Starting phenix.real_space_refine on Sat Mar 23 18:31:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu2_3957/03_2024/6eu2_3957.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu2_3957/03_2024/6eu2_3957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu2_3957/03_2024/6eu2_3957.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu2_3957/03_2024/6eu2_3957.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu2_3957/03_2024/6eu2_3957.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu2_3957/03_2024/6eu2_3957.pdb" } resolution = 3.4 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= 0.001 sd= 0.009 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: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 Mg 1 5.21 5 S 207 5.16 5 C 24312 2.51 5 N 6585 2.21 5 O 7218 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A ARG 259": "NH1" <-> "NH2" Residue "A ARG 1187": "NH1" <-> "NH2" Residue "A ARG 1259": "NH1" <-> "NH2" Residue "B ARG 227": "NH1" <-> "NH2" Residue "B ARG 481": "NH1" <-> "NH2" Residue "B ARG 607": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B ARG 867": "NH1" <-> "NH2" Residue "B ARG 1048": "NH1" <-> "NH2" Residue "B ARG 1054": "NH1" <-> "NH2" Residue "B ARG 1056": "NH1" <-> "NH2" Residue "C TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 277": "NH1" <-> "NH2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "G PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 42": "NH1" <-> "NH2" Residue "M ARG 93": "NH1" <-> "NH2" Residue "M PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 303": "NH1" <-> "NH2" Residue "N ARG 364": "NH1" <-> "NH2" Residue "N ARG 411": "NH1" <-> "NH2" Residue "O ARG 228": "NH1" <-> "NH2" Residue "O ARG 238": "NH1" <-> "NH2" Residue "O ARG 286": "NH1" <-> "NH2" Residue "O ARG 292": "NH1" <-> "NH2" Residue "O ARG 303": "NH1" <-> "NH2" Residue "O ARG 317": "NH1" <-> "NH2" Residue "O ARG 509": "NH1" <-> "NH2" Residue "O ARG 512": "NH1" <-> "NH2" Residue "O ARG 534": "NH1" <-> "NH2" Residue "O ARG 557": "NH1" <-> "NH2" Residue "O ARG 561": "NH1" <-> "NH2" Residue "O ARG 643": "NH1" <-> "NH2" Residue "P TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 313": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 38329 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 10980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1402, 10980 Classifications: {'peptide': 1402} Link IDs: {'PTRANS': 63, 'TRANS': 1338} Chain breaks: 3 Chain: "B" Number of atoms: 8788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8788 Classifications: {'peptide': 1114} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 1070} Chain: "C" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2655 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 20, 'TRANS': 314} Chain: "D" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 977 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain breaks: 2 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 671 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1544 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 12, 'TRANS': 178} Chain breaks: 2 Chain: "H" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1120 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 135} Chain breaks: 1 Chain: "I" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 321 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "J" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 558 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "K" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 792 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "L" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1347 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 8, 'TRANS': 156} Chain breaks: 1 Chain: "N" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 802 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain breaks: 1 Chain: "O" Number of atoms: 4315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4315 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 17, 'TRANS': 519} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1024 Classifications: {'peptide': 123} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "Q" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 311 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 5, 'TRANS': 34} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 510 SG CYS A 70 78.753 66.943 79.309 1.00 66.93 S ATOM 795 SG CYS A 107 61.364 111.694 95.439 1.00 48.48 S ATOM 1184 SG CYS A 154 62.664 114.580 93.523 1.00 68.31 S ATOM 1208 SG CYS A 157 58.803 114.034 93.724 1.00 70.16 S ATOM 19341 SG CYS B1095 82.241 82.925 76.225 1.00 37.65 S ATOM 19430 SG CYS B1107 79.320 81.301 74.903 1.00 46.23 S ATOM 28552 SG CYS I 8 61.485 104.888 159.568 1.00 81.51 S ATOM 28703 SG CYS I 29 59.675 107.936 160.450 1.00 90.89 S ATOM 28892 SG CYS J 10 131.323 38.271 125.391 1.00 24.11 S ATOM 29172 SG CYS J 45 129.207 41.878 128.080 1.00 29.06 S ATOM 29178 SG CYS J 46 129.442 38.035 128.413 1.00 23.95 S ATOM 30215 SG CYS L 31 86.293 24.890 124.388 1.00 46.89 S ATOM 30235 SG CYS L 34 86.320 21.438 125.514 1.00 58.37 S ATOM 30362 SG CYS L 51 83.267 23.842 126.230 1.00 62.35 S Time building chain proxies: 18.50, per 1000 atoms: 0.48 Number of scatterers: 38329 At special positions: 0 Unit cell: (190.05, 159.6, 207.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 207 16.00 Mg 1 11.99 O 7218 8.00 N 6585 7.00 C 24312 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: 13.14 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 70 " pdb="ZN ZN A2000 " - pdb=" ND1 HIS A 80 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 157 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 107 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1107 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 8 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9114 Finding SS restraints... Secondary structure from input PDB file: 161 helices and 50 sheets defined 34.5% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.25 Creating SS restraints... Processing helix chain 'A' and resid 22 through 29 removed outlier: 3.669A pdb=" N VAL A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 104 Processing helix chain 'A' and resid 118 through 128 removed outlier: 3.506A pdb=" N ARG A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 148 removed outlier: 3.560A pdb=" N GLY A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 191 through 208 Processing helix chain 'A' and resid 223 through 231 removed outlier: 3.604A pdb=" N ASN A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.502A pdb=" N ILE A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 303 removed outlier: 3.603A pdb=" N THR A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 327 removed outlier: 3.806A pdb=" N ILE A 327 " --> pdb=" O VAL A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 423 removed outlier: 3.626A pdb=" N GLN A 417 " --> pdb=" O ARG A 413 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLU A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 456 removed outlier: 3.550A pdb=" N LYS A 454 " --> pdb=" O MET A 450 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN A 455 " --> pdb=" O LYS A 451 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 450 through 456' Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing helix chain 'A' and resid 504 through 509 removed outlier: 4.169A pdb=" N TYR A 508 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 533 removed outlier: 3.794A pdb=" N ILE A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 528 through 533' Processing helix chain 'A' and resid 554 through 565 removed outlier: 3.678A pdb=" N THR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER A 561 " --> pdb=" O PHE A 557 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE A 564 " --> pdb=" O GLY A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 583 removed outlier: 3.532A pdb=" N MET A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 615 removed outlier: 4.102A pdb=" N PHE A 610 " --> pdb=" O GLY A 606 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 612 " --> pdb=" O GLN A 608 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 614 " --> pdb=" O PHE A 610 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS A 615 " --> pdb=" O SER A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 685 Processing helix chain 'A' and resid 685 through 709 removed outlier: 4.295A pdb=" N GLU A 689 " --> pdb=" O TYR A 685 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA A 690 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA A 702 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG A 703 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN A 707 " --> pdb=" O ARG A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 740 removed outlier: 3.653A pdb=" N LYS A 726 " --> pdb=" O ASP A 722 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU A 732 " --> pdb=" O GLU A 728 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS A 736 " --> pdb=" O GLU A 732 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 740 " --> pdb=" O HIS A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 746 removed outlier: 3.588A pdb=" N ASN A 746 " --> pdb=" O ILE A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 777 removed outlier: 3.718A pdb=" N GLU A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG A 774 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU A 775 " --> pdb=" O SER A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 784 removed outlier: 3.960A pdb=" N ASN A 783 " --> pdb=" O ASP A 779 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU A 784 " --> pdb=" O VAL A 780 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 779 through 784' Processing helix chain 'A' and resid 789 through 797 Processing helix chain 'A' and resid 802 through 810 Processing helix chain 'A' and resid 857 through 877 removed outlier: 3.535A pdb=" N SER A 867 " --> pdb=" O PHE A 863 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY A 871 " --> pdb=" O SER A 867 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR A 875 " --> pdb=" O GLY A 871 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 876 " --> pdb=" O LEU A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 882 removed outlier: 3.778A pdb=" N THR A 882 " --> pdb=" O THR A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 890 Processing helix chain 'A' and resid 915 through 919 Processing helix chain 'A' and