0.7171 (mmm160) REVERT: D 214 LYS cc_start: 0.8063 (pptt) cc_final: 0.7092 (ptpp) REVERT: D 294 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8400 (tp) REVERT: D 309 GLU cc_start: 0.7126 (tt0) cc_final: 0.6878 (mt-10) REVERT: D 362 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8668 (p) REVERT: D 435 MET cc_start: 0.7404 (tmm) cc_final: 0.6836 (tmm) REVERT: D 456 GLN cc_start: 0.7785 (tp40) cc_final: 0.7058 (tt0) REVERT: E 44 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7356 (mtt90) REVERT: E 80 THR cc_start: 0.9168 (m) cc_final: 0.8727 (p) REVERT: E 154 MET cc_start: 0.8644 (mmm) cc_final: 0.8379 (mmt) REVERT: E 314 ARG cc_start: 0.7011 (mmm160) cc_final: 0.6661 (tpt90) REVERT: E 403 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8120 (mtmm) REVERT: E 456 GLN cc_start: 0.7552 (tm-30) cc_final: 0.7321 (tp40) REVERT: Z 271 GLU cc_start: 0.3507 (OUTLIER) cc_final: 0.3065 (mp0) REVERT: X 115 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7661 (ttp) REVERT: X 161 MET cc_start: 0.7877 (tpt) cc_final: 0.7566 (tpt) REVERT: X 166 TYR cc_start: 0.7667 (m-10) cc_final: 0.7378 (m-80) REVERT: X 180 LYS cc_start: 0.7736 (ttpp) cc_final: 0.7226 (tppt) REVERT: X 243 GLN cc_start: 0.7515 (mt0) cc_final: 0.7114 (mm-40) REVERT: G 45 ARG cc_start: 0.7848 (ttm170) cc_final: 0.7508 (mmm-85) REVERT: G 56 MET cc_start: 0.4899 (mmp) cc_final: 0.3233 (ptm) REVERT: G 58 MET cc_start: 0.4714 (tmm) cc_final: 0.4298 (ttp) REVERT: G 215 LYS cc_start: 0.7016 (ttpt) cc_final: 0.6794 (ttpp) REVERT: N 73 MET cc_start: 0.6899 (OUTLIER) cc_final: 0.6537 (tmm) REVERT: W 333 MET cc_start: 0.6612 (mmt) cc_final: 0.5798 (mmt) REVERT: W 378 LYS cc_start: 0.8740 (mtpp) cc_final: 0.8515 (mmtt) REVERT: F 239 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7408 (tm-30) REVERT: F 299 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.7904 (t0) REVERT: F 321 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8085 (tpp80) REVERT: F 435 MET cc_start: 0.6112 (mmm) cc_final: 0.5532 (tpt) REVERT: F 456 GLN cc_start: 0.7490 (mm-40) cc_final: 0.6991 (mp-120) REVERT: F 475 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7330 (pm20) outliers start: 187 outliers final: 131 residues processed: 1088 average time/residue: 0.6770 time to fit residues: 1275.9955 Evaluate side-chains 1070 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 917 time to evaluate : 6.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 333 ILE Chi-restraints excluded: chain R residue 418 LEU Chi-restraints excluded: chain R residue 535 PHE Chi-restraints excluded: chain R residue 588 ILE Chi-restraints excluded: chain R residue 751 LEU Chi-restraints excluded: chain R residue 801 HIS Chi-restraints excluded: chain J residue 66 GLN Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain M residue 27 LYS Chi-restraints excluded: chain M residue 79 GLU Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 102 PHE Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain T residue 101 TYR Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain U residue 262 ASP Chi-restraints excluded: chain U residue 374 VAL Chi-restraints excluded: chain U residue 383 LEU Chi-restraints excluded: chain U residue 407 VAL Chi-restraints excluded: chain V residue 299 TYR Chi-restraints excluded: chain 0 residue 72 THR Chi-restraints excluded: chain 0 residue 76 ILE Chi-restraints excluded: chain 1 residue 59 VAL Chi-restraints excluded: chain 1 residue 129 VAL Chi-restraints excluded: chain 2 residue 57 ILE Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 148 VAL Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 4 residue 136 ILE Chi-restraints excluded: chain 5 residue 59 VAL Chi-restraints excluded: chain 5 residue 65 ILE Chi-restraints excluded: chain 5 residue 70 LEU Chi-restraints excluded: chain 6 residue 57 ILE Chi-restraints excluded: chain 7 residue 57 ILE Chi-restraints excluded: chain 7 residue 126 ARG Chi-restraints excluded: chain 8 residue 39 THR Chi-restraints excluded: