Starting phenix.real_space_refine on Fri Mar 22 08:36:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hlq_0239/03_2024/6hlq_0239_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hlq_0239/03_2024/6hlq_0239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hlq_0239/03_2024/6hlq_0239.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hlq_0239/03_2024/6hlq_0239.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hlq_0239/03_2024/6hlq_0239_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hlq_0239/03_2024/6hlq_0239_updated.pdb" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 7 6.06 5 P 76 5.49 5 Mg 1 5.21 5 S 168 5.16 5 C 20445 2.51 5 N 5704 2.21 5 O 6330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 99": "NH1" <-> "NH2" Residue "A ARG 201": "NH1" <-> "NH2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A ARG 397": "NH1" <-> "NH2" Residue "A ARG 468": "NH1" <-> "NH2" Residue "A ARG 481": "NH1" <-> "NH2" Residue "A TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 591": "NH1" <-> "NH2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A ARG 701": "NH1" <-> "NH2" Residue "A ARG 834": "NH1" <-> "NH2" Residue "A ARG 878": "NH1" <-> "NH2" Residue "A ARG 884": "NH1" <-> "NH2" Residue "A ARG 985": "NH1" <-> "NH2" Residue "A ARG 1003": "NH1" <-> "NH2" Residue "A ARG 1015": "NH1" <-> "NH2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A PHE 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1176": "NH1" <-> "NH2" Residue "A TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1494": "NH1" <-> "NH2" Residue "A ARG 1559": "NH1" <-> "NH2" Residue "A ARG 1580": "NH1" <-> "NH2" Residue "A ARG 1640": "NH1" <-> "NH2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B ARG 204": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ARG 316": "NH1" <-> "NH2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B ARG 379": "NH1" <-> "NH2" Residue "B ARG 429": "NH1" <-> "NH2" Residue "B ARG 448": "NH1" <-> "NH2" Residue "B ARG 452": "NH1" <-> "NH2" Residue "B ARG 501": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B ARG 609": "NH1" <-> "NH2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B ARG 648": "NH1" <-> "NH2" Residue "B ARG 651": "NH1" <-> "NH2" Residue "B ARG 714": "NH1" <-> "NH2" Residue "B ARG 736": "NH1" <-> "NH2" Residue "B PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B ARG 908": "NH1" <-> "NH2" Residue "B ARG 909": "NH1" <-> "NH2" Residue "B ARG 920": "NH1" <-> "NH2" Residue "B ARG 1023": "NH1" <-> "NH2" Residue "B ARG 1063": "NH1" <-> "NH2" Residue "B ARG 1065": "NH1" <-> "NH2" Residue "B ARG 1070": "NH1" <-> "NH2" Residue "B ARG 1129": "NH1" <-> "NH2" Residue "B ARG 1130": "NH1" <-> "NH2" Residue "B ARG 1134": "NH1" <-> "NH2" Residue "B PHE 1167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 295": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 167": "NH1" <-> "NH2" Residue "F ARG 119": "NH1" <-> "NH2" Residue "F PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "I ARG 61": "NH1" <-> "NH2" Residue "K ARG 77": "NH1" <-> "NH2" Residue "L ARG 54": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32731 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 11498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1456, 11498 Classifications: {'peptide': 1456} Link IDs: {'PCIS': 5, 'PTRANS': 54, 'TRANS': 1396} Chain breaks: 8 Chain: "B" Number of atoms: 9279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1167, 9279 Classifications: {'peptide': 1167} Link IDs: {'PTRANS': 59, 'TRANS': 1107} Chain breaks: 3 Chain: "C" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2415 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 19, 'TRANS': 284} Chain: "D" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 452 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 3, 'TRANS': 53} Chain breaks: 1 Chain: "E" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1747 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "G" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1386 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 10, 'TRANS': 165} Chain breaks: 1 Chain: "H" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1052 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain breaks: 1 Chain: "I" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 844 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain breaks: 1 Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 766 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "L" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 352 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'TRANS': 43} Chain: "R" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 195 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna3p': 8} Chain: "S" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 581 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain breaks: 1 Chain: "T" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 732 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 461 SG CYS A 62 67.782 53.472 56.339 1.00 19.73 S ATOM 480 SG CYS A 65 71.584 52.050 55.947 1.00 17.69 S ATOM 535 SG CYS A 72 70.598 53.987 59.156 1.00 18.35 S ATOM 781 SG CYS A 102 68.410 103.667 45.223 1.00 38.28 S ATOM 806 SG CYS A 105 70.997 103.152 42.657 1.00 39.53 S ATOM 1597 SG CYS A 233 71.812 105.479 45.386 1.00 37.90 S ATOM 1619 SG CYS A 236 69.337 106.296 41.729 1.00 47.04 S ATOM 20107 SG CYS B1104 82.015 62.651 48.576 1.00 12.25 S ATOM 20133 SG CYS B1107 79.991 65.648 48.376 1.00 13.03 S ATOM 20280 SG CYS B1128 78.435 62.337 48.323 1.00 21.65 S ATOM 28715 SG CYS I 10 40.952 128.595 106.167 1.00 34.82 S ATOM 28737 SG CYS I 13 40.079 124.619 105.120 1.00 38.95 S ATOM 28857 SG CYS I 30 41.307 126.792 102.096 1.00 43.34 S ATOM 29187 SG CYS I 86 74.938 90.571 154.102 1.00 63.72 S ATOM 29407 SG CYS I 114 76.925 88.424 150.907 1.00 62.33 S ATOM 29550 SG CYS J 7 88.296 42.953 126.708 1.00 6.20 S ATOM 29573 SG CYS J 10 91.755 42.305 127.284 1.00 7.07 S ATOM 29853 SG CYS J 45 91.756 46.367 128.002 1.00 8.28 S ATOM 29859 SG CYS J 46 89.793 43.567 130.009 1.00 7.04 S ATOM 30874 SG CYS L 31 47.141 42.103 110.843 1.00 22.91 S ATOM 30894 SG CYS L 34 45.457 40.469 113.658 1.00 26.64 S ATOM 30998 SG CYS L 48 44.414 39.161 110.412 1.00 35.97 S ATOM 31021 SG CYS L 51 43.370 43.262 112.414 1.00 40.02 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="ZN ZN I3002 " occ=0.75 Time building chain proxies: 15.44, per 1000 atoms: 0.47 Number of scatterers: 32731 At special positions: 0 Unit cell: (167.44, 163.28, 169.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 S 168 16.00 P 76 15.00 Mg 1 11.99 O 6330 8.00 N 5704 7.00 C 20445 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.52 Conformation dependent library (CDL) restraints added in 5.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 72 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 62 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 65 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 233 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 236 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 105 " pdb=" ZN B3001 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1107 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1104 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1128 " pdb=" ZN I3001 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 10 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 13 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 30 " pdb=" ZN I3002 " pdb="ZN ZN I3002 " - pdb=" SG CYS I 86 " pdb="ZN ZN I3002 " - pdb=" SG CYS I 114 " pdb=" ZN J3001 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 45 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 46 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 10 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 7 " pdb=" ZN L3001 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 34 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 31 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 51 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 48 " Number of angles added : 21 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7374 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 137 helices and 35 sheets defined 29.9% alpha, 12.0% beta 16 base pairs and 51 stacking pairs defined. Time for finding SS restraints: 14.89 Creating SS restraints... Processing helix chain 'A' and resid 23 through 26 No H-bonds generated for 'chain 'A' and resid 23 through 26' Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 91 through 98 removed outlier: 3.897A pdb=" N ILE A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.503A pdb=" N TYR A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 124 " --> pdb=" O CYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 177 through 198 removed outlier: 3.637A pdb=" N ALA A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 227 removed outlier: 3.535A pdb=" N GLU A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 265 No H-bonds generated for 'chain 