resid 934 through 946 removed outlier: 3.579A pdb=" N ASN A 944 " --> pdb=" O ASP A 940 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 963 Processing helix chain 'A' and resid 968 through 973 removed outlier: 3.898A pdb=" N ARG A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1025 removed outlier: 3.903A pdb=" N ARG A1002 " --> pdb=" O TYR A 998 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS A1015 " --> pdb=" O TYR A1011 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A1016 " --> pdb=" O ILE A1012 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A1018 " --> pdb=" O GLY A1014 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER A1025 " --> pdb=" O ASN A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1060 removed outlier: 3.539A pdb=" N VAL A1056 " --> pdb=" O VAL A1052 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1080 removed outlier: 3.526A pdb=" N GLU A1072 " --> pdb=" O ARG A1068 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR A1078 " --> pdb=" O ALA A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1102 removed outlier: 3.629A pdb=" N ILE A1097 " --> pdb=" O GLY A1093 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY A1098 " --> pdb=" O ALA A1094 " (cutoff:3.500A) Proline residue: A1100 - end of helix Processing helix chain 'A' and resid 1122 through 1131 removed outlier: 3.508A pdb=" N ILE A1126 " --> pdb=" O GLY A1122 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS A1127 " --> pdb=" O VAL A1123 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU A1128 " --> pdb=" O PRO A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1160 Processing helix chain 'A' and resid 1164 through 1169 removed outlier: 4.370A pdb=" N SER A1167 " --> pdb=" O THR A1164 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL A1169 " --> pdb=" O LEU A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1196 Processing helix chain 'A' and resid 1201 through 1211 Processing helix chain 'A' and resid 1255 through 1266 Processing helix chain 'A' and resid 1318 through 1326 removed outlier: 3.692A pdb=" N VAL A1325 " --> pdb=" O GLU A1321 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1345 removed outlier: 3.711A pdb=" N TYR A1333 " --> pdb=" O GLU A1329 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER A1334 " --> pdb=" O ALA A1330 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG A1337 " --> pdb=" O TYR A1333 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A1339 " --> pdb=" O ILE A1335 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN A1340 " --> pdb=" O ILE A1336 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN A1345 " --> pdb=" O TYR A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1352 through 1362 removed outlier: 3.807A pdb=" N MET A1362 " --> pdb=" O LEU A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1402 removed outlier: 4.074A pdb=" N ASP A1398 " --> pdb=" O ASP A1394 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A1399 " --> pdb=" O HIS A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1413 through 1418 removed outlier: 3.748A pdb=" N LEU A1417 " --> pdb=" O GLU A1413 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1427 removed outlier: 3.683A pdb=" N GLY A1426 " --> pdb=" O ILE A1423 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER A1427 " --> pdb=" O GLY A1424 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1423 through 1427' Processing helix chain 'A' and resid 1449 through 1455 removed outlier: 3.937A pdb=" N GLU A1454 " --> pdb=" O SER A1450 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA A1455 " --> pdb=" O LEU A1451 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 45 removed outlier: 3.567A pdb=" N TRP B 45 " --> pdb=" O GLN B 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 42 through 45' Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.597A pdb=" N ALA B 50 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 71 removed outlier: 4.361A pdb=" N SER B 64 " --> pdb=" O GLN B 60 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 65 " --> pdb=" O HIS B 61 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP B 70 " --> pdb=" O ASN B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 78 removed outlier: 4.373A pdb=" N ILE B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 removed outlier: 3.563A pdb=" N LEU B 120 " --> pdb=" O HIS B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 252 through 260 removed outlier: 3.580A pdb=" N VAL B 256 " --> pdb=" O PRO B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 289 removed outlier: 4.765A pdb=" N VAL B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ASN B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 308 removed outlier: 3.603A pdb=" N ILE B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS B 308 " --> pdb=" O TYR B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 removed outlier: 4.017A pdb=" N ILE B 319 " --> pdb=" O LYS B 316 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 320 " --> pdb=" O LEU B 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 316 through 320' Processing helix chain 'B' and resid 322 through 329 removed outlier: 4.330A pdb=" N ALA B 326 " --> pdb=" O GLU B 322 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 327 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 328 " --> pdb=" O ILE B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 362 removed outlier: 3.775A pdb=" N ALA B 350 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG B 355 " --> pdb=" O MET B 351 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL B 356 " --> pdb=" O MET B 352 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA B 359 " --> pdb=" O ARG B 355 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 379 through 404 removed outlier: 4.108A pdb=" N LEU B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 439 removed outlier: 3.999A pdb=" N LEU B 433 " --> pdb=" O ILE B 429 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 470 removed outlier: 3.602A pdb=" N ALA B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET B 470 " --> pdb=" O ALA B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 494 removed outlier: 3.646A pdb=" N GLN B 493 " --> pdb=" O GLN B 490 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE B 494 " --> pdb=" O PRO B 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 490 through 494' Processing helix chain 'B' and resid 526 through 537 removed outlier: 4.201A pdb=" N LYS B 530 " --> pdb=" O GLU B 526 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR B 534 " --> pdb=" O LYS B 530 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B 535 " --> pdb=" O LYS B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 544 removed outlier: 3.806A pdb=" N ILE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 583 removed outlier: 3.884A pdb=" N THR B 581 " --> pdb=" O HIS B 577 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 582 " --> pdb=" O LEU B 578 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 631 removed outlier: 3.862A pdb=" N LEU B 627 " --> pdb=" O LYS B 623 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS B 629 " --> pdb=" O ILE B 625 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU B 630 " --> pdb=" O HIS B 626 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 657 Processing helix chain 'B' and resid 676 through 680 removed outlier: 3.898A pdb=" N THR B 679 " --> pdb=" O GLU B 676 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 680 " --> pdb=" O PRO B 677 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 676 through 680' Processing helix chain 'B' and resid 684 through 688 removed outlier: 3.992A pdb=" N ILE B 688 " --> pdb=" O ALA B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 706 removed outlier: 4.204A pdb=" N GLN B 702 " --> pdb=" O ARG B 698 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N CYS B 703 " --> pdb=" O ASN B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 822 removed outlier: 3.733A pdb=" N GLN B 822 " --> pdb=" O TRP B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 949 removed outlier: 3.665A pdb=" N GLY B 948 " --> pdb=" O ASN B 945 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B 949 " --> pdb=" O PRO B 946 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 945 through 949' Processing helix chain 'B' and resid 955 through 970 removed outlier: 3.515A pdb=" N GLU B 960 " --> pdb=" O GLY B 956 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 961 " --> pdb=" O LYS B 957 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 962 " --> pdb=" O MET B 958 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY B 967 " --> pdb=" O SER B 963 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU B 969 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASN B 970 " --> pdb=" O ALA B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 993 removed outlier: 3.543A pdb=" N LYS B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 990 " --> pdb=" O ASP B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1074 removed outlier: 3.616A pdb=" N CYS B1069 " --> pdb=" O MET B1065 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL B1070 " --> pdb=" O GLU B1066 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B1071 " --> pdb=" O ARG B1067 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B1072 " --> pdb=" O ASP B1068 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1084 removed outlier: 3.765A pdb=" N LEU B1080 " --> pdb=" O SER B1076 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1088 Processing helix chain 'B' and resid 1123 through 1135 removed outlier: 3.742A pdb=" N MET B1135 " --> pdb=" O GLU B1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 40 removed outlier: 3.588A pdb=" N LYS C 38 " --> pdb=" O GLU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 71 removed outlier: 3.699A pdb=" N ALA C 64 " --> pdb=" O ASP C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 103 removed outlier: 3.562A pdb=" N ILE C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU C 103 " --> pdb=" O HIS C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.643A pdb=" N LEU C 113 " --> pdb=" O PRO C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 removed outlier: 4.590A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 241 through 251 removed outlier: 3.865A pdb=" N CYS C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 removed outlier: 3.579A pdb=" N LYS C 272 " --> pdb=" O ASP C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 