chain 8 residue 56 ILE Chi-restraints excluded: chain 8 residue 60 VAL Chi-restraints excluded: chain 8 residue 104 LEU Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 56 ILE Chi-restraints excluded: chain 9 residue 93 LEU Chi-restraints excluded: chain 9 residue 108 PHE Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 107 ASP Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 150 LEU Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 358 ASN Chi-restraints excluded: chain E residue 403 LYS Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain Z residue 146 THR Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 221 ASP Chi-restraints excluded: chain Z residue 271 GLU Chi-restraints excluded: chain X residue 10 MET Chi-restraints excluded: chain X residue 115 MET Chi-restraints excluded: chain X residue 168 ILE Chi-restraints excluded: chain X residue 177 GLN Chi-restraints excluded: chain X residue 241 VAL Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Y residue 74 CYS Chi-restraints excluded: chain Y residue 169 THR Chi-restraints excluded: chain Y residue 179 PHE Chi-restraints excluded: chain Y residue 256 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain N residue 73 MET Chi-restraints excluded: chain W residue 206 VAL Chi-restraints excluded: chain W residue 245 ILE Chi-restraints excluded: chain W residue 280 SER Chi-restraints excluded: chain W residue 292 CYS Chi-restraints excluded: chain W residue 373 ASP Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 321 ARG Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 475 GLU Chi-restraints excluded: chain F residue 499 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 833 optimal weight: 8.9990 chunk 878 optimal weight: 20.0000 chunk 801 optimal weight: 1.9990 chunk 854 optimal weight: 50.0000 chunk 877 optimal weight: 5.9990 chunk 514 optimal weight: 1.9990 chunk 372 optimal weight: 7.9990 chunk 670 optimal weight: 0.0570 chunk 262 optimal weight: 5.9990 chunk 771 optimal weight: 9.9990 chunk 807 optimal weight: 0.7980 overall best weight: 2.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 67 GLN U 348 HIS ** Q 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 ASN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 72859 Z= 0.257 Angle : 0.638 14.665 98827 Z= 0.326 Chirality : 0.044 0.471 11476 Planarity : 0.004 0.067 12780 Dihedral : 5.012 142.592 10472 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.52 % Allowed : 19.31 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.55 (0.09), residues: 9526 helix: 1.84 (0.07), residues: 5500 sheet: -1.06 (0.18), residues: 773 loop : -1.96 (0.11), residues: 3253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP 0 49 HIS 0.010 0.001 HIS R 801 PHE 0.038 0.002 PHE 1 137 TYR 0.064 0.002 TYR 2 144 ARG 0.009 0.000 ARG 1 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1142 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 964 time to evaluate : 6.397 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: symmetry clash REVERT: R 9 GLU cc_start: 0.2841 (tm-30) cc_final: 0.1954 (pm20) REVERT: R 17 LEU cc_start: 0.3845 (OUTLIER) cc_final: 0.3472 (mp) REVERT: R 80 MET cc_start: 0.5489 (mpp) cc_final: 0.5140 (mmt) REVERT: R 280 GLN cc_start: 0.6083 (mp10) cc_final: 0.5704 (mp10) REVERT: R 358 ASN cc_start: 0.4881 (p0) cc_final: 0.4384 (m-40) REVERT: R 439 MET cc_start: 0.4155 (ppp) cc_final: 0.2019 (tpp) REVERT: R 479 TRP cc_start: 0.4844 (m100) cc_final: 0.4236 (m100) REVERT: R 484 MET cc_start: 0.5042 (mmm) cc_final: 0.4815 (mmt) REVERT: R 539 MET cc_start: 0.8215 (tmm) cc_final: 0.7768 (ttt) REVERT: R 588 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8307 (tp) REVERT: R 615 MET cc_start: 0.7596 (tmm) cc_final: 0.7354 (tmm) REVERT: R 801 HIS cc_start: 0.5382 (OUTLIER) cc_final: 0.5009 (m-70) REVERT: O 313 PRO cc_start: 0.7314 (Cg_endo) cc_final: 0.6951 (Cg_exo) REVERT: J 65 GLU cc_start: 0.8070 (tt0) cc_final: 0.7333 (tp30) REVERT: J 111 ARG cc_start: 0.8259 (mtm180) cc_final: 