'A' and resid 263 through 265' Processing helix chain 'A' and resid 317 through 330 removed outlier: 3.841A pdb=" N THR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 338 removed outlier: 3.538A pdb=" N GLN A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 332 through 338' Processing helix chain 'A' and resid 352 through 354 No H-bonds generated for 'chain 'A' and resid 352 through 354' Processing helix chain 'A' and resid 365 through 368 removed outlier: 3.530A pdb=" N ARG A 368 " --> pdb=" O THR A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 368' Processing helix chain 'A' and resid 381 through 405 removed outlier: 3.703A pdb=" N LYS A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ASP A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 438 removed outlier: 3.894A pdb=" N VAL A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A 422 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 438 " --> pdb=" O VAL A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 442 No H-bonds generated for 'chain 'A' and resid 440 through 442' Processing helix chain 'A' and resid 499 through 504 removed outlier: 3.901A pdb=" N LYS A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 525 removed outlier: 3.550A pdb=" N VAL A 523 " --> pdb=" O LEU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 559 removed outlier: 3.734A pdb=" N ALA A 556 " --> pdb=" O GLU A 552 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN A 559 " --> pdb=" O LYS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 599 No H-bonds generated for 'chain 'A' and resid 597 through 599' Processing helix chain 'A' and resid 641 through 644 No H-bonds generated for 'chain 'A' and resid 641 through 644' Processing helix chain 'A' and resid 672 through 680 removed outlier: 3.615A pdb=" N VAL A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TRP A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 697 removed outlier: 3.700A pdb=" N ILE A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 697 " --> pdb=" O GLN A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 704 No H-bonds generated for 'chain 'A' and resid 702 through 704' Processing helix chain 'A' and resid 728 through 739 removed outlier: 3.579A pdb=" N ILE A 732 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 734 " --> pdb=" O GLN A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 800 removed outlier: 3.513A pdb=" N GLU A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 821 removed outlier: 3.665A pdb=" N SER A 811 " --> pdb=" O ALA A 807 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 818 " --> pdb=" O GLY A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 833 No H-bonds generated for 'chain 'A' and resid 831 through 833' Processing helix chain 'A' and resid 837 through 850 removed outlier: 4.242A pdb=" N THR A 849 " --> pdb=" O ASP A 845 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER A 850 " --> pdb=" O ILE A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 861 Processing helix chain 'A' and resid 873 through 883 Processing helix chain 'A' and resid 888 through 892 Processing helix chain 'A' and resid 896 through 911 removed outlier: 3.767A pdb=" N ALA A 902 " --> pdb=" O SER A 898 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A 906 " --> pdb=" O ALA A 902 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 907 " --> pdb=" O ILE A 903 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 909 " --> pdb=" O SER A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 930 removed outlier: 3.592A pdb=" N ALA A 929 " --> pdb=" O MET A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 944 Processing helix chain 'A' and resid 977 through 979 No H-bonds generated for 'chain 'A' and resid 977 through 979' Processing helix chain 'A' and resid 992 through 1011 removed outlier: 3.615A pdb=" N ALA A1010 " --> pdb=" O LEU A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 removed outlier: 3.734A pdb=" N LEU A1019 " --> pdb=" O ARG A1015 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A1020 " --> pdb=" O SER A1016 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG A1021 " --> pdb=" O GLY A1017 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN A1026 " --> pdb=" O CYS A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1052 No H-bonds generated for 'chain 'A' and resid 1050 through 1052' Processing helix chain 'A' and resid 1057 through 1059 No H-bonds generated for 'chain 'A' and resid 1057 through 1059' Processing helix chain 'A' and resid 1066 through 1071 removed outlier: 3.628A pdb=" N ASP A1071 " --> pdb=" O GLU A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1080 removed outlier: 3.996A pdb=" N LYS A1078 " --> pdb=" O TYR A1074 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS A1079 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1107 removed outlier: 4.315A pdb=" N LEU A1095 " --> pdb=" O VAL A1091 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS A1096 " --> pdb=" O GLU A1092 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A1097 " --> pdb=" O SER A1093 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR A1104 " --> pdb=" O LYS A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1126 No H-bonds generated for 'chain 'A' and resid 1123 through 1126' Processing helix chain 'A' and resid 1138 through 1150 removed outlier: 3.525A pdb=" N SER A1146 " --> pdb=" O ASP A1142 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP A1149 " --> pdb=" O GLU A1145 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS A1150 " --> pdb=" O SER A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1176 removed outlier: 3.605A pdb=" N ARG A1167 " --> pdb=" O GLU A1163 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A1169 " --> pdb=" O LYS A1165 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN A1171 " --> pdb=" O ARG A1167 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A1172 " --> pdb=" O ALA A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1194 removed outlier: 3.825A pdb=" N VAL A1193 " --> pdb=" O ALA A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1225 removed outlier: 3.595A pdb=" N LEU A1222 " --> pdb=" O ILE A1219 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A1223 " --> pdb=" O PRO A1220 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A1225 " --> pdb=" O LEU A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1252 Processing helix chain 'A' and resid 1264 through 1266 No H-bonds generated for 'chain 'A' and resid 1264 through 1266' Processing helix chain 'A' and resid 1299 through 1305 removed outlier: 4.254A pdb=" N GLU A1304 " --> pdb=" O ASN A1300 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU A1305 " --> pdb=" O GLU A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1310 through 1319 removed outlier: 3.550A pdb=" N ILE A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1321 through 1335 removed outlier: 3.825A pdb=" N ALA A1327 " --> pdb=" O HIS A1323 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A1332 " --> pdb=" O ALA A1328 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1453 Processing helix chain 'A' and resid 1487 through 1493 removed outlier: 3.520A pdb=" N GLU A1491 " --> pdb=" O ASN A1487 " (cutoff:3.500A) Processing helix chain 'A' and resid 1513 through 1515 No H-bonds generated for 'chain 'A' and resid 1513 through 1515' Processing helix chain 'A' and resid 1538 through 1540 No H-bonds generated for 'chain 'A' and resid 1538 through 1540' Processing helix chain 'A' and resid 1546 through 1552 removed outlier: 3.519A pdb=" N LEU A1550 " --> pdb=" O VAL A1546 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A1551 " --> pdb=" O ALA A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1567 removed outlier: 3.537A pdb=" N ASN A1564 " --> pdb=" O ASN A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1581 through 1589 Processing helix chain 'A' and resid 1609 through 1615 Processing helix chain 'A' and resid 1618 through 1627 removed outlier: 4.171A pdb=" N THR A1623 " --> pdb=" O CYS A1619 " (cutoff:3.500A) Processing helix chain 'A' and resid 1639 through 1642 No H-bonds generated for 'chain 'A' and resid 1639 through 1642' Processing helix chain 'A' and resid 1650 through 1652 No H-bonds generated for 'chain 'A' and resid 1650 through 1652' Processing helix chain 'B' and resid 21 through 26 removed outlier: 3.500A pdb=" N ILE B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 39 No H-bonds generated for 'chain 'B' and resid 36 through 39' Processing helix chain 'B' and resid 43 through 49 removed outlier: 4.073A pdb=" N SER B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 60 through 68 Processing helix chain 'B' and resid 123 through 128 Processing helix chain 'B' and resid 177 through 182 removed outlier: 3.639A pdb=" N VAL B 181 " --> pdb=" O PRO B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 225 removed outlier: 3.625A pdb=" N ARG B 225 " --> pdb=" O PHE B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 280 Processing helix