removed outlier: 4.035A pdb=" N ARG C 281 " --> pdb=" O GLU C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 327 removed outlier: 3.565A pdb=" N ILE C 313 " --> pdb=" O THR C 309 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA C 325 " --> pdb=" O LEU C 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 24 removed outlier: 3.739A pdb=" N VAL D 16 " --> pdb=" O SER D 12 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU D 24 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 66 removed outlier: 3.758A pdb=" N VAL D 63 " --> pdb=" O THR D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 100 through 113 removed outlier: 4.062A pdb=" N PHE D 113 " --> pdb=" O LYS D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 127 removed outlier: 4.360A pdb=" N LEU D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 138 removed outlier: 3.712A pdb=" N SER D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 161 removed outlier: 4.051A pdb=" N GLU D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE D 157 " --> pdb=" O MET D 153 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA D 161 " --> pdb=" O ILE D 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 6 removed outlier: 3.807A pdb=" N GLU E 6 " --> pdb=" O GLN E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 26 removed outlier: 3.617A pdb=" N LEU E 12 " --> pdb=" O ASN E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 47 removed outlier: 4.510A pdb=" N ALA E 44 " --> pdb=" O GLU E 40 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LYS E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS E 47 " --> pdb=" O LYS E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 72 Processing helix chain 'E' and resid 90 through 103 Processing helix chain 'E' and resid 117 through 121 removed outlier: 3.821A pdb=" N MET E 121 " --> pdb=" O PRO E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 168 removed outlier: 3.631A pdb=" N ARG E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.861A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 102 removed outlier: 3.708A pdb=" N ALA F 91 " --> pdb=" O LYS F 87 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE F 93 " --> pdb=" O GLU F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 128 removed outlier: 3.645A pdb=" N MET F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS F 123 " --> pdb=" O ARG F 119 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU F 124 " --> pdb=" O ILE F 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 32 removed outlier: 3.580A pdb=" N ASN G 32 " --> pdb=" O HIS G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 115 removed outlier: 3.659A pdb=" N MET G 114 " --> pdb=" O PRO G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 168 removed outlier: 3.985A pdb=" N GLU G 167 " --> pdb=" O LYS G 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.626A pdb=" N ASP H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 88 through 92' Processing helix chain 'J' and resid 18 through 27 Processing helix chain 'J' and resid 31 through 38 Processing helix chain 'J' and resid 47 through 52 Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'J' and resid 62 through 64 No H-bonds generated for 'chain 'J' and resid 62 through 64' Processing helix chain 'K' and resid 50 through 54 removed outlier: 3.882A pdb=" N ALA K 53 " --> pdb=" O LEU K 50 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR K 54 " --> pdb=" O THR K 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 50 through 54' Processing helix chain 'K' and resid 69 through 82 removed outlier: 3.724A pdb=" N GLY K 73 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 142 removed outlier: 3.759A pdb=" N GLN K 118 " --> pdb=" O VAL K 114 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP K 123 " --> pdb=" O LYS K 119 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU K 124 " --> pdb=" O GLY K 120 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N MET K 125 " --> pdb=" O LEU K 121 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR K 136 " --> pdb=" O GLU K 132 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU K 137 " --> pdb=" O SER K 133 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS K 138 " --> pdb=" O LYS K 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 139 removed outlier: 3.613A pdb=" N GLU M 137 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU M 139 " --> pdb=" O LYS M 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 184 through 193 removed outlier: 3.611A pdb=" N THR M 192 " --> pdb=" O ASP M 188 " (cutoff:3.500A) Processing helix chain 'M' and resid 231 through 236 Processing helix chain 'M' and resid 251 through 256 removed outlier: 3.608A pdb=" N LYS M 256 " --> pdb=" O PHE M 252 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 282 removed outlier: 3.759A pdb=" N LEU N 282 " --> pdb=" O ALA N 278 " (cutoff:3.500A) Processing helix chain 'N' and resid 282 through 295 removed outlier: 3.772A pdb=" N HIS N 287 " --> pdb=" O LEU N 283 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLN N 288 " --> pdb=" O ASN N 284 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS N 295 " --> pdb=" O LEU N 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 55 removed outlier: 3.610A pdb=" N VAL O 53 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA O 55 " --> pdb=" O GLU O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 71 removed outlier: 3.553A pdb=" N VAL O 64 " --> pdb=" O ARG O 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET O 67 " --> pdb=" O SER O 63 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU O 68 " --> pdb=" O VAL O 64 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL O 69 " --> pdb=" O ILE O 65 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA O 70 " --> pdb=" O GLY O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 84 removed outlier: 3.912A pdb=" N ASP O 84 " --> pdb=" O VAL O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 101 removed outlier: 3.860A pdb=" N THR O 93 " --> pdb=" O ASP O 89 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL O 96 " --> pdb=" O LYS O 92 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER O 97 " --> pdb=" O THR O 93 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU O 101 " --> pdb=" O SER O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 123 through 133 removed outlier: 3.618A pdb=" N ILE O 127 " --> pdb=" O ASN O 123 " (cutoff:3.500A) Processing helix chain 'O' and resid 135 through 140 Processing helix chain 'O' and resid 155 through 167 removed outlier: 3.934A pdb=" N GLN O 161 " --> pdb=" O ALA O 157 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 176 removed outlier: 3.830A pdb=" N SER O 176 " --> pdb=" O GLU O 172 " (cutoff:3.500A) Processing helix chain 'O' and resid 185 through 195 removed outlier: 3.802A pdb=" N LEU O 190 " --> pdb=" O THR O 186 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN O 193 " --> pdb=" O SER O 189 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS O 195 " --> pdb=" O PHE O 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 222 removed outlier: 3.520A pdb=" N LEU O 214 " --> pdb=" O PRO O 210 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU O 218 " --> pdb=" O LEU O 214 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS O 222 " --> pdb=" O LEU O 218 " (cutoff:3.500A) Processing helix chain 'O' and resid 236 through 254 removed outlier: 3.724A pdb=" N GLN O 240 " --> pdb=" O LYS O 236 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ALA O 245 " --> pdb=" O ALA O 241 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LYS O 246 " --> pdb=" O LYS O 242 " (cutoff:3.500A) Processing helix chain 'O' and resid 285 through 304 removed outlier: 3.751A pdb=" N LYS O 289 " --> pdb=" O ASP O 285 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER O 293 " --> pdb=" O LYS O 289 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS O 294 " --> pdb=" O GLY O 290 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN O 295 " --> pdb=" O ARG O 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 306 through 318 Processing helix chain 'O' and resid 338 through 344 Processing helix chain 'O' and resid 345 through 355 removed outlier: 3.501A pdb=" N GLU O 350 " --> pdb=" O GLN O 346 " (cutoff:3.500A) Processing helix chain 'O' and resid 363 through 369 Processing helix chain 'O' and resid 451 through 462 Processing helix chain 'O' and resid 483 through 497 removed outlier: 3.755A pdb=" N VAL O 491 " --> pdb=" O LEU O 487 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR O 492 " --> pdb=" O LYS O 488 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR O 494 " --> pdb=" O SER O 490 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL O 495 " --> pdb=" O VAL O 491 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE O 496 " --> pdb=" O TYR O 492 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA O 497 " --> pdb=" O GLU O 493 " (cutoff:3.500A) Processing helix chain 'O' and resid 501 through 514 removed outlier: 3.989A pdb=" N ILE O 511 " --> pdb=" O LEU O 507 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG O 512 " --> pdb=" O SER O 508 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASN O 514 " --> pdb=" O CYS O 510 " (cutoff:3.500A) Processing helix chain 'O' and resid 518 through 523 removed outlier: 3.930A pdb=" N ASN O 523 " --> pdb=" O GLU O 519 " (cutoff:3.500A) Processing helix chain 'O' and resid 532 through 543 Processing helix chain 'O' and resid 572 through 591 removed outlier: 3.569A pdb=" N PHE O 576 " --> pdb=" O HIS O 572 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE O 590 " --> pdb=" O ALA O 586 " (cutoff:3.500A) Processing helix chain 'O' and resid 629 through 649 removed outlier: 4.107A pdb=" N ARG O 633 " --> pdb=" O MET O 629 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL O 637 " --> pdb=" O ARG O 633 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE O 638 " --> pdb=" O GLU O 634 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG O 643 " --> pdb=" O ALA O 639 " (cutoff:3.500A) Processing helix chain 'O' and resid 650 through 653 removed outlier: 3.744A pdb=" N MET O 653 " --> pdb=" O VAL O 650 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 650 through 653' Processing helix chain 'P' and resid 172 through 191 removed outlier: 3.941A pdb=" N ASN P 176 " --> pdb=" O ILE P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 201 through 209 Processing helix