0.7938 (mtm180) REVERT: M 53 LYS cc_start: 0.8136 (pttt) cc_final: 0.7754 (tttt) REVERT: M 105 ASP cc_start: 0.6090 (t0) cc_final: 0.5579 (p0) REVERT: I 74 ASN cc_start: 0.8184 (t0) cc_final: 0.7849 (m-40) REVERT: I 92 THR cc_start: 0.9095 (OUTLIER) cc_final: 0.8664 (p) REVERT: I 132 MET cc_start: 0.8546 (mmt) cc_final: 0.8310 (mmt) REVERT: I 172 TYR cc_start: 0.6813 (m-80) cc_final: 0.6485 (m-10) REVERT: L 85 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7767 (mt0) REVERT: L 112 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7892 (pp20) REVERT: H 63 GLN cc_start: 0.8027 (tm-30) cc_final: 0.7702 (tm-30) REVERT: H 117 ASP cc_start: 0.7838 (t0) cc_final: 0.7032 (m-30) REVERT: K 74 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7269 (tp30) REVERT: K 83 ILE cc_start: 0.8445 (tt) cc_final: 0.8055 (mt) REVERT: K 94 GLU cc_start: 0.8250 (pm20) cc_final: 0.7760 (pm20) REVERT: K 98 ASN cc_start: 0.8325 (t0) cc_final: 0.8043 (t0) REVERT: S 34 ARG cc_start: 0.3239 (tpt90) cc_final: 0.2920 (tpt90) REVERT: S 40 MET cc_start: 0.8335 (ptp) cc_final: 0.7724 (ppp) REVERT: T 55 ILE cc_start: 0.6533 (mt) cc_final: 0.6081 (pt) REVERT: T 64 MET cc_start: 0.4515 (mmp) cc_final: 0.3831 (mtp) REVERT: T 67 MET cc_start: 0.7249 (mtt) cc_final: 0.6665 (tpt) REVERT: U 262 ASP cc_start: 0.6012 (OUTLIER) cc_final: 0.5229 (p0) REVERT: U 453 MET cc_start: 0.2779 (mmm) cc_final: 0.2511 (mmt) REVERT: V 299 TYR cc_start: 0.0889 (OUTLIER) cc_final: -0.0049 (t80) REVERT: 1 44 MET cc_start: 0.6236 (tmm) cc_final: 0.5558 (tmm) REVERT: 1 47 MET cc_start: 0.7160 (ppp) cc_final: 0.5914 (mmt) REVERT: 1 59 VAL cc_start: 0.1432 (OUTLIER) cc_final: 0.0925 (m) REVERT: 2 137 PHE cc_start: 0.6128 (m-80) cc_final: 0.5265 (m-10) REVERT: 3 53 MET cc_start: 0.3124 (mmp) cc_final: 0.1607 (ptm) REVERT: 3 134 ILE cc_start: 0.6522 (OUTLIER) cc_final: 0.6032 (tp) REVERT: 6 47 MET cc_start: 0.6529 (mpp) cc_final: 0.6300 (mpp) REVERT: 8 119 ARG cc_start: 0.6531 (mmt-90) cc_final: 0.6118 (mpt180) REVERT: 9 126 ARG cc_start: 0.6373 (ptt-90) cc_final: 0.5877 (ttp-170) REVERT: Q 117 LEU cc_start: 0.5639 (mp) cc_final: 0.4609 (tp) REVERT: C 203 PHE cc_start: 0.6322 (t80) cc_final: 0.5822 (t80) REVERT: C 283 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8034 (tt0) REVERT: C 438 LYS cc_start: 0.7421 (tmtt) cc_final: 0.7168 (tttm) REVERT: C 586 PHE cc_start: 0.7548 (m-80) cc_final: 0.7225 (m-80) REVERT: A 81 ARG cc_start: 0.6053 (mtt180) cc_final: 0.5079 (ptp-170) REVERT: A 353 ARG cc_start: 0.7165 (mmt-90) cc_final: 0.6871 (mmp80) REVERT: A 399 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: A 443 LYS cc_start: 0.8270 (tttm) cc_final: 0.8038 (mmtm) REVERT: A 510 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7398 (tp30) REVERT: A 596 LYS cc_start: 0.7730 (tptp) cc_final: 0.6972 (tmtt) REVERT: A 600 ASP cc_start: 0.7027 (m-30) cc_final: 0.6654 (m-30) REVERT: B 20 TYR cc_start: 0.8013 (m-80) cc_final: 0.7801 (m-80) REVERT: B 61 MET cc_start: 0.8546 (tpp) cc_final: 0.7564 (mmm) REVERT: B 136 THR cc_start: 0.7768 (OUTLIER) cc_final: 0.7484 (t) REVERT: B 142 ARG cc_start: 0.8568 (mtm-85) cc_final: 0.8160 (mtm110) REVERT: B 203 PHE cc_start: 0.6784 (t80) cc_final: 0.6005 (t80) REVERT: B 213 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.7944 (mt0) REVERT: B 299 ASP cc_start: 0.6561 (p0) cc_final: 0.6307 (p0) REVERT: B 459 ARG cc_start: 0.8506 (tpp-160) cc_final: 0.8032 (mmm-85) REVERT: B 588 ASP cc_start: 0.8270 (t0) cc_final: 0.7996 (t0) REVERT: B 594 GLU cc_start: 0.6297 (tm-30) cc_final: 0.5792 (tm-30) REVERT: D 141 ARG cc_start: 0.7665 (tpt170) cc_final: 0.7157 (mmm160) REVERT: D 214 LYS cc_start: 0.8035 (pptt) cc_final: 0.7072 (ptpp) REVERT: D 309 GLU cc_start: 0.7116 (tt0) cc_final: 0.6859 (mt-10) REVERT: D 435 MET cc_start: 0.7429 (tmm) cc_final: 0.6865 (tmm) REVERT: D 456 GLN cc_start: 0.7750 (tp40) cc_final: 0.7067 (tt0) REVERT: E 44 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7343 (mtt90) REVERT: E 80 THR cc_start: 0.9169 (m) cc_final: 0.8725 (p) REVERT: E 141 ARG cc_start: 0.8527 (ttt180) cc_final: 0.8279 (mtp180) REVERT: E 154 MET cc_start: 0.8635 (mmm) cc_final: 0.8368 (mmt) REVERT: E 403 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8108 (mtmm) REVERT: E 456 GLN cc_start: 0.7530 (tm-30) cc_final: 0.7292 (tp40) REVERT: Z 59 ASN cc_start: 0.6996 (m-40) cc_final: 0.6364 (p0) REVERT: Z 161 MET cc_start: 0.7322 (mmt) cc_final: 0.7114 (mmt) REVERT: Z 188 MET cc_start: 0.6369 (tpp) cc_final: 0.5964 (mmp) REVERT: Z 271 GLU cc_start: 0.3486 (OUTLIER) cc_final: 0.3027 (mp0) REVERT: X 115 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7668 (ttp) REVERT: X 161 MET cc_start: 0.7974 (tpt) cc_final: 0.7701 (tpt) REVERT: X 166 TYR cc_start: 0.7698 (m-10) cc_final: 0.7460 (m-80) REVERT: X 180 LYS cc_start: 0.7728 (ttpp) cc_final: 0.7133 (tppt) REVERT: X 181 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7771 (tp) REVERT: X 243 GLN cc_start: 0.7490 (mt0) cc_final: 0.7111 (mm-40) REVERT: Y 109 GLU cc_start: 0.6333 (mm-30) cc_final: 0.5673 (tt0) REVERT: G 45 ARG cc_start: 0.7838 (ttm170) cc_final: 0.7501 (mmm-85) REVERT: G 56 MET cc_start: 0.4866 (mmp) cc_final: 0.3228 (ptm) REVERT: G 58 MET cc_start: 0.4749 (tmm) cc_final: 0.4356 (ttp) REVERT: N 73 MET cc_start: 0.6801 (OUTLIER) cc_final: 0.6455 (tmm) REVERT: W 333 MET cc_start: 0.6557 (mmt) cc_final: 0.5706 (mmt) REVERT: W 378 LYS cc_start: 0.8737 (mtpp) cc_final: 0.8507 (mmtt) REVERT: F 39 TYR cc_start: 0.6356 (m-10) cc_final: 0.6095 (m-10) REVERT: F 297 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8459 (mt) REVERT: F 299 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7817 (t0) REVERT: F 321 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8091 (tpp80) REVERT: F 435 MET cc_start: 0.6142 (mmm) cc_final: 0.5582 (tpt) REVERT: F 456 GLN cc_start: 0.7492 (mm-40) cc_final: 0.6981 (mp-120) REVERT: F 475 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7328 (pm20) outliers start: 178 outliers final: 134 residues processed: 1090 average time/residue: 0.6809 time to fit residues: 1283.1380 Evaluate side-chains 1088 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 932 time to evaluate : 6.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 333 ILE Chi-restraints excluded: chain R residue 418 LEU Chi-restraints excluded: chain R residue 535 PHE Chi-restraints excluded: chain R residue 588 ILE Chi-restraints excluded: chain R residue 717 MET Chi-restraints excluded: chain R residue 801 HIS Chi-restraints excluded: chain J residue 66 GLN Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain M residue 27 LYS Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 102 PHE Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain U residue 262 ASP Chi-restraints excluded: chain U residue 374 VAL Chi-restraints excluded: chain U residue 383 LEU Chi-restraints excluded: chain U residue 407 VAL Chi-restraints excluded: chain V residue 299 TYR Chi-restraints excluded: chain V residue 335 TYR Chi-restraints excluded: chain 0 residue 72 THR Chi-restraints excluded: chain 0 residue 76 ILE Chi-restraints excluded: chain 1 residue 59 VAL Chi-restraints excluded: chain 1 residue 129 VAL Chi-restraints excluded: chain 2 residue 57 ILE Chi-restraints excluded: chain 2 residue 135 LEU Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 134 ILE Chi-restraints excluded: chain 3 residue 148 VAL Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 4 residue 136 ILE Chi-restraints excluded: chain 5 residue 70 LEU Chi-restraints excluded: chain 6 residue 57 ILE Chi-restraints excluded: chain 7 residue 57 ILE Chi-restraints excluded: chain 7 residue 126 ARG Chi-restraints excluded: chain 8 residue 39 THR Chi-restraints excluded: chain 8 residue 56 ILE Chi-restraints excluded: chain 8 residue 60 VAL Chi-restraints excluded: chain 8 residue 104 LEU Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 56 ILE Chi-restraints excluded: chain 9 residue 93 LEU Chi-restraints excluded: chain 9 residue 108 PHE Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 