chain 'B' and resid 286 through 292 removed outlier: 3.756A pdb=" N ILE B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 316 removed outlier: 3.553A pdb=" N ASP B 304 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 309 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 314 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 333 removed outlier: 3.958A pdb=" N GLN B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 356 removed outlier: 3.509A pdb=" N GLN B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 385 removed outlier: 3.620A pdb=" N ARG B 379 " --> pdb=" O LEU B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 399 No H-bonds generated for 'chain 'B' and resid 397 through 399' Processing helix chain 'B' and resid 406 through 432 removed outlier: 3.552A pdb=" N GLU B 415 " --> pdb=" O MET B 411 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL B 428 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET B 430 " --> pdb=" O ALA B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 450 Processing helix chain 'B' and resid 458 through 467 Processing helix chain 'B' and resid 494 through 500 removed outlier: 3.566A pdb=" N SER B 498 " --> pdb=" O TYR B 494 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS B 499 " --> pdb=" O ARG B 495 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 494 through 500' Processing helix chain 'B' and resid 522 through 524 No H-bonds generated for 'chain 'B' and resid 522 through 524' Processing helix chain 'B' and resid 536 through 538 No H-bonds generated for 'chain 'B' and resid 536 through 538' Processing helix chain 'B' and resid 561 through 565 Processing helix chain 'B' and resid 573 through 575 No H-bonds generated for 'chain 'B' and resid 573 through 575' Processing helix chain 'B' and resid 598 through 613 removed outlier: 3.618A pdb=" N ALA B 605 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 607 " --> pdb=" O ILE B 603 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU B 608 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 671 removed outlier: 3.677A pdb=" N VAL B 670 " --> pdb=" O PRO B 666 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N TYR B 671 " --> pdb=" O PHE B 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 666 through 671' Processing helix chain 'B' and resid 693 through 695 No H-bonds generated for 'chain 'B' and resid 693 through 695' Processing helix chain 'B' and resid 699 through 703 removed outlier: 3.647A pdb=" N LEU B 703 " --> pdb=" O ILE B 699 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 699 through 703' Processing helix chain 'B' and resid 707 through 709 No H-bonds generated for 'chain 'B' and resid 707 through 709' Processing helix chain 'B' and resid 712 through 721 removed outlier: 3.569A pdb=" N GLN B 718 " --> pdb=" O ARG B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 764 No H-bonds generated for 'chain 'B' and resid 762 through 764' Processing helix chain 'B' and resid 791 through 794 No H-bonds generated for 'chain 'B' and resid 791 through 794' Processing helix chain 'B' and resid 834 through 837 removed outlier: 3.782A pdb=" N LEU B 837 " --> pdb=" O LYS B 834 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 834 through 837' Processing helix chain 'B' and resid 933 through 935 No H-bonds generated for 'chain 'B' and resid 933 through 935' Processing helix chain 'B' and resid 951 through 953 No H-bonds generated for 'chain 'B' and resid 951 through 953' Processing helix chain 'B' and resid 960 through 975 removed outlier: 3.709A pdb=" N HIS B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 1003 removed outlier: 3.552A pdb=" N GLU B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B1003 " --> pdb=" O GLN B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1073 through 1081 removed outlier: 4.162A pdb=" N ALA B1078 " --> pdb=" O MET B1074 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1092 removed outlier: 3.504A pdb=" N GLN B1089 " --> pdb=" O SER B1085 " (cutoff:3.500A) Processing helix chain 'B' and resid 1094 through 1097 No H-bonds generated for 'chain 'B' and resid 1094 through 1097' Processing helix chain 'B' and resid 1180 through 1191 Processing helix chain 'C' and resid 33 through 39 Processing helix chain 'C' and resid 61 through 73 removed outlier: 3.845A pdb=" N ILE C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 103 Processing helix chain 'C' and resid 153 through 156 No H-bonds generated for 'chain 'C' and resid 153 through 156' Processing helix chain 'C' and resid 164 through 166 No H-bonds generated for 'chain 'C' and resid 164 through 166' Processing helix chain 'C' and resid 173 through 178 removed outlier: 3.875A pdb=" N SER C 176 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C 177 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR C 178 " --> pdb=" O GLN C 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 173 through 178' Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 241 through 247 removed outlier: 3.708A pdb=" N ALA C 244 " --> pdb=" O GLY C 241 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG C 245 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE C 247 " --> pdb=" O ALA C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 281 No H-bonds generated for 'chain 'C' and resid 279 through 281' Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 310 through 330 removed outlier: 3.520A pdb=" N ARG C 319 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN C 330 " --> pdb=" O GLU C 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 48 removed outlier: 3.690A pdb=" N ILE D 44 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP D 45 " --> pdb=" O GLU D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 93 removed outlier: 4.217A pdb=" N ARG D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 25 removed outlier: 3.590A pdb=" N SER E 10 " --> pdb=" O GLU E 6 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG E 14 " --> pdb=" O SER E 10 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET E 22 " --> pdb=" O THR E 18 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP E 25 " --> pdb=" O GLU E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 35 No H-bonds generated for 'chain 'E' and resid 32 through 35' Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 66 through 71 removed outlier: 3.567A pdb=" N LYS E 71 " --> pdb=" O GLU E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 102 removed outlier: 3.521A pdb=" N ILE E 100 " --> pdb=" O PHE E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 158 through 167 Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'F' and resid 57 through 70 removed outlier: 3.795A pdb=" N LEU F 69 " --> pdb=" O ARG F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 102 removed outlier: 3.565A pdb=" N ALA F 91 " --> pdb=" O LYS F 87 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 126 removed outlier: 3.548A pdb=" N ALA F 121 " --> pdb=" O PRO F 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 53 No H-bonds generated for 'chain 'G' and resid 51 through 53' Processing helix chain 'G' and resid 57 through 64 Processing helix chain 'H' and resid 89 through 92 removed outlier: 3.935A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 89 through 92' Processing helix chain 'I' and resid 61 through 66 removed outlier: 3.688A pdb=" N SER I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL I 66 " --> pdb=" O ALA I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 66' Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 32 through 38 Processing helix chain 'J' and resid 44 through 50 removed outlier: 3.972A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 4.163A pdb=" N LEU J 61 " --> pdb=" O GLU J 58 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG J 62 " --> pdb=" O LYS J 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 82 removed outlier: 3.879A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 139 removed outlier: 3.540A pdb=" N LYS K 134 " --> pdb=" O VAL K 130 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE K 135 " --> pdb=" O VAL K 131 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 371 through 373 removed outlier: 3.619A pdb=" N SER A 371 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS A 378 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 479 through 483 removed outlier: 3.736A pdb=" N SER A 482 " --> pdb=" O MET A 633 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 484 through 486 removed outlier: 6.013A pdb=" N LEU A 614 " --> pdb=" O SER A 485 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 506 through 510 removed outlier: 3.926A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N HIS A 580 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ALA A 533 " --> pdb=" O HIS A 580 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 748 through 752 Processing sheet with id= F, first strand: chain 'A' and resid 1238 through 1241 removed outlier: 3.909A pdb=" N MET A1238 " --> pdb=" O THR A1521 