chain 'P' and resid 219 through 227 Processing helix chain 'P' and resid 239 through 248 Processing helix chain 'P' and resid 265 through 271 removed outlier: 3.621A pdb=" N MET P 271 " --> pdb=" O SER P 267 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 68 removed outlier: 3.673A pdb=" N ALA Q 55 " --> pdb=" O GLU Q 51 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 removed outlier: 6.386A pdb=" N GLU A 3 " --> pdb=" O ILE G 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 19 removed outlier: 5.138A pdb=" N ILE A 13 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLU B1144 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY A 15 " --> pdb=" O ARG B1142 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG B1142 " --> pdb=" O GLY A 15 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 30 through 33 removed outlier: 6.882A pdb=" N HIS A 83 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU A 33 " --> pdb=" O HIS A 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 85 through 90 removed outlier: 12.023A pdb=" N LEU A 88 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N TYR A 260 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 163 through 166 Processing sheet with id=AA6, first strand: chain 'A' and resid 371 through 372 removed outlier: 4.110A pdb=" N LYS A 371 " --> pdb=" O LEU B1062 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1036 through 1038 removed outlier: 3.591A pdb=" N LYS A 491 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG A 499 " --> pdb=" O ALA A 393 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N PHE A 498 " --> pdb=" O ARG A 378 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL A 380 " --> pdb=" O PHE A 498 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU A 500 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N SER A 382 " --> pdb=" O LEU A 500 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 404 through 407 removed outlier: 4.198A pdb=" N TYR A 432 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 570 through 571 Processing sheet with id=AB1, first strand: chain 'A' and resid 627 through 628 removed outlier: 6.210A pdb=" N ILE A 653 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 897 through 898 removed outlier: 3.752A pdb=" N SER A 897 " --> pdb=" O ARG A 905 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N VAL A 904 " --> pdb=" O VAL A 912 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 912 " --> pdb=" O VAL A 904 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1281 through 1285 removed outlier: 3.648A pdb=" N THR A1315 " --> pdb=" O ASN A1142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1176 through 1178 Processing sheet with id=AB5, first strand: chain 'F' and resid 132 through 135 Processing sheet with id=AB6, first strand: chain 'B' and resid 95 through 100 removed outlier: 6.582A pdb=" N ASP B 132 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE B 98 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N TYR B 130 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL B 100 " --> pdb=" O PRO B 128 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY B 150 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL B 131 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N GLU B 148 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ILE B 133 " --> pdb=" O ASP B 146 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ASP B 146 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N TYR B 135 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N HIS B 144 " --> pdb=" O TYR B 135 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AB8, first strand: chain 'B' and resid 375 through 378 removed outlier: 6.067A pdb=" N VAL B 196 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 205 through 208 removed outlier: 3.617A pdb=" N ILE B 206 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 519 through 520 Processing sheet with id=AC2, first strand: chain 'B' and resid 519 through 520 Processing sheet with id=AC3, first strand: chain 'B' and resid 560 through 561 removed outlier: 5.952A pdb=" N GLY B 554 " --> pdb=" O VAL B 599 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ILE B 601 " --> pdb=" O GLY B 554 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N TYR B 556 " --> pdb=" O ILE B 601 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 724 through 728 removed outlier: 3.529A pdb=" N GLU B 786 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA B 894 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN B 883 " --> pdb=" O LEU B 899 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG B 901 " --> pdb=" O ILE B 881 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ILE B 881 " --> pdb=" O ARG B 901 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ASN B 903 " --> pdb=" O SER B 879 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N SER B 879 " --> pdb=" O ASN B 903 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 724 through 728 removed outlier: 3.529A pdb=" N GLU B 786 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA B 894 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN B 883 " --> pdb=" O LEU B 899 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG B 901 " --> pdb=" O ILE B 881 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ILE B 881 " --> pdb=" O ARG B 901 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ASN B 903 " --> pdb=" O SER B 879 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N SER B 879 " --> pdb=" O ASN B 903 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1001 through 1002 removed outlier: 4.016A pdb=" N GLN B1025 " --> pdb=" O SER B 913 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU B 771 " --> pdb=" O GLY B 923 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE B 925 " --> pdb=" O LEU B 771 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU B 773 " --> pdb=" O ILE B 925 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL B 772 " --> pdb=" O ILE B 943 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 943 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA B 758 " --> pdb=" O ILE B 942 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE B1018 " --> pdb=" O VAL B 759 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 841 through 843 removed outlier: 4.235A pdb=" N ILE B 843 " --> pdb=" O VAL B 871 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 846 through 848 Processing sheet with id=AC9, first strand: chain 'B' and resid 1089 through 1095 Processing sheet with id=AD1, first strand: chain 'C' and resid 41 through 47 removed outlier: 3.776A pdb=" N GLU C 41 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU C 47 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 10.434A pdb=" N ARG C 293 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 10.102A pdb=" N ASN C 234 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 10.344A pdb=" N ARG C 295 " --> pdb=" O GLN C 232 " (cutoff:3.500A) removed outlier: 11.724A pdb=" N GLN C 232 " --> pdb=" O ARG C 295 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N HIS C 297 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU C 230 " --> pdb=" O HIS C 297 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER C 226 " --> pdb=" O ASN C 301 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.632A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR C 82 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C 83 " --> pdb=" O PHE L 67 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE C 85 " --> pdb=" O VAL L 65 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL L 65 " --> pdb=" O PHE C 85 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 106 through 107 removed outlier: 3.878A pdb=" N VAL C 185 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AD5, first strand: chain 'D' and resid 3 through 5 removed outlier: 3.505A pdb=" N GLU D 5 " --> pdb=" O LYS G 6 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 107 through 110 removed outlier: 3.626A pdb=" N GLY E 108 " --> pdb=" O THR E 131 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 152 through 155 removed outlier: 4.110A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE E 199 " --> pdb=" O LYS E 152 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 3 through 4 removed outlier: 3.912A pdb=" N LEU G 44 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AE1, first strand: chain 'G' and resid 51 through 52 Processing sheet with id=AE2, first strand: chain 'G' and resid 84 through 86 Processing sheet with id=AE3, first strand: chain 'G' and resid 88 through 91 removed outlier: 7.972A pdb=" N LYS G 98 " --> pdb=" O SER G 90 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 153 through 154 removed outlier: 3.833A pdb=" N VAL G 154 " --> pdb=" O ALA G 195 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ALA G 195 " --> pdb=" O VAL G 154 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'H' and resid 95 through 96 removed outlier: 6.825A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU H 121 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 14 through 17 removed outlier: 3.766A pdb=" N VAL I 21 " --> pdb=" O GLY I 17 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 47 through 48 removed outlier: 3.611A pdb=" N GLN K 64 " --> pdb=" O LYS K 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 76 through 77 removed outlier: 6.307A pdb=" N LYS M 77 " --> pdb=" O LEU M 170 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE M 162 " --> pdb=" O TYR M 169 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL N 306 " --> pdb=" O ILE N 416 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 84 through 87 removed outlier: 4.608A pdb=" N SER M 84 " --> pdb=" O ILE N 399 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ALA N 396 " --> pdb=" O LEU N 408 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU N 408 " --> pdb=" O ALA N 396 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N SER N 398 " --> pdb=" O ALA N 406 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 119 through 122 removed outlier: 3.583A pdb=" N ILE M 121 " --> pdb=" O LEU M 148 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 153 through 154 removed outlier: 3.643A pdb=" N VAL M 153 " --> pdb=" O VAL M 176 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL M 176 " --> pdb=" O VAL M 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'O' and resid 104 through 109 Processing sheet with id=AF4, first strand: chain 'O' and resid 200 through 202 Processing sheet with id=AF5, first strand: chain 'O' and resid 548 through 552 1094 hydrogen bonds defined for protein. 