150 LEU Chi-restraints excluded: chain Q residue 197 CYS Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 403 LYS Chi-restraints excluded: chain Z residue 54 ILE Chi-restraints excluded: chain Z residue 74 CYS Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain Z residue 146 THR Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 221 ASP Chi-restraints excluded: chain Z residue 271 GLU Chi-restraints excluded: chain X residue 10 MET Chi-restraints excluded: chain X residue 115 MET Chi-restraints excluded: chain X residue 168 ILE Chi-restraints excluded: chain X residue 177 GLN Chi-restraints excluded: chain X residue 181 LEU Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Y residue 74 CYS Chi-restraints excluded: chain Y residue 169 THR Chi-restraints excluded: chain Y residue 179 PHE Chi-restraints excluded: chain Y residue 256 THR Chi-restraints excluded: chain Y residue 266 ILE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain N residue 73 MET Chi-restraints excluded: chain W residue 206 VAL Chi-restraints excluded: chain W residue 280 SER Chi-restraints excluded: chain W residue 292 CYS Chi-restraints excluded: chain W residue 373 ASP Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 321 ARG Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 475 GLU Chi-restraints excluded: chain F residue 499 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 851 optimal weight: 7.9990 chunk 560 optimal weight: 1.9990 chunk 903 optimal weight: 10.0000 chunk 551 optimal weight: 2.9990 chunk 428 optimal weight: 8.9990 chunk 627 optimal weight: 0.8980 chunk 947 optimal weight: 4.9990 chunk 872 optimal weight: 40.0000 chunk 754 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 582 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 272 GLN U 348 HIS ** Q 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN A 449 ASN B 317 ASN B 449 ASN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 207 GLN ** Y 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 270 ASN ** W 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 72859 Z= 0.221 Angle : 0.640 15.484 98827 Z= 0.326 Chirality : 0.043 0.377 11476 Planarity : 0.004 0.061 12780 Dihedral : 4.907 141.524 10472 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.39 % Allowed : 19.65 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.60 (0.09), residues: 9526 helix: 1.87 (0.07), residues: 5498 sheet: -0.96 (0.19), residues: 764 loop : -1.91 (0.11), residues: 3264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP 0 49 HIS 0.009 0.001 HIS R 801 PHE 0.038 0.002 PHE 1 137 TYR 0.086 0.002 TYR 2 144 ARG 0.009 0.000 ARG 1 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1145 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 976 time to evaluate : 6.350 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: R 9 GLU cc_start: 0.2649 (tm-30) cc_final: 0.1752 (pm20) REVERT: R 10 MET cc_start: 0.5197 (tpp) cc_final: 0.4893 (tpp) REVERT: R 17 LEU cc_start: 0.3819 (OUTLIER) cc_final: 0.3454 (mp) REVERT: R 80 MET cc_start: 0.5507 (mpp) cc_final: 0.5182 (mmt) REVERT: R 108 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7160 (mt) REVERT: R 280 GLN cc_start: 0.6104 (mp10) cc_final: 0.5739 (mp10) REVERT: R 406 MET cc_start: 0.5803 (mmm) cc_final: 0.5553 (tpp) REVERT: R 423 MET cc_start: 0.5030 (tpp) cc_final: 0.4171 (tpp) REVERT: R 439 MET cc_start: 0.4150 (ppp) cc_final: 0.2020 (tpp) REVERT: R 479 TRP cc_start: 0.4847 (m100) cc_final: 0.4265 (m100) REVERT: R 484 MET cc_start: 0.5097 (mmm) cc_final: 0.4785 (mmt) REVERT: R 539 MET cc_start: 0.8108 (tmm) cc_final: 0.7264 (tmm) REVERT: R 588 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8304 (tp) REVERT: R 615 MET cc_start: 0.7564 (tmm) cc_final: 0.7329 (tmm) REVERT: R 801 HIS cc_start: 0.5334 (OUTLIER) cc_final: 0.5033 (m-70) REVERT: O 313 PRO cc_start: 0.7412 (Cg_endo) cc_final: 0.7069 (Cg_exo) REVERT: J 65 GLU cc_start: 0.8056 (tt0) cc_final: 0.7331 (tp30) REVERT: J 111 ARG cc_start: 0.8275 (mtm180) cc_final: 0.7982 (mtm180) REVERT: M 53 LYS cc_start: 0.8012 (pttt) cc_final: 0.7683 (mttt) REVERT: M 105 ASP cc_start: 0.6106 (t0) cc_final: 0.5607 (p0) REVERT: I 74 ASN cc_start: 0.8009 (t0) cc_final: 0.7698 (m-40) REVERT: I 92 THR cc_start: 0.9101 (OUTLIER) cc_final: 0.8639 (p) REVERT: I 172 TYR cc_start: 0.6826 (m-80) cc_final: 0.6511 (m-10) REVERT: L 75 LYS cc_start: 0.9070 (tptt) cc_final: 0.8623 (pttp) REVERT: L 85 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7760 (mt0) REVERT: L 112 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7859 (pp20) REVERT: H 63 GLN cc_start: 0.8031 (tm-30) cc_final: 0.7701 (tm-30) REVERT: H 117 ASP cc_start: 0.7824 (t0) cc_final: 0.7036 (m-30) REVERT: K 74 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7313 (tp30) REVERT: K 83 ILE cc_start: 0.8418 (tt) cc_final: 0.8035 (mt) REVERT: K 94 GLU cc_start: 0.8226 (pm20) cc_final: 0.7747 (pm20) REVERT: K 98 ASN cc_start: 0.8352 (t0) cc_final: 0.8050 (t0) REVERT: S 13 MET cc_start: 0.4225 (tmm) cc_final: 0.3879 (tmm) REVERT: S 17 TRP cc_start: 0.6481 (m-90) cc_final: 0.6146 (m100) REVERT: S 34 ARG cc_start: 0.3203 (tpt90) cc_final: 0.2897 (tpt90) REVERT: S 40 MET cc_start: 0.8294 (ptp) cc_final: 0.7644 (ppp) REVERT: T 55 ILE cc_start: 0.6531 (mt) cc_final: 0.6083 (pt) REVERT: T 64 MET cc_start: 0.4525 (mmp) cc_final: 0.4005 (mtp) REVERT: T 67 MET cc_start: 0.7193 (mtt) cc_final: 0.6623 (tpt) REVERT: U 262 ASP cc_start: 0.6138 (OUTLIER) cc_final: 0.5371 (p0) REVERT: U 453 MET cc_start: 0.2959 (mmm) cc_final: 0.2678 (mmt) REVERT: V 299 TYR cc_start: 0.0896 (OUTLIER) cc_final: 0.0021 (t80) REVERT: 0 41 LEU cc_start: 0.4493 (mm) cc_final: 0.4014 (mm) REVERT: 1 44 MET cc_start: 0.6153 (tmm) cc_final: 0.5545 (tmm) REVERT: 1 47 MET cc_start: 0.7181 (ppp) cc_final: 0.5921 (mmt) REVERT: 1 59 VAL cc_start: 0.1415 (OUTLIER) cc_final: 0.0907 (m) REVERT: 1 146 LEU cc_start: 0.7945 (tt) cc_final: 0.7358 (mm) REVERT: 2 137 PHE cc_start: 0.6131 (m-80) cc_final: 0.5342 (m-10) REVERT: 3 53 MET cc_start: 0.3178 (mmp) cc_final: 0.1750 (ptm) REVERT: 4 17 MET cc_start: 0.6128 (mtp) cc_final: 0.5457 (mmt) REVERT: 4 44 MET cc_start: 0.4735 (tmm) cc_final: 0.4280 (tmm) REVERT: 4 150 LEU cc_start: 0.6442 (OUTLIER) cc_final: 0.6166 (mt) REVERT: 6 47 MET cc_start: 0.6465 (mpp) cc_final: 0.6252 (mpp) REVERT: 7 10 TYR cc_start: 0.4899 (p90) cc_final: 0.4490 (p90) REVERT: 7 125 PRO cc_start: 0.6430 (Cg_exo) cc_final: 0.5948 (Cg_endo) REVERT: 8 81 ASN cc_start: 0.3216 (p0) cc_final: 0.2444 (m-40) REVERT: 9 126 ARG cc_start: 0.6345 (ptt-90) cc_final: 0.5852 (ttp-170) REVERT: Q 117 LEU cc_start: 0.5655 (mp) cc_final: 0.4722 (tp) REVERT: C 203 PHE cc_start: 0.6291 (t80) cc_final: 0.5815 (t80) REVERT: C 283 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8005 (tt0) REVERT: C 438 LYS cc_start: 0.7524 (tmtt) cc_final: 0.7264 (tttm) REVERT: C 586 PHE cc_start: 0.7531 (m-80) cc_final: 0.7203 (m-80) REVERT: A 81 ARG cc_start: 0.5599 (mtt180) cc_final: 0.5026 (ptp-170) REVERT: A 353 ARG cc_start: 0.7164 (mmt-90) cc_final: 0.6869 (mmp80) REVERT: A 399 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: A 443 LYS cc_start: 0.8261 (tttm) cc_final: 0.8047 (mmtm) REVERT: A 463 GLU cc_start: 0.7759 (tp30) cc_final: 0.7441 (tp30) REVERT: A 510 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7386 (tp30) REVERT: A 518 ASP cc_start: 0.8182 (t0) cc_final: 0.7968 (t0) REVERT: A 596 LYS cc_start: 0.7576 (tptp) cc_final: 0.6893 (tmtt) REVERT: A 600 ASP cc_start: 0.6936 (m-30) cc_final: 0.6631 (m-30) REVERT: B 20 TYR cc_start: 0.7980 (m-80) cc_final: 0.7770 (m-80) REVERT: B 61 MET cc_start: 0.8548 (tpp) cc_final: 0.8259 (mmm) REVERT: B 136 THR cc_start: 0.7641 (OUTLIER) cc_final: 0.7368 (t) REVERT: B 142 ARG cc_start: 0.8561 (mtm-85) cc_final: 0.8156 (mtm110) REVERT: B 203 PHE cc_start: 0.6771 (t80) cc_final: 0.6039 (t80) REVERT: B 213 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.7926 (mt0) REVERT: B 299 ASP cc_start: 0.6503 (p0) cc_final: 0.6275 (p0) REVERT: B 317 ASN