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1469 through 1473 Processing sheet with id= H, first strand: chain 'B' and resid 134 through 136 Processing sheet with id= I, first strand: chain 'B' and resid 150 through 157 removed outlier: 4.094A pdb=" N GLU B 150 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU B 154 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN B 101 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LYS B 142 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N VAL B 99 " --> pdb=" O LYS B 142 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 194 through 196 Processing sheet with id= K, first strand: chain 'B' and resid 206 through 209 Processing sheet with id= L, first strand: chain 'B' and resid 233 through 239 removed outlier: 3.806A pdb=" N ILE B 236 " --> pdb=" O ASN B 248 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 625 through 629 removed outlier: 6.457A pdb=" N ILE B 588 " --> pdb=" O ILE B 592 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 651 through 655 removed outlier: 3.631A pdb=" N LYS B 660 " --> pdb=" O TYR B 655 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 740 through 744 removed outlier: 3.518A pdb=" N GLY B 801 " --> pdb=" O ARG B 909 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR B 900 " --> pdb=" O ILE B 888 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU B 884 " --> pdb=" O LYS B 904 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG B 906 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE B 882 " --> pdb=" O ARG B 906 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 769 through 772 Processing sheet with id= Q, first strand: chain 'B' and resid 773 through 775 removed outlier: 6.693A pdb=" N ILE B 947 " --> pdb=" O ALA B 774 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE B 788 " --> pdb=" O ILE B 948 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 823 through 825 removed outlier: 6.985A pdb=" N LYS B 872 " --> pdb=" O ILE B 858 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ALA B 860 " --> pdb=" O LYS B 870 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LYS B 870 " --> pdb=" O ALA B 860 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N PHE B 862 " --> pdb=" O LYS B 868 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LYS B 868 " --> pdb=" O PHE B 862 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 916 through 918 Processing sheet with id= T, first strand: chain 'B' and resid 1098 through 1104 Processing sheet with id= U, first strand: chain 'B' and resid 1158 through 1160 Processing sheet with id= V, first strand: chain 'C' and resid 51 through 56 removed outlier: 3.948A pdb=" N SER C 226 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR C 224 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 132 through 139 removed outlier: 6.540A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 231 through 235 Processing sheet with id= Y, first strand: chain 'C' and resid 256 through 258 Processing sheet with id= Z, first strand: chain 'E' and resid 60 through 62 removed outlier: 7.022A pdb=" N THR E 107 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N GLU E 81 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE E 109 " --> pdb=" O GLU E 81 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.812A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET E 215 " --> pdb=" O ILE E 178 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 133 through 137 Processing sheet with id= AC, first strand: chain 'G' and resid 38 through 49 removed outlier: 6.195A pdb=" N TRP G 125 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL G 81 " --> pdb=" O TRP G 125 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 153 through 157 removed outlier: 5.637A pdb=" N LEU G 148 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ILE G 137 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 232 through 237 removed outlier: 6.857A pdb=" N ASP G 246 " --> pdb=" O ARG G 234 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL G 236 " --> pdb=" O SER G 244 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N SER G 244 " --> pdb=" O VAL G 236 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 23 through 29 removed outlier: 5.369A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR H 56 " --> pdb=" O ARG H 145 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'I' and resid 95 through 99 Processing sheet with id= AH, first strand: chain 'K' and resid 47 through 50 removed outlier: 4.483A pdb=" N SER K 62 " --> pdb=" O LEU K 50 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'L' and resid 29 through 31 783 hydrogen bonds defined for protein. 2253 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 41 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 51 stacking parallelities Total time for adding SS restraints: 15.55 Time building geometry restraints manager: 12.69 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: 9551 1.33 - 1.45: 5995 1.45 - 1.58: 17554 1.58 - 1.70: 147 1.70 - 1.82: 266 Bond restraints: 33513 Sorted by residual: bond pdb=" O3B G2P T3000 " pdb=" PG G2P T3000 " ideal model delta sigma weight residual 1.716 1.611 0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" O2A G2P T3000 " pdb=" PA G2P T3000 " ideal model delta sigma weight residual 1.513 1.611 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" O2B G2P T3000 " pdb=" PB G2P T3000 " ideal model delta sigma weight residual 1.517 1.609 -0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" C4 G2P T3000 " pdb=" C5 G2P T3000 " ideal model delta sigma weight residual 1.384 1.470 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" CA PRO A 716 " pdb=" C PRO A 716 " ideal model delta sigma weight residual 1.517 1.540 -0.023 6.70e-03 2.23e+04 1.16e+01 ... (remaining 33508 not shown) Histogram of bond angle deviations from ideal: 97.60 - 105.22: 968 105.22 - 112.84: 17488 112.84 - 120.46: 14362 120.46 - 128.08: 12471 128.08 - 135.70: 321 Bond angle restraints: 45610 Sorted by residual: angle pdb=" N ILE A1641 " pdb=" CA ILE A1641 " pdb=" C ILE A1641 " ideal model delta sigma weight residual 112.96 107.65 5.31 1.00e+00 1.00e+00 2.82e+01 angle pdb=" C LYS E 103 " pdb=" N ASN E 104 " pdb=" CA ASN E 104 " ideal model delta sigma weight residual 121.54 131.02 -9.48 1.91e+00 2.74e-01 2.46e+01 angle pdb=" C ARG L 42 " pdb=" N THR L 43 " pdb=" CA THR L 43 " ideal model delta sigma weight residual 121.54 129.78 -8.24 1.91e+00 2.74e-01 1.86e+01 angle pdb=" N PHE B 954 " pdb=" CA PHE B 954 " pdb=" C PHE B 954 " ideal model delta sigma weight residual 109.81 119.31 -9.50 2.21e+00 2.05e-01 1.85e+01 angle pdb=" C GLY K 109 " pdb=" N GLU K 110 " pdb=" CA GLU K 110 " ideal model delta sigma weight residual 121.54 129.11 -7.57 1.91e+00 2.74e-01 1.57e+01 ... (remaining 45605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 18968 17.55 - 35.09: 898 35.09 - 52.64: 308 52.64 - 70.18: 70 70.18 - 87.73: 18 Dihedral angle restraints: 20262 sinusoidal: 8845 harmonic: 11417 Sorted by residual: dihedral pdb=" CA ASN A 863 " pdb=" C ASN A 863 " pdb=" N LEU A 864 " pdb=" CA LEU A 864 " ideal model delta harmonic sigma weight residual 180.00 150.61 29.39 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ASP B 794 " pdb=" C ASP B 794 " pdb=" N GLU B 795 " pdb=" CA GLU B 795 " ideal model delta harmonic sigma weight residual 180.00 152.74 27.26 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA LEU A 781 " pdb=" C LEU A 781 " pdb=" N ASP A 782 " pdb=" CA ASP A 782 " ideal model delta harmonic sigma weight residual -180.00 -152.86 -27.14 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 20259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 4113 0.066 - 0.133: 835 0.133 - 0.199: 122 0.199 - 0.266: 22 0.266 - 0.332: 5 Chirality restraints: 5097 Sorted by residual: chirality pdb=" CB ILE A1219 " pdb=" CA ILE A1219 " pdb=" CG1 ILE A1219 " pdb=" CG2 ILE A1219 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CB ILE B 207 " pdb=" CA ILE B 207 " pdb=" CG1 ILE B 207 " pdb=" CG2 ILE B 207 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CB ILE A 581 " pdb=" CA ILE A 581 " pdb=" CG1 ILE A 581 " pdb=" CG2 ILE A 581 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 5094 not shown) Planarity restraints: 5637 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 150 " 0.055 5.00e-02 4.00e+02 8.36e-02 1.12e+01 pdb=" N PRO E 151 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO E 151 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO E 151 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1033 " 0.025 2.00e-02 2.50e+03 2.25e-02 1.01e+01 pdb=" CG TYR B1033 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR B1033 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR B1033 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B1033 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B1033 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR B1033 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B1033 