3063 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.84 Time building geometry restraints manager: 14.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12413 1.34 - 1.46: 7858 1.46 - 1.58: 18407 1.58 - 1.70: 0 1.70 - 1.82: 337 Bond restraints: 39015 Sorted by residual: bond pdb=" C PHE Q 36 " pdb=" N PRO Q 37 " ideal model delta sigma weight residual 1.333 1.380 -0.047 1.01e-02 9.80e+03 2.16e+01 bond pdb=" C LEU A 88 " pdb=" N PRO A 89 " ideal model delta sigma weight residual 1.330 1.367 -0.037 1.19e-02 7.06e+03 9.61e+00 bond pdb=" C GLY P 201 " pdb=" N PRO P 202 " ideal model delta sigma weight residual 1.331 1.364 -0.033 1.20e-02 6.94e+03 7.38e+00 bond pdb=" C VAL E 124 " pdb=" N PRO E 125 " ideal model delta sigma weight residual 1.334 1.391 -0.057 2.34e-02 1.83e+03 6.01e+00 bond pdb=" C PRO E 128 " pdb=" N PRO E 129 " ideal model delta sigma weight residual 1.334 1.387 -0.053 2.34e-02 1.83e+03 5.21e+00 ... (remaining 39010 not shown) Histogram of bond angle deviations from ideal: 90.66 - 99.47: 11 99.47 - 108.28: 1835 108.28 - 117.10: 25888 117.10 - 125.91: 24362 125.91 - 134.72: 589 Bond angle restraints: 52685 Sorted by residual: angle pdb=" N LEU N 409 " pdb=" CA LEU N 409 " pdb=" C LEU N 409 " ideal model delta sigma weight residual 110.80 90.66 20.14 2.13e+00 2.20e-01 8.94e+01 angle pdb=" C GLY O 198 " pdb=" N TYR O 199 " pdb=" CA TYR O 199 " ideal model delta sigma weight residual 120.82 129.53 -8.71 1.50e+00 4.44e-01 3.37e+01 angle pdb=" C SER B 889 " pdb=" N ASP B 890 " pdb=" CA ASP B 890 " ideal model delta sigma weight residual 120.82 129.43 -8.61 1.50e+00 4.44e-01 3.30e+01 angle pdb=" C GLY K 58 " pdb=" N THR K 59 " pdb=" CA THR K 59 " ideal model delta sigma weight residual 121.31 129.71 -8.40 1.49e+00 4.50e-01 3.18e+01 angle pdb=" C GLY N 410 " pdb=" N ARG N 411 " pdb=" CA ARG N 411 " ideal model delta sigma weight residual 121.54 132.29 -10.75 1.91e+00 2.74e-01 3.17e+01 ... (remaining 52680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 22547 17.29 - 34.57: 1132 34.57 - 51.86: 234 51.86 - 69.15: 18 69.15 - 86.44: 25 Dihedral angle restraints: 23956 sinusoidal: 9878 harmonic: 14078 Sorted by residual: dihedral pdb=" CA GLU P 308 " pdb=" C GLU P 308 " pdb=" N VAL P 309 " pdb=" CA VAL P 309 " ideal model delta harmonic sigma weight residual -180.00 -93.56 -86.44 0 5.00e+00 4.00e-02 2.99e+02 dihedral pdb=" CA LYS P 307 " pdb=" C LYS P 307 " pdb=" N GLU P 308 " pdb=" CA GLU P 308 " ideal model delta harmonic sigma weight residual -180.00 -113.62 -66.38 0 5.00e+00 4.00e-02 1.76e+02 dihedral pdb=" CA LYS B 583 " pdb=" C LYS B 583 " pdb=" N VAL B 584 " pdb=" CA VAL B 584 " ideal model delta harmonic sigma weight residual -180.00 -123.56 -56.44 0 5.00e+00 4.00e-02 1.27e+02 ... (remaining 23953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 5208 0.086 - 0.173: 689 0.173 - 0.259: 54 0.259 - 0.346: 8 0.346 - 0.432: 1 Chirality restraints: 5960 Sorted by residual: chirality pdb=" CB ILE A 551 " pdb=" CA ILE A 551 " pdb=" CG1 ILE A 551 " pdb=" CG2 ILE A 551 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.67e+00 chirality pdb=" CA LEU N 409 " pdb=" N LEU N 409 " pdb=" C LEU N 409 " pdb=" CB LEU N 409 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CB VAL B 888 " pdb=" CA VAL B 888 " pdb=" CG1 VAL B 888 " pdb=" CG2 VAL B 888 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 5957 not shown) Planarity restraints: 6778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS O 236 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C LYS O 236 " 0.055 2.00e-02 2.50e+03 pdb=" O LYS O 236 " -0.021 2.00e-02 2.50e+03 pdb=" N LYS O 237 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS L 28 " -0.014 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" C LYS L 28 " 0.051 2.00e-02 2.50e+03 pdb=" O LYS L 28 " -0.019 2.00e-02 2.50e+03 pdb=" N TYR L 29 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN O 43 " -0.047 5.00e-02 4.00e+02 7.10e-02 8.06e+00 pdb=" N PRO O 44 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO O 44 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO O 44 " -0.039 5.00e-02 4.00e+02 ... (remaining 6775 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 56 2.41 - 3.03: 19200 3.03 - 3.65: 56018 3.65 - 4.28: 80136 4.28 - 4.90: 133566 Nonbonded interactions: 288976 Sorted by model distance: nonbonded pdb=" O GLU D 139 " pdb=" O GLU D 140 " model vdw 1.787 3.040 nonbonded pdb=" O ALA D 143 " pdb=" N PHE D 145 " model vdw 1.792 2.520 nonbonded pdb=" NZ LYS A 232 " pdb=" O TRP P 315 " model vdw 1.829 2.520 nonbonded pdb=" CE1 TYR D 135 " pdb=" CA ASP D 142 " model vdw 2.228 3.770 nonbonded pdb=" O LEU E 123 " pdb=" OG SER E 126 " model vdw 2.269 2.440 ... (remaining 288971 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.030 Extract box with map and model: 8.220 Check model and map are aligned: 0.550 Set scattering table: 0.370 Process input model: 98.950 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.140 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0571 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 : 0.004 0.073 39015 Z= 0.280 Angle : 1.042 20.142 52685 Z= 0.546 Chirality : 0.059 0.432 5960 Planarity : 0.007 0.071 6778 Dihedral : 11.347 86.436 14842 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.52 % Allowed : 12.97 % Favored : 86.51 % Rotamer: Outliers : 0.40 % Allowed : 6.28 % Favored : 93.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.96 % Twisted General : 0.57 % 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: -5.22 (0.09), residues: 4765 helix: -3.85 (0.07), residues: 1554 sheet: -2.18 (0.21), residues: 502 loop : -3.62 (0.09), residues: 2709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 88 HIS 0.012 0.002 HIS B 947 PHE 0.041 0.002 PHE D 145 TYR 0.028 0.002 TYR B1103 ARG 0.010 0.001 ARG B 915 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 614 time to evaluate : 4.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 613 LEU cc_start: 0.0319 (pp) cc_final: -0.0177 (pp) REVERT: A 1032 LEU cc_start: 0.1190 (OUTLIER) cc_final: 0.0868 (tp) REVERT: B 269 MET cc_start: 0.0825 (tpt) cc_final: 0.0261 (ppp) REVERT: D 156 ILE cc_start: 0.4417 (OUTLIER) cc_final: 0.3378 (tt) REVERT: F 151 LEU cc_start: -0.0418 (mt) cc_final: -0.0779 (mt) REVERT: L 40 LEU cc_start: 0.4339 (pp) cc_final: 0.3167 (pp) REVERT: M 77 LYS cc_start: 0.5668 (mppt) cc_final: 0.5062 (tptt) REVERT: M 226 ARG cc_start: 0.3925 (pmm150) cc_final: 0.3675 (ptt-90) REVERT: P 263 VAL cc_start: -0.0018 (OUTLIER) cc_final: -0.0408 (p) REVERT: Q 66 LYS cc_start: 0.4236 (ttmm) cc_final: 0.3786 (mmtt) outliers start: 17 outliers final: 3 residues processed: 631 average time/residue: 0.5721 time to fit residues: 580.1893 Evaluate side-chains 343 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 337 time to evaluate : 4.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain N residue 409 LEU Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 312 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 401 optimal weight: 3.9990 chunk 360 optimal weight: 0.9990 chunk 200 optimal weight: 0.0470 chunk 123 optimal weight: 6.9990 chunk 243 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 373 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 chunk 226 optimal weight: 0.8980 chunk 277 optimal weight: 5.9990 chunk 432 optimal weight: 0.9990 overall best weight: 0.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 125 HIS A 229 ASN ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 HIS A 578 GLN A 589 HIS A 643 ASN A 805 ASN A 948 ASN A 990 ASN A1174 GLN A1218 GLN A1254 ASN ** A1262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1346 HIS ** A1354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1419 GLN A1453 ASN B 39 ASN B 159 ASN ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN B 286 ASN B 300 GLN B 362 ASN B 396 ASN B 626 HIS B 774 ASN B 801 HIS B 861 ASN B 880 HIS B 893 GLN ** B 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1025 GLN B1049 GLN C 137 ASN C 143 ASN C 161 HIS C 207 HIS C 323 ASN D 61 ASN D 71 ASN E 5 ASN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN E 136 ASN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN H 33 GLN H 128 ASN ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 155 ASN M 158 GLN M 190 ASN ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 298 ASN O 143 GLN ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 202 GLN O 225 ASN O 244 ASN O 254 ASN O 362 ASN O 464 ASN O 469 ASN O 544 ASN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1173 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 39015 Z= 0.213 Angle : 0.729 14.367 52685 Z= 0.374 Chirality : 0.046 0.500 5960 Planarity : 0.006 0.080 6778 Dihedral : 6.517 84.636 5237 Min Nonbonded Distance : 1.657 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.82 % Favored : 87.76 % Rotamer: Outliers : 1.92 % Allowed : 9.87 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.37 % 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: -4.17 (0.10), residues: 4765 helix: -2.40 (0.11), residues: 1587 sheet: -1.76 (0.22), residues: 513 loop : -3.34 (0.10), residues: 2665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 119 HIS 0.015 0.001 HIS B 244 PHE 0.024 0.002 PHE D 103 TYR 0.033 0.002 TYR P 249 ARG 0.008 0.001 ARG O 643 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 399 time to evaluate : 4.