cc_start: 0.7950 (t0) cc_final: 0.7668 (t0) REVERT: B 459 ARG cc_start: 0.8507 (tpp-160) cc_final: 0.8029 (mmm-85) REVERT: B 594 GLU cc_start: 0.6269 (tm-30) cc_final: 0.5888 (tm-30) REVERT: D 124 SER cc_start: 0.8700 (t) cc_final: 0.8319 (m) REVERT: D 141 ARG cc_start: 0.7663 (tpt170) cc_final: 0.7152 (mmm160) REVERT: D 214 LYS cc_start: 0.7990 (pptt) cc_final: 0.7044 (ptpp) REVERT: D 309 GLU cc_start: 0.7094 (tt0) cc_final: 0.6838 (mt-10) REVERT: D 435 MET cc_start: 0.7451 (tmm) cc_final: 0.6866 (tmm) REVERT: D 456 GLN cc_start: 0.7741 (tp40) cc_final: 0.7093 (tm-30) REVERT: E 44 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7330 (mtt90) REVERT: E 80 THR cc_start: 0.9175 (m) cc_final: 0.8730 (p) REVERT: E 141 ARG cc_start: 0.8546 (ttt180) cc_final: 0.8290 (mtp180) REVERT: E 154 MET cc_start: 0.8620 (mmm) cc_final: 0.8366 (mmt) REVERT: E 314 ARG cc_start: 0.6933 (mmm160) cc_final: 0.6630 (tpt90) REVERT: E 341 VAL cc_start: 0.8896 (OUTLIER) cc_final: 0.8662 (t) REVERT: E 403 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8099 (mtmm) REVERT: E 456 GLN cc_start: 0.7574 (tm-30) cc_final: 0.7340 (tp40) REVERT: Z 59 ASN cc_start: 0.6995 (m-40) cc_final: 0.6378 (p0) REVERT: Z 161 MET cc_start: 0.7302 (mmt) cc_final: 0.7099 (mmt) REVERT: Z 188 MET cc_start: 0.6279 (tpp) cc_final: 0.5907 (mmp) REVERT: Z 271 GLU cc_start: 0.3478 (OUTLIER) cc_final: 0.3019 (mp0) REVERT: X 115 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7638 (ttp) REVERT: X 161 MET cc_start: 0.7971 (tpt) cc_final: 0.7695 (tpt) REVERT: X 166 TYR cc_start: 0.7655 (m-10) cc_final: 0.7406 (m-80) REVERT: X 180 LYS cc_start: 0.7716 (ttpp) cc_final: 0.7107 (tppt) REVERT: X 181 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7768 (tp) REVERT: X 243 GLN cc_start: 0.7445 (mt0) cc_final: 0.7090 (mm-40) REVERT: X 251 SER cc_start: 0.7445 (t) cc_final: 0.7228 (p) REVERT: Y 103 MET cc_start: 0.4402 (ptm) cc_final: 0.4106 (ppp) REVERT: Y 172 ASN cc_start: 0.5338 (t0) cc_final: 0.5123 (t0) REVERT: G 45 ARG cc_start: 0.7833 (ttm170) cc_final: 0.7497 (mmm-85) REVERT: G 56 MET cc_start: 0.4776 (mmp) cc_final: 0.3196 (ptm) REVERT: G 58 MET cc_start: 0.4725 (tmm) cc_final: 0.4335 (ttp) REVERT: N 73 MET cc_start: 0.6867 (OUTLIER) cc_final: 0.6522 (tmm) REVERT: W 333 MET cc_start: 0.6527 (mmt) cc_final: 0.5685 (mmt) REVERT: W 378 LYS cc_start: 0.8723 (mtpp) cc_final: 0.8491 (mmtt) REVERT: F 39 TYR cc_start: 0.6318 (m-10) cc_final: 0.6068 (m-10) REVERT: F 297 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8435 (mt) REVERT: F 299 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7584 (t0) REVERT: F 321 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8081 (tpp80) REVERT: F 435 MET cc_start: 0.6546 (mmm) cc_final: 0.6008 (tpt) REVERT: F 456 GLN cc_start: 0.7466 (mm-40) cc_final: 0.6955 (mp-120) REVERT: F 475 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7327 (pm20) outliers start: 169 outliers final: 128 residues processed: 1098 average time/residue: 0.6718 time to fit residues: 1281.2745 Evaluate side-chains 1086 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 934 time to evaluate : 6.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 333 ILE Chi-restraints excluded: chain R residue 418 LEU Chi-restraints excluded: chain R residue 535 PHE Chi-restraints excluded: chain R residue 588 ILE Chi-restraints excluded: chain R residue 717 MET Chi-restraints excluded: chain R residue 751 LEU Chi-restraints excluded: chain R residue 801 HIS Chi-restraints excluded: chain J residue 66 GLN Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain M residue 27 LYS Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain U residue 262 ASP Chi-restraints excluded: chain U residue 374 VAL Chi-restraints excluded: chain U residue 383 LEU Chi-restraints excluded: chain U residue 407 VAL Chi-restraints excluded: chain U residue 426 ILE Chi-restraints excluded: chain V residue 299 TYR Chi-restraints excluded: chain V residue 335 TYR Chi-restraints excluded: chain 0 residue 