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 836 " 0.023 2.00e-02 2.50e+03 1.69e-02 7.13e+00 pdb=" CG TRP B 836 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP B 836 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 836 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 836 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 836 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 836 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 836 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 836 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 836 " 0.007 2.00e-02 2.50e+03 ... (remaining 5634 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 37 2.37 - 3.01: 15308 3.01 - 3.64: 48351 3.64 - 4.27: 78426 4.27 - 4.90: 127734 Nonbonded interactions: 269856 Sorted by model distance: nonbonded pdb=" O3' C R 20 " pdb="MG MG R 101 " model vdw 1.742 2.170 nonbonded pdb=" OD1 ASP A 629 " pdb="MG MG R 101 " model vdw 1.824 2.170 nonbonded pdb=" OD1 ASP A 627 " pdb="MG MG R 101 " model vdw 1.981 2.170 nonbonded pdb=" OG1 THR A 621 " pdb=" O ALA A 626 " model vdw 2.229 2.440 nonbonded pdb=" O VAL A 483 " pdb=" OG1 THR A 613 " model vdw 2.248 2.440 ... (remaining 269851 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 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: 0.020 Extract box with map and model: 5.750 Check model and map are aligned: 0.450 Set scattering table: 0.250 Process input model: 93.740 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 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 0.105 33513 Z= 0.357 Angle : 0.896 11.968 45610 Z= 0.472 Chirality : 0.056 0.332 5097 Planarity : 0.007 0.084 5637 Dihedral : 12.531 87.728 12888 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.09 % Allowed : 3.69 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.49 (0.10), residues: 3870 helix: -4.36 (0.06), residues: 1260 sheet: -2.36 (0.19), residues: 577 loop : -2.15 (0.12), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP B 836 HIS 0.014 0.002 HIS C 297 PHE 0.030 0.003 PHE B 545 TYR 0.055 0.003 TYR B1033 ARG 0.015 0.001 ARG B 920 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1023 residues out of total 3473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1020 time to evaluate : 3.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.8120 (tp) cc_final: 0.7842 (tp) REVERT: A 179 ASN cc_start: 0.8031 (t0) cc_final: 0.7250 (m-40) REVERT: A 399 LEU cc_start: 0.8550 (mm) cc_final: 0.8242 (mm) REVERT: A 769 VAL cc_start: 0.9321 (m) cc_final: 0.9087 (t) REVERT: A 924 SER cc_start: 0.9143 (t) cc_final: 0.8923 (m) REVERT: A 937 ASN cc_start: 0.7462 (t0) cc_final: 0.7235 (m-40) REVERT: A 938 VAL cc_start: 0.9252 (p) cc_final: 0.8919 (t) REVERT: A 1120 TYR cc_start: 0.6880 (m-80) cc_final: 0.6407 (m-80) REVERT: A 1170 MET cc_start: 0.8824 (mmp) cc_final: 0.8482 (mmm) REVERT: A 1292 ILE cc_start: 0.8872 (mm) cc_final: 0.8551 (mt) REVERT: A 1466 SER cc_start: 0.7085 (m) cc_final: 0.6696 (m) REVERT: B 550 ARG cc_start: 0.7722 (ptp90) cc_final: 0.7358 (mmt-90) REVERT: B 763 ASP cc_start: 0.7920 (m-30) cc_final: 0.7700 (m-30) REVERT: C 183 PRO cc_start: 0.8776 (Cg_endo) cc_final: 0.8439 (Cg_exo) REVERT: E 14 ARG cc_start: 0.7805 (mtp180) cc_final: 0.7520 (mtm-85) REVERT: G 72 LYS cc_start: 0.8482 (mptt) cc_final: 0.8169 (mptt) REVERT: K 138 LYS cc_start: 0.8652 (mmtt) cc_final: 0.8318 (mmmt) REVERT: L 64 LEU cc_start: 0.8839 (tp) cc_final: 0.8546 (tp) outliers start: 3 outliers final: 2 residues processed: 1022 average time/residue: 0.4866 time to fit residues: 766.0469 Evaluate side-chains 590 residues out of total 3473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 588 time to evaluate : 3.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 10.0000 chunk 297 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 200 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 chunk 307 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 186 optimal weight: 0.8980 chunk 228 optimal weight: 0.9980 chunk 355 optimal weight: 9.9990 overall best weight: 4.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN A 384 GLN A 634 ASN A 656 GLN A 673 HIS A 863 ASN A 880 GLN A 923 ASN A1237 GLN A1244 ASN A1629 ASN A1648 ASN B 171 HIS B 182 GLN B 224 ASN B 600 GLN B 724 GLN B 745 GLN B1010 ASN B1094 ASN C 32 ASN C 65 ASN C 137 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN C 248 GLN D 17 ASN D 26 GLN D 29 GLN E 101 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN F 78 GLN G 59 GLN G 64 GLN G 140 GLN G 161 ASN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 33513 Z= 0.477 Angle : 0.743 8.692 45610 Z= 0.387 Chirality : 0.050 0.213 5097 Planarity : 0.006 0.068 5637 Dihedral : 13.692 89.215 5140 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.06 % Allowed : 10.25 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.11), residues: 3870 helix: -2.77 (0.11), residues: 1288 sheet: -1.98 (0.19), residues: 594 loop : -1.69 (0.12), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 836 HIS 0.010 0.002 HIS B1082 PHE 0.031 0.003 PHE A 637 TYR 0.040 0.003 TYR B1033 ARG 0.008 0.001 ARG A 884 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 3473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 614 time to evaluate : 3.702 Fit side-chains REVERT: A 399 LEU cc_start: 0.8491 (mm) cc_final: 0.8271 (mm) REVERT: A 433 ASP cc_start: 0.7146 (m-30) cc_final: 0.6914 (m-30) REVERT: A 611 GLU cc_start: 0.6156 (mm-30) cc_final: 0.5876 (mm-30) REVERT: A 646 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8292 (mt-10) REVERT: A 937 ASN cc_start: 0.7760 (t0) cc_final: 0.7493 (m-40) REVERT: A 1170 MET cc_start: 0.9125 (mmp) cc_final: 0.8725 (mmp) REVERT: A 1266 VAL cc_start: 0.8876 (OUTLIER) cc_final: 0.8551 (m) REVERT: B 219 ARG cc_start: 0.8740 (ttm110) cc_final: 0.8480 (ttm170) REVERT: B 397 THR cc_start: 0.9073 (t) cc_final: 0.8840 (m) REVERT: B 454 ASN cc_start: 0.8396 (t0) cc_final: 0.8155 (t0) REVERT: B 550 ARG cc_start: 0.7675 (ptp90) cc_final: 0.7395 (mmt-90) REVERT: B 762 MET cc_start: 0.8870 (mmt) cc_final: 0.8432 (mmt) REVERT: B 783 MET cc_start: 0.7947 (ttm) cc_final: 0.7638 (ttm) REVERT: B 1111 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8132 (pp) REVERT: C 183 PRO cc_start: 0.8733 (Cg_endo) cc_final: 0.8487 (Cg_exo) REVERT: C 222 VAL cc_start: 0.8773 (t) cc_final: 0.8548 (m) REVERT: E 215 MET cc_start: 0.8762 (mmt) cc_final: 0.8538 (mmt) REVERT: G 72 LYS cc_start: 0.8812 (mptt) cc_final: 0.8559 (mptt) REVERT: H 27 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7968 (mt-10) REVERT: I 94 MET cc_start: 0.3258 (ttm) cc_final: 0.2747 (ttt) REVERT: K 122 LYS cc_start: 0.8778 (tptt) cc_final: 0.8492 (tptp) outliers start: 141 outliers final: 97 residues processed: 701 average time/residue: 0.4536 time to fit residues: 500.6475 Evaluate side-chains 630 residues out of total 3473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 530 time to evaluate : 4.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1458 THR Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain A residue 1577 VAL Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain A residue 1638 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 479 GLN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 987 ASN Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1199 ASN Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 38 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 296 optimal weight: 0.6980 chunk 242 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 356 optimal weight: 4.9990 chunk 385 optimal weight: 9.9990 chunk 317 optimal weight: 6.9990 chunk 353 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 286 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 HIS A 263 ASN A 384 GLN ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 ASN A1293 HIS A1629 ASN B 767 ASN B 823 GLN D 38 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN G 56 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33513 Z= 0.219 Angle : 0.573 8.038 45610 Z= 0.302 Chirality : 0.043 0.176 5097 Planarity : 0.004 0.055 5637 Dihedral : 13.368 89.270 5140 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.46 % Allowed : 12.38 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.12), residues: 3870 helix: -1.67 (0.13), residues: 1274 sheet: -1.59 (0.20), residues: 570 loop : -1.39 (0.13), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 836 HIS 0.006 0.001 HIS A 596 PHE 0.013 0.001 PHE B1167 TYR 0.017 0.002 TYR B 655 ARG 0.004 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 3473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 585 time to evaluate : 4.036 Fit side-chains REVERT: A 399 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8177 (mm) REVERT: A 432 ASN cc_start: 0.8712 (m-40) cc_final: 0.8505 (t0) REVERT: A 433 ASP cc_start: 0.7049 (m-30) cc_final: 0.6773 (m-30) REVERT: A 937 ASN cc_start: 0.7713 (t0) cc_final: 0.7456 (m-40) REVERT: A 965 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8507 (p) REVERT: A 1120 TYR cc_start: 0.7192 (m-80) cc_final: 0.6943 (m-10) REVERT: A 1170 MET cc_start: 0.9064 (mmp) cc_final: 0.8632 (mmp) REVERT: A 1266 VAL cc_start: 0.8957 (p) cc_final: 0.8671 (m) REVERT: B 307 GLU cc_start: 0.8267 (tp30) cc_final: 0.7931 (tp30) REVERT: B 397 THR cc_start: 0.8997 (t) cc_final: 0.8738 (m) REVERT: B 454 ASN cc_start: 0.8305 (t0) cc_final: 0.8093 (t0) REVERT: B 550 ARG cc_start: 0.7698 (ptp90) cc_final: 0.7423 (mmt-90) REVERT: B 762 MET cc_start: 0.8869 (mmt) cc_final: 0.8584 (mmt) REVERT: B 1006 ASN cc_start: 0.8031 (p0) cc_final: 0.7290 (t0) REVERT: C 183 PRO cc_start: 0.8704 (Cg_endo) cc_final: 0.8450 (Cg_exo) REVERT: F 152 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8312 (tp) REVERT: G 72 LYS cc_start: 0.8729 (mptt) cc_final: 0.8455 (mptt) REVERT: G 75 ASN cc_start: 0.7276 (t0) cc_final: 0.7071 (t0) REVERT: I 94 MET cc_start: 0.2878 (ttm) cc_final: 0.2566 (ttt) REVERT: K 131 VAL cc_start: 0.8913 (p) cc_final: 0.8674 (t) outliers start: 120 outliers final: 86 residues processed: 658 average time/residue: 0.4714 time to fit residues: 488.8275 Evaluate side-chains 635 residues out of total 3473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 546 time to evaluate : 3.