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.0077 (OUTLIER) cc_final: -0.1452 (mt) REVERT: A 145 LEU cc_start: 0.1858 (mp) cc_final: 0.0845 (mp) REVERT: A 273 MET cc_start: 0.2081 (ppp) cc_final: 0.1782 (ppp) REVERT: A 416 LEU cc_start: 0.4162 (OUTLIER) cc_final: 0.3806 (mt) REVERT: A 599 LYS cc_start: 0.4652 (tptp) cc_final: 0.4126 (mttp) REVERT: A 735 TYR cc_start: 0.0413 (m-80) cc_final: -0.0899 (m-80) REVERT: A 1095 GLN cc_start: 0.3092 (mt0) cc_final: 0.2602 (mt0) REVERT: A 1260 MET cc_start: 0.1535 (mmt) cc_final: 0.1165 (tmm) REVERT: B 245 ASN cc_start: 0.4945 (OUTLIER) cc_final: 0.4660 (t0) REVERT: B 269 MET cc_start: 0.1010 (tpt) cc_final: 0.0245 (ppp) REVERT: B 283 PHE cc_start: 0.1487 (t80) cc_final: 0.1211 (t80) REVERT: B 317 LEU cc_start: 0.3701 (OUTLIER) cc_final: 0.3499 (tt) REVERT: B 360 MET cc_start: 0.4236 (mmt) cc_final: 0.3780 (mmt) REVERT: B 470 MET cc_start: 0.3513 (mmp) cc_final: 0.2056 (mmp) REVERT: B 728 MET cc_start: 0.2569 (tpp) cc_final: 0.1121 (ttm) REVERT: B 958 MET cc_start: 0.0186 (tpp) cc_final: -0.0236 (mmp) REVERT: B 1035 MET cc_start: 0.0881 (ppp) cc_final: 0.0653 (tmm) REVERT: D 153 MET cc_start: 0.0844 (ppp) cc_final: 0.0305 (ttp) REVERT: E 50 MET cc_start: 0.1510 (ppp) cc_final: 0.0685 (ptt) REVERT: E 75 MET cc_start: 0.3393 (ppp) cc_final: 0.2539 (mtm) REVERT: F 115 THR cc_start: -0.1209 (OUTLIER) cc_final: -0.1437 (p) REVERT: H 146 ARG cc_start: -0.0426 (ttm110) cc_final: -0.2715 (ttm170) REVERT: I 1 MET cc_start: 0.0773 (ptm) cc_final: 0.0468 (tpp) REVERT: M 77 LYS cc_start: 0.6196 (mppt) cc_final: 0.5464 (tptp) REVERT: M 226 ARG cc_start: 0.3872 (pmm150) cc_final: 0.3525 (ptt-90) REVERT: P 263 VAL cc_start: -0.0360 (OUTLIER) cc_final: -0.0656 (p) REVERT: Q 56 VAL cc_start: 0.4186 (t) cc_final: 0.2891 (p) REVERT: Q 66 LYS cc_start: 0.4754 (ttmm) cc_final: 0.4172 (mmtt) outliers start: 82 outliers final: 38 residues processed: 459 average time/residue: 0.4767 time to fit residues: 366.8302 Evaluate side-chains 370 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 326 time to evaluate : 4.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1065 MET Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 140 PHE Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain M residue 141 ASN Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 252 ILE Chi-restraints excluded: chain O residue 468 LEU Chi-restraints excluded: chain O residue 522 ILE Chi-restraints excluded: chain O residue 641 LEU Chi-restraints excluded: chain P residue 193 ASN Chi-restraints excluded: chain P residue 197 ASN Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 312 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 240 optimal weight: 0.0040 chunk 134 optimal weight: 4.9990 chunk 359 optimal weight: 10.0000 chunk 294 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 433 optimal weight: 4.9990 chunk 467 optimal weight: 10.0000 chunk 385 optimal weight: 0.7980 chunk 429 optimal weight: 1.9990 chunk 147 optimal weight: 0.0770 chunk 347 optimal weight: 6.9990 overall best weight: 1.5754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 386 ASN A 488 HIS A 520 HIS ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 HIS A 815 GLN A1021 ASN A1218 GLN A1262 GLN B 159 ASN ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN B 396 ASN B 519 HIS B 552 ASN ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 GLN B 753 GLN ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 837 GLN B 893 GLN ** B1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN C 248 GLN D 27 HIS D 56 GLN ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 123 ASN O 207 HIS O 584 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2418 moved from start: 0.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.148 39015 Z= 0.331 Angle : 0.922 14.249 52685 Z= 0.474 Chirality : 0.052 0.314 5960 Planarity : 0.007 0.111 6778 Dihedral : 6.881 82.925 5231 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.47 % Favored : 86.21 % Rotamer: Outliers : 3.89 % Allowed : 12.08 % Favored : 84.03 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.41 % 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: -3.72 (0.10), residues: 4765 helix: -1.91 (0.11), residues: 1543 sheet: -1.48 (0.22), residues: 474 loop : -3.13 (0.10), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP M 119 HIS 0.035 0.003 HIS A 80 PHE 0.080 0.003 PHE H 118 TYR 0.033 0.003 TYR B1073 ARG 0.015 0.001 ARG A 703 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 472 time to evaluate : 4.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 VAL cc_start: 0.6152 (t) cc_final: 0.4696 (m) REVERT: A 145 LEU cc_start: 0.2078 (OUTLIER) cc_final: 0.1266 (mt) REVERT: A 273 MET cc_start: 0.2050 (ppp) cc_final: 0.1725 (ppp) REVERT: A 295 THR cc_start: 0.6621 (t) cc_final: 0.6235 (m) REVERT: A 325 MET cc_start: 0.2457 (ppp) cc_final: 0.0552 (tpp) REVERT: A 416 LEU cc_start: 0.5744 (OUTLIER) cc_final: 0.5079 (mt) REVERT: A 449 ARG cc_start: 0.5021 (ptt-90) cc_final: 0.4643 (mmp80) REVERT: A 599 LYS cc_start: 0.5566 (tptp) cc_final: 0.4854 (mttp) REVERT: A 617 ASN cc_start: 0.2709 (OUTLIER) cc_final: 0.2175 (p0) REVERT: A 626 LEU cc_start: 0.1807 (OUTLIER) cc_final: -0.1364 (tp) REVERT: A 789 ASN cc_start: 0.3583 (OUTLIER) cc_final: 0.3368 (m110) REVERT: A 946 THR cc_start: 0.2613 (m) cc_final: 0.2335 (p) REVERT: A 1114 VAL cc_start: 0.0069 (OUTLIER) cc_final: -0.0425 (t) REVERT: A 1293 LEU cc_start: 0.1960 (OUTLIER) cc_final: 0.1513 (mm) REVERT: A 1328 ILE cc_start: 0.0918 (OUTLIER) cc_final: 0.0226 (pt) REVERT: A 1369 LEU cc_start: 0.2662 (OUTLIER) cc_final: 0.2440 (pt) REVERT: B 73 LEU cc_start: 0.3746 (OUTLIER) cc_final: 0.2961 (tp) REVERT: B 251 ILE cc_start: 0.4204 (OUTLIER) cc_final: 0.3618 (mp) REVERT: B 269 MET cc_start: 0.1836 (tpt) cc_final: 0.0962 (ppp) REVERT: B 317 LEU cc_start: 0.4103 (OUTLIER) cc_final: 0.3534 (tt) REVERT: B 320 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.6390 (tp) REVERT: B 439 THR cc_start: 0.5862 (m) cc_final: 0.4285 (t) REVERT: B 449 MET cc_start: 0.0301 (mmt) cc_final: 0.0053 (tpp) REVERT: B 517 MET cc_start: -0.1119 (ptp) cc_final: -0.1569 (mmp) REVERT: B 597 MET cc_start: 0.5231 (tmm) cc_final: 0.4965 (tpp) REVERT: B 727 LEU cc_start: 0.4416 (mt) cc_final: 0.3482 (mp) REVERT: B 1084 MET cc_start: 0.2378 (mmm) cc_final: 0.2122 (mtm) REVERT: C 198 PRO cc_start: 0.6626 (Cg_endo) cc_final: 0.6194 (Cg_exo) REVERT: D 69 ASN cc_start: 0.5494 (OUTLIER) cc_final: 0.5246 (t0) REVERT: D 131 MET cc_start: 0.1045 (mmm) cc_final: 0.0822 (mmm) REVERT: E 50 MET cc_start: 0.2080 (ppp) cc_final: 0.1220 (ptt) REVERT: E 52 ARG cc_start: 0.3745 (ptp-170) cc_final: 0.3060 (mmm160) REVERT: E 215 MET cc_start: 0.3054 (mmp) cc_final: 0.2593 (mtt) REVERT: F 103 MET cc_start: 0.3802 (tpt) cc_final: 0.3539 (tpp) REVERT: G 114 MET cc_start: 0.6873 (mmt) cc_final: 0.5753 (ptt) REVERT: G 207 LEU cc_start: 0.1397 (OUTLIER) cc_final: 0.1157 (tt) REVERT: H 146 ARG cc_start: 0.0458 (ttm110) cc_final: -0.2370 (ttm170) REVERT: J 49 MET cc_start: 0.3637 (tpp) cc_final: 0.2608 (tpp) REVERT: K 103 ILE cc_start: 0.4575 (tt) cc_final: 0.4244 (tt) REVERT: N 305 MET cc_start: 0.5908 (mpp) cc_final: 0.5154 (tmm) REVERT: O 368 ARG cc_start: 0.4995 (tpm170) cc_final: 0.4255 (tpt170) outliers start: 166 outliers final: 74 residues processed: 589 average time/residue: 0.4910 time to fit residues: 479.1148 Evaluate side-chains 458 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 369 time to evaluate : 4.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 617 ASN Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 789 ASN Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1328 ILE Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 765 TYR Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 931 MET Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1065 MET Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 125 ASN Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 162 PHE Chi-restraints excluded: chain M residue 259 ILE Chi-restraints excluded: chain N residue 286 ASP Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 207 HIS Chi-restraints excluded: chain O residue 247 THR Chi-restraints excluded: chain O residue 263 LEU Chi-restraints excluded: chain O residue 468 LEU Chi-restraints excluded: chain O residue 503 SER Chi-restraints excluded: chain O residue 575 ASN Chi-restraints excluded: chain O residue 641 LEU Chi-restraints excluded: chain P residue 186 ILE Chi-restraints excluded: chain P residue 197 ASN Chi-restraints excluded: chain P residue 215 TYR Chi-restraints excluded: chain P residue 312 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 427 optimal weight: 8.9990 chunk 325 optimal weight: 0.7980 chunk 224 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 206 optimal weight: 0.8980 chunk 290 optimal weight: 3.9990 chunk 434 optimal weight: 8.9990 chunk 460 optimal weight: 10.0000 chunk 227 optimal weight: 1.9990 chunk 411 optimal weight: 1.9990 chunk 123 optimal weight: 0.0270 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 HIS B 61 HIS B 197 GLN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 ASN ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 GLN ** B1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1130 GLN ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN C 248 GLN ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 GLN ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 95 HIS M 167 GLN N 287 HIS ** O 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 193 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2584 moved from start: 0.6312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 39015 Z= 0.200 Angle : 0.716 17.276 52685 Z= 0.362 Chirality : 0.046 0.215 5960 Planarity : 0.005 0.081 6778 Dihedral : 6.165 79.162 5229 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.56 % Favored : 88.14 % Rotamer: Outliers : 2.56 % Allowed : 14.70 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.35 % 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: -3.24 (0.11), residues: 4765 helix: -1.31 (0.12), residues: 1569 sheet: -1.29 (0.23), residues: 474 loop : -2.97 (0.10), residues: 2722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 88 HIS 0.019 0.001 HIS O 207 PHE 0.030 0.002 PHE H 118 TYR 0.027 0.001 TYR P 249 ARG 0.016 0.001 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 429 time to evaluate : 3.