49 TRP Chi-restraints excluded: chain 1 residue 59 VAL Chi-restraints excluded: chain 1 residue 129 VAL Chi-restraints excluded: chain 2 residue 57 ILE Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 148 VAL Chi-restraints excluded: chain 4 residue 136 ILE Chi-restraints excluded: chain 4 residue 150 LEU Chi-restraints excluded: chain 5 residue 70 LEU Chi-restraints excluded: chain 6 residue 57 ILE Chi-restraints excluded: chain 7 residue 57 ILE Chi-restraints excluded: chain 7 residue 126 ARG Chi-restraints excluded: chain 8 residue 39 THR Chi-restraints excluded: chain 8 residue 56 ILE Chi-restraints excluded: chain 8 residue 60 VAL Chi-restraints excluded: chain 8 residue 104 LEU Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 56 ILE Chi-restraints excluded: chain 9 residue 93 LEU Chi-restraints excluded: chain 9 residue 108 PHE Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 150 LEU Chi-restraints excluded: chain Q residue 197 CYS Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 358 ASN Chi-restraints excluded: chain E residue 403 LYS Chi-restraints excluded: chain Z residue 74 CYS Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain Z residue 146 THR Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 221 ASP Chi-restraints excluded: chain Z residue 271 GLU Chi-restraints excluded: chain X residue 10 MET Chi-restraints excluded: chain X residue 115 MET Chi-restraints excluded: chain X residue 168 ILE Chi-restraints excluded: chain X residue 177 GLN Chi-restraints excluded: chain X residue 181 LEU Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Y residue 169 THR Chi-restraints excluded: chain Y residue 179 PHE Chi-restraints excluded: chain Y residue 256 THR Chi-restraints excluded: chain Y residue 266 ILE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain N residue 15 ASP Chi-restraints excluded: chain N residue 73 MET Chi-restraints excluded: chain W residue 206 VAL Chi-restraints excluded: chain W residue 245 ILE Chi-restraints excluded: chain W residue 280 SER Chi-restraints excluded: chain W residue 292 CYS Chi-restraints excluded: chain W residue 295 VAL Chi-restraints excluded: chain W residue 373 ASP Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 321 ARG Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 475 GLU Chi-restraints excluded: chain F residue 499 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 462 optimal weight: 0.0980 chunk 599 optimal weight: 0.9990 chunk 803 optimal weight: 0.9980 chunk 231 optimal weight: 40.0000 chunk 695 optimal weight: 0.0980 chunk 111 optimal weight: 30.0000 chunk 209 optimal weight: 8.9990 chunk 755 optimal weight: 6.9990 chunk 316 optimal weight: 7.9990 chunk 775 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 30 ASN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 348 HIS ** V 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.189197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.167398 restraints weight = 117958.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.164240 restraints weight = 189243.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.161502 restraints weight = 171572.206| |-----------------------------------------------------------------------------| r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 72859 Z= 0.231 Angle : 0.694 59.199 98827 Z= 0.365 Chirality : 0.043 0.378 11476 Planarity : 0.004 0.059 12780 Dihedral : 4.905 141.472 10472 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.35 % Allowed : 20.01 % Favored : 77.64 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.61 (0.09), residues: 9526 helix: 1.87 (0.07), residues: 5498 sheet: -0.96 (0.19), residues: 764 loop : -1.91 (0.11), residues: 3264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP 0 49 HIS 0.020 0.001 HIS T 75 PHE 0.036 0.001 PHE 1 137 TYR 0.063 0.002 TYR 2 144 ARG 0.007 0.000 ARG 1 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19833.32 seconds wall clock time: 342 minutes 16.37 seconds (20536.37 seconds total)