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1014 SER Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1466 SER Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 479 GLN Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 902 SER Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 987 ASN Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 38 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 3.9990 chunk 268 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 239 optimal weight: 5.9990 chunk 357 optimal weight: 8.9990 chunk 378 optimal weight: 2.9990 chunk 186 optimal weight: 0.3980 chunk 339 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 HIS A 263 ASN A 384 GLN A 535 GLN A1323 HIS A1629 ASN B 739 ASN B 767 ASN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN J 53 HIS ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 33513 Z= 0.294 Angle : 0.605 11.059 45610 Z= 0.315 Chirality : 0.045 0.192 5097 Planarity : 0.004 0.053 5637 Dihedral : 13.332 89.703 5140 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.26 % Allowed : 12.96 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.12), residues: 3870 helix: -1.10 (0.13), residues: 1279 sheet: -1.49 (0.20), residues: 570 loop : -1.24 (0.13), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 836 HIS 0.006 0.001 HIS A 596 PHE 0.018 0.002 PHE B1167 TYR 0.018 0.002 TYR K 91 ARG 0.009 0.001 ARG A1444 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 3473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 535 time to evaluate : 3.827 Fit side-chains REVERT: A 399 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8221 (mm) REVERT: A 433 ASP cc_start: 0.7071 (m-30) cc_final: 0.6773 (m-30) REVERT: A 606 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7892 (ttt180) REVERT: A 611 GLU cc_start: 0.6168 (mm-30) cc_final: 0.5911 (mm-30) REVERT: A 1124 LEU cc_start: 0.8444 (mm) cc_final: 0.8211 (mt) REVERT: A 1170 MET cc_start: 0.9086 (mmp) cc_final: 0.8657 (mmp) REVERT: A 1266 VAL cc_start: 0.8974 (OUTLIER) cc_final: 0.8664 (m) REVERT: B 397 THR cc_start: 0.9048 (t) cc_final: 0.8845 (m) REVERT: B 508 PHE cc_start: 0.7638 (t80) cc_final: 0.7349 (t80) REVERT: B 550 ARG cc_start: 0.7644 (ptp90) cc_final: 0.7369 (mmt-90) REVERT: B 699 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8376 (mt) REVERT: B 762 MET cc_start: 0.8909 (mmt) cc_final: 0.8518 (mmt) REVERT: B 767 ASN cc_start: 0.8840 (OUTLIER) cc_final: 0.8629 (t0) REVERT: B 884 GLU cc_start: 0.8457 (pt0) cc_final: 0.8176 (pt0) REVERT: B 1006 ASN cc_start: 0.8085 (p0) cc_final: 0.7462 (t0) REVERT: C 34 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7180 (tp30) REVERT: C 128 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7396 (p0) REVERT: C 183 PRO cc_start: 0.8706 (Cg_endo) cc_final: 0.8465 (Cg_exo) REVERT: F 152 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8326 (tp) REVERT: G 72 LYS cc_start: 0.8779 (mptt) cc_final: 0.8481 (mptt) REVERT: K 131 VAL cc_start: 0.8913 (p) cc_final: 0.8698 (t) outliers start: 148 outliers final: 111 residues processed: 631 average time/residue: 0.4960 time to fit residues: 492.3117 Evaluate side-chains 628 residues out of total 3473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 510 time to evaluate : 3.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 606 ARG Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1014 SER Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 479 GLN Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 739 ASN Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 902 SER Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 987 ASN Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1199 ASN Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain L residue 38 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 282 optimal weight: 0.7980 chunk 156 optimal weight: 0.7980 chunk 323 optimal weight: 5.9990 chunk 261 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 193 optimal weight: 10.0000 chunk 340 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 HIS A 263 ASN A 384 GLN A1323 HIS B 454 ASN B 739 ASN B 767 ASN E 114 ASN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN F 78 GLN ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 33513 Z= 0.360 Angle : 0.629 10.958 45610 Z= 0.327 Chirality : 0.046 0.209 5097 Planarity : 0.005 0.054 5637 Dihedral : 13.345 89.697 5139 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 5.01 % Allowed : 13.19 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.13), residues: 3870 helix: -0.83 (0.14), residues: 1287 sheet: -1.44 (0.20), residues: 564 loop : -1.19 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 836 HIS 0.007 0.001 HIS A 596 PHE 0.021 0.002 PHE B1167 TYR 0.018 0.002 TYR A1302 ARG 0.007 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 519 time to evaluate : 3.616 Fit side-chains REVERT: A 399 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8251 (mm) REVERT: A 606 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7960 (ttt180) REVERT: A 611 GLU cc_start: 0.6237 (mm-30) cc_final: 0.5990 (mm-30) REVERT: A 1124 LEU cc_start: 0.8446 (mm) cc_final: 0.8203 (mt) REVERT: A 1170 MET cc_start: 0.9080 (mmp) cc_final: 0.8637 (mmp) REVERT: A 1266 VAL cc_start: 0.8994 (OUTLIER) cc_final: 0.8707 (m) REVERT: B 96 SER cc_start: 0.8709 (t) cc_final: 0.8488 (p) REVERT: B 508 PHE cc_start: 0.7823 (t80) cc_final: 0.7534 (t80) REVERT: B 550 ARG cc_start: 0.7644 (ptp90) cc_final: 0.7372 (mmt-90) REVERT: B 762 MET cc_start: 0.8925 (mmt) cc_final: 0.8527 (mmt) REVERT: B 767 ASN cc_start: 0.8991 (OUTLIER) cc_final: 0.8755 (t0) REVERT: B 884 GLU cc_start: 0.8506 (pt0) cc_final: 0.8203 (pt0) REVERT: B 1006 ASN cc_start: 0.8237 (p0) cc_final: 0.7589 (t0) REVERT: C 34 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7230 (tp30) REVERT: C 128 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7426 (p0) REVERT: C 183 PRO cc_start: 0.8719 (Cg_endo) cc_final: 0.8482 (Cg_exo) REVERT: F 152 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8340 (tp) REVERT: G 72 LYS cc_start: 0.8801 (mptt) cc_final: 0.8448 (mptt) REVERT: J 27 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7206 (mp0) outliers start: 174 outliers final: 136 residues processed: 632 average time/residue: 0.4678 time to fit residues: 464.8915 Evaluate side-chains 647 residues out of total 3473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 504 time to evaluate : 3.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 606 ARG Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1014 SER Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1466 SER Chi-restraints excluded: chain A residue 1638 SER Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 479 GLN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 739 ASN Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 902 SER Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 987 ASN Chi-restraints excluded: chain B residue 1025 ASP Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1199 ASN Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 165 ARG Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain L residue 38 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 9.9990 chunk 341 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 222 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 379 optimal weight: 0.8980 chunk 314 optimal weight: 0.6980 chunk 175 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 chunk 199 optimal weight: 5.