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 VAL cc_start: 0.6078 (t) cc_final: 0.4604 (m) REVERT: A 215 VAL cc_start: 0.0327 (OUTLIER) cc_final: 0.0046 (p) REVERT: A 219 MET cc_start: 0.0141 (ttt) cc_final: -0.1712 (mtp) REVERT: A 273 MET cc_start: 0.2291 (ppp) cc_final: 0.1983 (ppp) REVERT: A 295 THR cc_start: 0.6465 (t) cc_final: 0.6131 (m) REVERT: A 325 MET cc_start: 0.2413 (ppp) cc_final: 0.0371 (tpp) REVERT: A 449 ARG cc_start: 0.4839 (ptt-90) cc_final: 0.4486 (mmp-170) REVERT: A 450 MET cc_start: 0.3719 (ptt) cc_final: 0.1500 (mmm) REVERT: A 599 LYS cc_start: 0.5689 (tptp) cc_final: 0.4730 (mttp) REVERT: A 717 VAL cc_start: 0.2214 (OUTLIER) cc_final: 0.1965 (t) REVERT: A 1114 VAL cc_start: 0.0527 (OUTLIER) cc_final: 0.0077 (t) REVERT: A 1296 GLU cc_start: 0.4270 (tt0) cc_final: 0.4043 (tt0) REVERT: A 1362 MET cc_start: 0.2240 (tpp) cc_final: 0.1509 (tpp) REVERT: B 73 LEU cc_start: 0.3400 (OUTLIER) cc_final: 0.2902 (tp) REVERT: B 251 ILE cc_start: 0.4408 (OUTLIER) cc_final: 0.3903 (mp) REVERT: B 269 MET cc_start: 0.1676 (tpt) cc_final: 0.0891 (ppp) REVERT: B 317 LEU cc_start: 0.4025 (OUTLIER) cc_final: 0.3339 (tt) REVERT: B 320 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.6465 (tt) REVERT: B 356 VAL cc_start: 0.3368 (OUTLIER) cc_final: 0.2267 (p) REVERT: B 439 THR cc_start: 0.6419 (m) cc_final: 0.5011 (t) REVERT: B 449 MET cc_start: 0.0281 (mmt) cc_final: 0.0030 (tpp) REVERT: B 470 MET cc_start: 0.4607 (mmp) cc_final: 0.4259 (mmt) REVERT: B 597 MET cc_start: 0.5398 (tmm) cc_final: 0.5106 (tpp) REVERT: B 760 MET cc_start: 0.1835 (tmm) cc_final: 0.0470 (ttt) REVERT: B 886 MET cc_start: 0.3629 (tpp) cc_final: 0.2589 (mtp) REVERT: B 990 ILE cc_start: 0.2953 (mt) cc_final: 0.2649 (mt) REVERT: E 50 MET cc_start: 0.1870 (ppp) cc_final: 0.0581 (ptt) REVERT: E 215 MET cc_start: 0.3373 (mmp) cc_final: 0.2792 (mtt) REVERT: G 114 MET cc_start: 0.6851 (mmt) cc_final: 0.5684 (ptt) REVERT: H 102 TYR cc_start: 0.3021 (p90) cc_final: 0.1426 (p90) REVERT: H 146 ARG cc_start: 0.0352 (ttm110) cc_final: -0.1950 (ttm170) REVERT: J 2 ILE cc_start: 0.2327 (OUTLIER) cc_final: 0.1023 (mt) REVERT: K 81 MET cc_start: 0.3643 (ttt) cc_final: 0.1955 (ttp) REVERT: K 103 ILE cc_start: 0.5105 (tt) cc_final: 0.4831 (tt) REVERT: K 125 MET cc_start: 0.4020 (mmp) cc_final: 0.3142 (mmp) REVERT: M 190 ASN cc_start: 0.3040 (OUTLIER) cc_final: 0.2435 (m110) REVERT: O 263 LEU cc_start: 0.0022 (OUTLIER) cc_final: -0.0824 (tm) REVERT: O 368 ARG cc_start: 0.5348 (tpm170) cc_final: 0.4672 (tpt170) outliers start: 109 outliers final: 63 residues processed: 512 average time/residue: 0.4883 time to fit residues: 416.9397 Evaluate side-chains 451 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 377 time to evaluate : 4.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 441 ASN Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 1047 THR Chi-restraints excluded: chain B residue 1065 MET Chi-restraints excluded: chain B residue 1080 LEU Chi-restraints excluded: chain B residue 1114 GLU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 88 TRP Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 190 ASN Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 263 LEU Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 468 LEU Chi-restraints excluded: chain O residue 498 SER Chi-restraints excluded: chain O residue 500 LEU Chi-restraints excluded: chain O residue 503 SER Chi-restraints excluded: chain O residue 641 LEU Chi-restraints excluded: chain P residue 181 ILE Chi-restraints excluded: chain P residue 193 ASN Chi-restraints excluded: chain P residue 215 TYR Chi-restraints excluded: chain P residue 312 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 383 optimal weight: 0.8980 chunk 261 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 342 optimal weight: 10.0000 chunk 189 optimal weight: 3.9990 chunk 392 optimal weight: 0.9990 chunk 318 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 234 optimal weight: 4.9990 chunk 412 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 208 ASN A 367 ASN A 555 GLN ** A 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 ASN A1197 GLN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 ASN ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 GLN B 997 ASN B1025 GLN B1130 GLN ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN C 175 GLN D 61 ASN ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN H 33 GLN ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 123 ASN O 337 GLN O 584 ASN ** P 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3461 moved from start: 0.8238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.138 39015 Z= 0.309 Angle : 0.831 19.336 52685 Z= 0.431 Chirality : 0.049 0.463 5960 Planarity : 0.006 0.113 6778 Dihedral : 6.313 75.365 5229 Min Nonbonded Distance : 1.228 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.29 % Allowed : 13.87 % Favored : 85.83 % Rotamer: Outliers : 3.49 % Allowed : 15.94 % Favored : 80.56 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.33 % 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: -3.18 (0.11), residues: 4765 helix: -1.16 (0.13), residues: 1539 sheet: -1.35 (0.22), residues: 505 loop : -2.97 (0.11), residues: 2721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 442 HIS 0.017 0.002 HIS A 589 PHE 0.043 0.002 PHE A 852 TYR 0.027 0.002 TYR P 249 ARG 0.013 0.001 ARG O 578 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 501 time to evaluate : 4.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.0871 (ttt) cc_final: -0.1149 (mtp) REVERT: A 325 MET cc_start: 0.2839 (ppp) cc_final: 0.0754 (tpp) REVERT: A 519 LEU cc_start: 0.5743 (tt) cc_final: 0.5299 (tt) REVERT: A 521 VAL cc_start: 0.6010 (m) cc_final: 0.4677 (t) REVERT: A 599 LYS cc_start: 0.6023 (tptp) cc_final: 0.5151 (ttmt) REVERT: A 946 THR cc_start: 0.3576 (m) cc_final: 0.3296 (p) REVERT: A 1114 VAL cc_start: 0.0311 (OUTLIER) cc_final: -0.0193 (t) REVERT: A 1397 PHE cc_start: 0.5292 (m-80) cc_final: 0.3698 (m-10) REVERT: B 73 LEU cc_start: 0.4009 (OUTLIER) cc_final: 0.3273 (tp) REVERT: B 75 LYS cc_start: 0.6663 (mtpt) cc_final: 0.6424 (mttt) REVERT: B 251 ILE cc_start: 0.4875 (OUTLIER) cc_final: 0.4413 (mp) REVERT: B 269 MET cc_start: 0.1828 (tpt) cc_final: 0.0604 (ppp) REVERT: B 320 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.6345 (tp) REVERT: B 335 LEU cc_start: 0.3147 (OUTLIER) cc_final: 0.2897 (mp) REVERT: B 356 VAL cc_start: 0.3939 (OUTLIER) cc_final: 0.2811 (p) REVERT: B 395 PHE cc_start: 0.2680 (t80) cc_final: 0.2455 (t80) REVERT: B 441 ASN cc_start: 0.4691 (OUTLIER) cc_final: 0.4490 (p0) REVERT: B 470 MET cc_start: 0.5356 (mmp) cc_final: 0.4754 (mmt) REVERT: B 652 ASN cc_start: 0.1066 (OUTLIER) cc_final: -0.1671 (p0) REVERT: C 82 TYR cc_start: 0.5844 (m-10) cc_final: 0.5628 (m-80) REVERT: E 50 MET cc_start: 0.1395 (ppp) cc_final: -0.0015 (ptt) REVERT: E 52 ARG cc_start: 0.3670 (ptp-170) cc_final: 0.2944 (mmm160) REVERT: E 215 MET cc_start: 0.3813 (mmp) cc_final: 0.3262 (mtt) REVERT: G 114 MET cc_start: 0.6735 (mmt) cc_final: 0.5788 (ptt) REVERT: H 102 TYR cc_start: 0.3594 (p90) cc_final: 0.1649 (p90) REVERT: H 123 MET cc_start: 0.5585 (pmm) cc_final: 0.5104 (ptp) REVERT: H 135 LEU cc_start: 0.5792 (OUTLIER) cc_final: 0.5183 (tp) REVERT: J 2 ILE cc_start: 0.4265 (OUTLIER) cc_final: 0.3931 (mt) REVERT: K 81 MET cc_start: 0.3463 (ttt) cc_final: 0.2844 (tmm) REVERT: K 121 LEU cc_start: 0.3078 (tp) cc_final: 0.2719 (mp) REVERT: N 305 MET cc_start: 0.6082 (mpp) cc_final: 0.5280 (tmm) REVERT: O 368 ARG cc_start: 0.5417 (tpm170) cc_final: 0.4771 (tpt170) REVERT: O 496 ILE cc_start: 0.5867 (mp) cc_final: 0.5665 (pt) REVERT: O 537 LEU cc_start: 0.2952 (OUTLIER) cc_final: 0.2750 (tt) REVERT: P 229 GLN cc_start: 0.4297 (mp10) cc_final: 0.3954 (tt0) outliers start: 149 outliers final: 78 residues processed: 602 average time/residue: 0.4832 time to fit residues: 482.7248 Evaluate side-chains 483 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 394 time to evaluate : 3.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 441 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 785 CYS Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 930 ASP Chi-restraints excluded: chain B residue 931 MET Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1065 MET Chi-restraints excluded: chain B residue 1114 GLU Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 125 ASN Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 180 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 140 PHE Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 162 PHE Chi-restraints excluded: chain N residue 286 ASP Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 247 THR Chi-restraints excluded: chain O residue 500 LEU Chi-restraints excluded: chain O residue 537 LEU Chi-restraints excluded: chain O residue 577 MET Chi-restraints excluded: chain P residue 215 TYR Chi-restraints excluded: chain P residue 312 PHE Chi-restraints excluded: chain Q residue 43 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 154 optimal weight: 0.6980 chunk 414 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 270 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 460 optimal weight: 6.9990 chunk 382 optimal weight: 8.9990 chunk 213 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 152 optimal weight: 0.0000 chunk 241 optimal weight: 0.9990 overall best weight: 1.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 125 HIS A 233 GLN A 518 ASN ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 ASN B 456 HIS ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 GLN B 754 ASN B1130 GLN ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN C 234 ASN ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN E 113 GLN ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 178 GLN ** O 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 337 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4491 moved from start: 1.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.141 39015 Z= 0.363 Angle : 0.919 18.105 52685 Z= 0.470 Chirality : 0.053 0.546 5960 Planarity : 0.007 0.124 6778 Dihedral : 6.595 71.770 5229 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.34 % Allowed : 12.38 % Favored : 87.28 % Rotamer: Outliers : 3.75 % Allowed : 17.84 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.33 % 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: -3.32 (0.11), residues: 4765 helix: -1.38 (0.12), residues: 1553 sheet: -1.15 (0.23), residues: 484 loop : -3.05 (0.10), residues: 2728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP J 18 HIS 0.030 0.002 HIS A 156 PHE 0.054 0.003 PHE A 852 TYR 0.044 0.003 TYR P 249 ARG 0.034 0.001 ARG J 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 557 time to evaluate : 4.