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN A 221 HIS A 263 ASN A 384 GLN A 489 ASN A1323 HIS B 739 ASN B 767 ASN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN G 59 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 33513 Z= 0.254 Angle : 0.575 10.636 45610 Z= 0.300 Chirality : 0.044 0.206 5097 Planarity : 0.004 0.054 5637 Dihedral : 13.224 89.334 5138 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.43 % Allowed : 14.28 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.13), residues: 3870 helix: -0.53 (0.14), residues: 1284 sheet: -1.32 (0.20), residues: 572 loop : -1.08 (0.13), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 836 HIS 0.005 0.001 HIS A 596 PHE 0.017 0.001 PHE B1167 TYR 0.015 0.002 TYR A1302 ARG 0.006 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 516 time to evaluate : 3.277 Fit side-chains REVERT: A 399 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8260 (mm) REVERT: A 611 GLU cc_start: 0.6192 (mm-30) cc_final: 0.5938 (mm-30) REVERT: A 654 ASP cc_start: 0.8125 (m-30) cc_final: 0.7896 (m-30) REVERT: A 1120 TYR cc_start: 0.7231 (m-80) cc_final: 0.6987 (m-10) REVERT: A 1124 LEU cc_start: 0.8391 (mm) cc_final: 0.8153 (mt) REVERT: A 1170 MET cc_start: 0.9057 (mmp) cc_final: 0.8602 (mmp) REVERT: A 1266 VAL cc_start: 0.9020 (OUTLIER) cc_final: 0.8710 (m) REVERT: B 96 SER cc_start: 0.8695 (t) cc_final: 0.8483 (p) REVERT: B 100 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7592 (pp20) REVERT: B 508 PHE cc_start: 0.7836 (t80) cc_final: 0.7558 (t80) REVERT: B 550 ARG cc_start: 0.7650 (ptp90) cc_final: 0.7363 (mmp80) REVERT: B 685 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8400 (t) REVERT: B 762 MET cc_start: 0.8896 (mmt) cc_final: 0.8480 (mmt) REVERT: B 884 GLU cc_start: 0.8499 (pt0) cc_final: 0.8192 (pt0) REVERT: C 128 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7478 (p0) REVERT: C 183 PRO cc_start: 0.8720 (Cg_endo) cc_final: 0.8482 (Cg_exo) REVERT: C 273 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7635 (p0) REVERT: E 93 MET cc_start: 0.7002 (tpp) cc_final: 0.6727 (tpp) REVERT: F 152 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8361 (tp) REVERT: G 72 LYS cc_start: 0.8766 (mptt) cc_final: 0.8416 (mptt) REVERT: G 75 ASN cc_start: 0.7327 (t0) cc_final: 0.7125 (t0) REVERT: G 111 THR cc_start: 0.8903 (p) cc_final: 0.8651 (p) REVERT: J 27 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7255 (mp0) outliers start: 154 outliers final: 127 residues processed: 614 average time/residue: 0.4756 time to fit residues: 459.9426 Evaluate side-chains 640 residues out of total 3473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 505 time to evaluate : 3.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1014 SER Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1233 ILE Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1466 SER Chi-restraints excluded: chain A residue 1638 SER Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 479 GLN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 584 CYS Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 739 ASN Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 902 SER Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 987 ASN Chi-restraints excluded: chain B residue 1025 ASP Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1199 ASN Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 165 ARG Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain L residue 38 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 216 optimal weight: 7.9990 chunk 276 optimal weight: 0.0070 chunk 214 optimal weight: 6.9990 chunk 319 optimal weight: 0.9980 chunk 211 optimal weight: 0.7980 chunk 377 optimal weight: 4.9990 chunk 236 optimal weight: 0.9980 chunk 230 optimal weight: 7.9990 chunk 174 optimal weight: 0.1980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 HIS A 263 ASN A 380 ASN A 384 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 ASN ** B 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 923 GLN C 58 ASN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 HIS F 78 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 33513 Z= 0.142 Angle : 0.511 9.505 45610 Z= 0.269 Chirality : 0.041 0.201 5097 Planarity : 0.004 0.051 5637 Dihedral : 13.000 89.642 5138 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.34 % Allowed : 15.92 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.13), residues: 3870 helix: -0.10 (0.15), residues: 1291 sheet: -1.11 (0.21), residues: 562 loop : -0.96 (0.13), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 836 HIS 0.004 0.001 HIS A1454 PHE 0.012 0.001 PHE B 301 TYR 0.012 0.001 TYR A1302 ARG 0.005 0.000 ARG H 130 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 554 time to evaluate : 4.176 Fit side-chains revert: symmetry clash REVERT: A 399 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8247 (mm) REVERT: A 1124 LEU cc_start: 0.8290 (mm) cc_final: 0.8003 (mt) REVERT: A 1170 MET cc_start: 0.9011 (mmp) cc_final: 0.8795 (mmm) REVERT: A 1266 VAL cc_start: 0.8993 (p) cc_final: 0.8697 (m) REVERT: B 96 SER cc_start: 0.8636 (t) cc_final: 0.8403 (p) REVERT: B 100 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7557 (pp20) REVERT: B 134 ARG cc_start: 0.7815 (ptt90) cc_final: 0.7343 (ptt180) REVERT: B 508 PHE cc_start: 0.7762 (t80) cc_final: 0.7507 (t80) REVERT: B 550 ARG cc_start: 0.7631 (ptp90) cc_final: 0.7319 (mmp80) REVERT: B 762 MET cc_start: 0.8879 (mmt) cc_final: 0.8578 (mmt) REVERT: B 803 MET cc_start: 0.8278 (ttm) cc_final: 0.8000 (ttp) REVERT: B 884 GLU cc_start: 0.8477 (pt0) cc_final: 0.8172 (pt0) REVERT: C 128 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7286 (p0) REVERT: C 183 PRO cc_start: 0.8701 (Cg_endo) cc_final: 0.8471 (Cg_exo) REVERT: E 93 MET cc_start: 0.6986 (tpp) cc_final: 0.6743 (tpp) REVERT: F 152 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8335 (tp) REVERT: G 75 ASN cc_start: 0.7199 (t0) cc_final: 0.6998 (t0) REVERT: G 106 LYS cc_start: 0.8406 (tttt) cc_final: 0.8193 (tttt) REVERT: I 48 VAL cc_start: 0.8690 (m) cc_final: 0.8465 (t) REVERT: J 27 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7271 (mp0) outliers start: 116 outliers final: 89 residues processed: 622 average time/residue: 0.4725 time to fit residues: 465.1671 Evaluate side-chains 606 residues out of total 3473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 512 time to evaluate : 3.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 479 GLN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 584 CYS Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 654 ARG Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 987 ASN Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain L residue 38 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 225 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 240 optimal weight: 8.9990 chunk 257 optimal weight: 0.7980 chunk 186 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 296 optimal weight: 2.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 HIS A 263 ASN A 384 GLN A 640 ASN A1323 HIS B 224 ASN B 923 GLN B 975 HIS ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN F 78 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 33513 Z= 0.358 Angle : 0.629 10.675 45610 Z= 0.325 Chirality : 0.046 0.227 5097 Planarity : 0.005 0.058 5637 Dihedral : 13.119 88.113 5138 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.97 % Allowed : 15.58 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.13), residues: 3870 helix: -0.21 (0.14), residues: 1278 sheet: -1.15 (0.20), residues: 565 loop : -0.94 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 836 HIS 0.006 0.001 HIS A 795 PHE 0.026 0.002 PHE B1167 TYR 0.020 0.002 TYR A1302 ARG 0.008 0.001 ARG B 634 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 502 time to evaluate : 3.669 Fit side-chains REVERT: A 59 ARG cc_start: 0.7280 (ttp-110) cc_final: 0.7054 (mtm-85) REVERT: A 399 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8284 (mm) REVERT: A 606 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.8013 (ttt180) REVERT: A 1170 MET cc_start: 0.9094 (mmp) cc_final: 0.8603 (mmp) REVERT: A 1266 VAL cc_start: 0.9022 (OUTLIER) cc_final: 0.8730 (m) REVERT: A 1444 ARG cc_start: 0.6178 (mpt180) cc_final: 0.5721 (mpt180) REVERT: B 96 SER cc_start: 0.8732 (t) cc_final: 0.8500 (p) REVERT: B 100 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7636 (pp20) REVERT: B 508 PHE cc_start: 0.7980 (t80) cc_final: 0.7706 (t80) REVERT: B 550 ARG cc_start: 0.7704 (ptp90) cc_final: 0.7435 (mmt-90) REVERT: B 762 MET cc_start: 0.8958 (mmt) cc_final: 0.8614 (mmt) REVERT: B 878 GLU cc_start: 0.8602 (tt0) cc_final: 0.8390 (tt0) REVERT: C 128 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7468 (p0) REVERT: C 183 PRO cc_start: 0.8722 (Cg_endo) cc_final: 0.8478 (Cg_exo) REVERT: E 93 MET cc_start: 0.7020 (tpp) cc_final: 0.6749 (tpp) REVERT: F 114 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6486 (tt0) REVERT: F 152 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8331 (tp) REVERT: J 27 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7219 (mp0) outliers start: 138 outliers final: 115 residues processed: 591 average time/residue: 0.4670 time to fit residues: 433.7737 Evaluate side-chains 616 residues out of total 3473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 493 time to evaluate : 3.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 606 ARG Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1233 ILE Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1466 SER Chi-restraints excluded: chain A residue 1638 SER Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 479 GLN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 584 CYS Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 654 ARG Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 902 SER Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 987 ASN Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1199 ASN Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 94 MET Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain L residue 38 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 30.0000 chunk 361 optimal weight: 8.9990 chunk 330 optimal weight: 8.9990 chunk 352 optimal weight: 2.9990 chunk 211 optimal weight: 5.9990 chunk 153 optimal weight: 7.9990 chunk 276 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 318 optimal weight: 8.9990 chunk 332 optimal weight: 9.9990 chunk 350 optimal weight: 0.0980 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 HIS A 263 ASN A 384 GLN A1323 HIS B 224 ASN ** B 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN H 128 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 33513 Z= 0.361 Angle : 0.630 10.596 45610 Z= 0.326 Chirality : 0.046 0.228 5097 Planarity : 0.005 0.056 5637 Dihedral : 13.154 86.846 5138 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.20 % Allowed : 15.75 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.13), residues: 3870 helix: -0.28 (0.14), residues: 1282 sheet: -1.14 (0.20), residues: 575 loop : -0.95 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 836 HIS 0.006 0.001 HIS A 596 PHE 0.026 0.002 PHE B1167 TYR 0.017 0.002 TYR A1302 ARG 0.010 0.001 ARG A 244 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 488 time to evaluate : 3.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.7281 (ttp-110) cc_final: 0.7074 (mtm-85) REVERT: A 399 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8294 (mm) REVERT: A 606 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.8024 (ttt180) REVERT: A 1170 MET cc_start: 0.9086 (mmp) cc_final: 0.8616 (mmp) REVERT: A 1266 VAL cc_start: 0.9060 (OUTLIER) cc_final: 0.8763 (m) REVERT: A 1583 ASP cc_start: 0.7885 (m-30) cc_final: 0.7681 (m-30) REVERT: B 100 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7688 (pp20) REVERT: B 337 VAL cc_start: 0.9000 (p) cc_final: 0.8769 (m) REVERT: B 508 PHE cc_start: 0.7938 (t80) cc_final: 0.7623 (t80) REVERT: B 550 ARG cc_start: 0.7747 (ptp90) cc_final: 0.7343 (mmt180) REVERT: B 699 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8440 (mt) REVERT: B 762 MET cc_start: 0.8916 (mmt) cc_final: 0.8571 (mmt) REVERT: C 128 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7451 (p0) REVERT: C 319 ARG cc_start: 0.7872 (tpp80) cc_final: 0.7311 (mtp180) REVERT: F 114 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6526 (tt0) REVERT: F 152 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8344 (tp) REVERT: J 27 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7181 (mp0) outliers start: 146 outliers final: 121 residues processed: 588 average time/residue: 0.4697 time to fit residues: 434.8736 Evaluate side-chains 611 residues out of total 3473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 481 time to evaluate : 3.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 606 ARG Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1233 ILE Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1466 SER Chi-restraints excluded: chain A residue 1473 LYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 479 GLN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 584 CYS Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 654 ARG Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 902 SER Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 987 ASN Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1199 ASN Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 94 MET Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 60 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 7.9990 chunk 372 optimal weight: 0.6980 chunk 227 optimal weight: 0.5980 chunk 176 optimal weight: 0.4980 chunk 258 optimal weight: 5.9990 chunk 390 optimal weight: 10.0000 chunk 359 optimal weight: 0.9980 chunk 310 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 240 optimal weight: 0.8980 chunk 190 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 HIS A 263 ASN A 384 GLN A 610 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1323 HIS B 224 ASN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 923 GLN B1165 ASN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN H 128 ASN I 32 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 33513 Z= 0.153 Angle : 0.528 9.497 45610 Z= 0.276 Chirality : 0.042 0.226 5097 Planarity : 0.004 0.056 5637 Dihedral : 12.946 87.235 5138 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.14 % Allowed : 16.84 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.13), residues: 3870 helix: 0.13 (0.15), residues: 1294 sheet: -1.01 (0.21), residues: 572 loop : -0.85 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 836 HIS 0.005 0.001 HIS A 596 PHE 0.012 0.001 PHE B1167 TYR 0.013 0.001 TYR A1302 ARG 0.007 0.000 ARG B 634 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 3473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 512 time to evaluate : 3.448 Fit side-chains revert: symmetry clash REVERT: A 59 ARG cc_start: 0.7309 (ttp-110) cc_final: 0.7103 (mtm-85) REVERT: A 92 ASN cc_start: 0.8206 (m-40) cc_final: 0.7886 (m-40) REVERT: A 399 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8270 (mm) REVERT: A 965 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8455 (p) REVERT: A 1266 VAL cc_start: 0.9029 (OUTLIER) cc_final: 0.8734 (m) REVERT: A 1583 ASP cc_start: 0.7828 (m-30) cc_final: 0.7625 (m-30) REVERT: B 65 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8248 (m) REVERT: B 100 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7768 (pp20) REVERT: B 550 ARG cc_start: 0.7658 (ptp90) cc_final: 0.7267 (mmt180) REVERT: B 699 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8120 (mt) REVERT: B 762 MET cc_start: 0.8856 (mmt) cc_final: 0.8553 (mmt) REVERT: B 1077 ASP cc_start: 0.8407 (p0) cc_final: 0.7884 (m-30) REVERT: B 1199 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.7275 (m110) REVERT: C 128 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7337 (p0) REVERT: C 183 PRO cc_start: 0.8724 (Cg_endo) cc_final: 0.8478 (Cg_exo) REVERT: C 315 PHE cc_start: 0.7633 (t80) cc_final: 0.7314 (t80) REVERT: F 152 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8326 (tp) REVERT: J 27 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7228 (mp0) outliers start: 109 outliers final: 90 residues processed: 586 average time/residue: 0.4865 time to fit residues: 451.8592 Evaluate side-chains 588 residues out of total 3473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 488 time to evaluate : 4.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 479 GLN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 584 CYS Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 654 ARG Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 902 SER Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 987 ASN Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1199 ASN Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain L residue 38 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 4.9990 chunk 331 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 286 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 311 optimal weight: 0.7980 chunk 130 optimal weight: 9.9990 chunk 319 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 HIS A 263 ASN A 384 GLN A 610 ASN A1237 GLN A1323 HIS B 224 ASN ** B 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 923 GLN B1165 ASN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN G 75 ASN H 128 ASN I 32 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.144718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.110837 restraints weight = 37488.099| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.20 r_work: 0.2898 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33513 Z= 0.229 Angle : 0.563 9.985 45610 Z= 0.292 Chirality : 0.044 0.244 5097 Planarity : 0.004 0.055 5637 Dihedral : 12.938 86.695 5138 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.63 % Allowed : 16.70 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.13), residues: 3870 helix: 0.13 (0.15), residues: 1293 sheet: -0.99 (0.21), residues: 571 loop : -0.77 (0.14), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 836 HIS 0.005 0.001 HIS A 596 PHE 0.019 0.001 PHE B1167 TYR 0.018 0.001 TYR A1302 ARG 0.006 0.000 ARG A 329 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9339.82 seconds wall clock time: 167 minutes 29.68 seconds (10049.68 seconds total)