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.0281 (ttt) cc_final: -0.1449 (mtp) REVERT: A 228 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7744 (tp) REVERT: A 325 MET cc_start: 0.3581 (ppp) cc_final: 0.1173 (tpp) REVERT: A 408 VAL cc_start: 0.7408 (OUTLIER) cc_final: 0.7169 (m) REVERT: A 450 MET cc_start: 0.5341 (ptt) cc_final: 0.5093 (ttp) REVERT: A 659 ILE cc_start: 0.4675 (mp) cc_final: 0.4218 (mt) REVERT: A 664 MET cc_start: 0.6128 (tmm) cc_final: 0.5919 (tmm) REVERT: B 75 LYS cc_start: 0.7120 (mtpt) cc_final: 0.6874 (mttt) REVERT: B 251 ILE cc_start: 0.4894 (OUTLIER) cc_final: 0.4494 (mp) REVERT: B 320 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6298 (tp) REVERT: B 464 ILE cc_start: 0.8213 (tp) cc_final: 0.7960 (tt) REVERT: B 652 ASN cc_start: 0.2819 (OUTLIER) cc_final: 0.2029 (p0) REVERT: B 765 TYR cc_start: 0.6387 (OUTLIER) cc_final: 0.5135 (m-10) REVERT: B 931 MET cc_start: 0.6457 (OUTLIER) cc_final: 0.5334 (mtm) REVERT: B 1033 ASP cc_start: 0.7014 (m-30) cc_final: 0.6774 (m-30) REVERT: C 68 ARG cc_start: 0.7847 (tmm160) cc_final: 0.7488 (tmt170) REVERT: C 320 ILE cc_start: 0.6951 (OUTLIER) cc_final: 0.6680 (mt) REVERT: E 4 GLU cc_start: 0.4594 (mt-10) cc_final: 0.3998 (mm-30) REVERT: E 50 MET cc_start: 0.1352 (ppp) cc_final: 0.0220 (ptt) REVERT: G 26 ILE cc_start: 0.8486 (mt) cc_final: 0.8240 (mt) REVERT: H 102 TYR cc_start: 0.3331 (p90) cc_final: 0.1646 (p90) REVERT: K 65 ILE cc_start: 0.7597 (mp) cc_final: 0.7325 (mp) REVERT: K 81 MET cc_start: 0.2927 (ttt) cc_final: 0.2292 (mmm) REVERT: M 77 LYS cc_start: 0.6080 (mtpp) cc_final: 0.4889 (tptt) REVERT: M 118 LEU cc_start: 0.6998 (mt) cc_final: 0.6795 (mp) REVERT: M 119 TRP cc_start: 0.4606 (OUTLIER) cc_final: 0.3867 (m-10) REVERT: N 398 SER cc_start: 0.6112 (m) cc_final: 0.5361 (p) REVERT: O 368 ARG cc_start: 0.5717 (tpm170) cc_final: 0.5101 (tpt170) REVERT: P 176 ASN cc_start: 0.7018 (t0) cc_final: 0.6283 (t0) REVERT: P 261 TYR cc_start: 0.3323 (OUTLIER) cc_final: 0.2211 (m-80) outliers start: 160 outliers final: 80 residues processed: 675 average time/residue: 0.4849 time to fit residues: 541.6683 Evaluate side-chains 526 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 436 time to evaluate : 4.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain A residue 901 ASP Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 765 TYR Chi-restraints excluded: chain B residue 821 HIS Chi-restraints excluded: chain B residue 847 VAL Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 910 ASP Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 931 MET Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1047 THR Chi-restraints excluded: chain B residue 1065 MET Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain C residue 281 ARG Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 64 ASN Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 119 TRP Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 117 THR Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 204 SER Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain O residue 500 LEU Chi-restraints excluded: chain O residue 577 MET Chi-restraints excluded: chain P residue 181 ILE Chi-restraints excluded: chain P residue 215 TYR Chi-restraints excluded: chain P residue 261 TYR Chi-restraints excluded: chain P residue 312 PHE Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 43 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 444 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 262 optimal weight: 0.4980 chunk 336 optimal weight: 30.0000 chunk 260 optimal weight: 0.6980 chunk 387 optimal weight: 10.0000 chunk 257 optimal weight: 0.9990 chunk 458 optimal weight: 3.9990 chunk 287 optimal weight: 2.9990 chunk 279 optimal weight: 0.5980 chunk 211 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS A 156 HIS A 233 GLN ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 GLN A1354 HIS B 116 HIS B 159 ASN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 GLN ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 287 HIS O 202 GLN Q 44 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4572 moved from start: 1.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 39015 Z= 0.194 Angle : 0.736 14.702 52685 Z= 0.370 Chirality : 0.046 0.292 5960 Planarity : 0.005 0.072 6778 Dihedral : 6.084 73.045 5229 Min Nonbonded Distance : 1.468 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.50 % Favored : 88.21 % Rotamer: Outliers : 2.70 % Allowed : 20.38 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.35 % 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: -2.94 (0.11), residues: 4765 helix: -0.96 (0.13), residues: 1555 sheet: -0.92 (0.24), residues: 477 loop : -2.89 (0.11), residues: 2733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP O 648 HIS 0.011 0.001 HIS A 156 PHE 0.039 0.002 PHE A 91 TYR 0.018 0.001 TYR K 108 ARG 0.009 0.001 ARG B 435 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 510 time to evaluate : 4.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 SER cc_start: 0.7396 (t) cc_final: 0.6989 (p) REVERT: A 219 MET cc_start: 0.0489 (ttt) cc_final: -0.1226 (mtp) REVERT: A 228 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7682 (tp) REVERT: A 325 MET cc_start: 0.3604 (ppp) cc_final: 0.1294 (tpp) REVERT: A 592 ILE cc_start: 0.5571 (mm) cc_final: 0.5360 (mm) REVERT: A 664 MET cc_start: 0.6123 (tmm) cc_final: 0.5362 (ttm) REVERT: B 251 ILE cc_start: 0.4754 (OUTLIER) cc_final: 0.4464 (mp) REVERT: B 269 MET cc_start: 0.2004 (tpt) cc_final: 0.0206 (ppp) REVERT: B 320 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6417 (tp) REVERT: B 385 SER cc_start: 0.6601 (t) cc_final: 0.6401 (t) REVERT: B 464 ILE cc_start: 0.8282 (tp) cc_final: 0.8051 (tt) REVERT: B 607 ARG cc_start: 0.3845 (tpt-90) cc_final: 0.3463 (tpt-90) REVERT: B 1065 MET cc_start: 0.5173 (OUTLIER) cc_final: 0.4942 (mpp) REVERT: B 1067 ARG cc_start: 0.6335 (mmp80) cc_final: 0.5335 (mtm110) REVERT: D 153 MET cc_start: 0.2664 (ppp) cc_final: 0.2334 (ppp) REVERT: E 50 MET cc_start: 0.1293 (ppp) cc_final: -0.0045 (ptt) REVERT: E 52 ARG cc_start: 0.3686 (ptp-170) cc_final: 0.3121 (mmm160) REVERT: G 26 ILE cc_start: 0.8635 (mt) cc_final: 0.8357 (mt) REVERT: H 1 MET cc_start: 0.1515 (ppp) cc_final: 0.1069 (ppp) REVERT: H 102 TYR cc_start: 0.3081 (p90) cc_final: 0.1618 (p90) REVERT: H 123 MET cc_start: 0.6152 (ptp) cc_final: 0.5774 (ptp) REVERT: M 77 LYS cc_start: 0.6046 (mtpp) cc_final: 0.5379 (mmmt) REVERT: M 119 TRP cc_start: 0.4551 (OUTLIER) cc_final: 0.3880 (m-10) REVERT: O 38 GLU cc_start: 0.6364 (pm20) cc_final: 0.5914 (mm-30) REVERT: O 202 GLN cc_start: 0.3110 (OUTLIER) cc_final: 0.2902 (tm-30) REVERT: O 368 ARG cc_start: 0.5654 (tpm170) cc_final: 0.5035 (tpt170) REVERT: O 585 MET cc_start: 0.5648 (mmt) cc_final: 0.5209 (mmt) REVERT: O 589 LEU cc_start: 0.5089 (OUTLIER) cc_final: 0.4868 (mp) REVERT: P 176 ASN cc_start: 0.6889 (t0) cc_final: 0.6187 (t0) REVERT: P 188 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.6995 (mp0) outliers start: 115 outliers final: 78 residues processed: 590 average time/residue: 0.4779 time to fit residues: 473.7364 Evaluate side-chains 530 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 444 time to evaluate : 4.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 589 HIS Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1416 ILE Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 382 GLN Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 804 ASP Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 919 LYS Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1065 MET Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 115 TRP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain C residue 281 ARG Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 125 ASN Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain H residue 64 ASN Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 60 PHE Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain M residue 119 TRP Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 162 PHE Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 117 THR Chi-restraints excluded: chain O residue 133 SER Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 202 GLN Chi-restraints excluded: chain O residue 263 LEU Chi-restraints excluded: chain O residue 460 LEU Chi-restraints excluded: chain O residue 493 GLU Chi-restraints excluded: chain O residue 503 SER Chi-restraints excluded: chain O residue 589 LEU Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain P residue 215 TYR Chi-restraints excluded: chain P residue 312 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 283 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 chunk 274 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 88 optimal weight: 0.0020 chunk 291 optimal weight: 0.1980 chunk 312 optimal weight: 1.9990 chunk 226 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 360 optimal weight: 0.9980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS A 648 ASN A 707 ASN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1130 GLN ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN E 8 ASN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 128 HIS ** P 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4711 moved from start: 1.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 39015 Z= 0.183 Angle : 0.721 16.970 52685 Z= 0.360 Chirality : 0.045 0.290 5960 Planarity : 0.005 0.074 6778 Dihedral : 5.853 71.358 5229 Min Nonbonded Distance : 1.597 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.61 % Favored : 88.12 % Rotamer: Outliers : 2.56 % Allowed : 20.73 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.31 % 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: -2.73 (0.12), residues: 4765 helix: -0.66 (0.13), residues: 1546 sheet: -1.07 (0.23), residues: 513 loop : -2.80 (0.11), residues: 2706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 648 HIS 0.008 0.001 HIS A 92 PHE 0.041 0.002 PHE O 47 TYR 0.020 0.001 TYR P 249 ARG 0.012 0.001 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 493 time to evaluate : 4.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 SER cc_start: 0.7724 (t) cc_final: 0.7386 (p) REVERT: A 219 MET cc_start: 0.0563 (ttt) cc_final: -0.1213 (mtp) REVERT: A 228 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7619 (tp) REVERT: A 325 MET cc_start: 0.3486 (ppp) cc_final: 0.1173 (tpp) REVERT: A 450 MET cc_start: 0.5777 (ptt) cc_final: 0.5458 (ttp) REVERT: A 592 ILE cc_start: 0.5656 (mm) cc_final: 0.5219 (mm) REVERT: A 664 MET cc_start: 0.6086 (tmm) cc_final: 0.5496 (ttm) REVERT: B 269 MET cc_start: 0.2007 (tpt) cc_final: -0.0123 (ppp) REVERT: B 320 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.6432 (tp) REVERT: B 464 ILE cc_start: 0.8298 (tp) cc_final: 0.8067 (tt) REVERT: B 607 ARG cc_start: 0.4143 (tpt-90) cc_final: 0.3535 (tpt-90) REVERT: B 930 ASP cc_start: 0.5679 (m-30) cc_final: 0.4986 (m-30) REVERT: B 1067 ARG cc_start: 0.6552 (mmp80) cc_final: 0.5748 (mtm110) REVERT: C 88 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8215 (p0) REVERT: C 166 ASP cc_start: 0.7806 (t0) cc_final: 0.7500 (t0) REVERT: E 50 MET cc_start: 0.1292 (ppp) cc_final: 0.0104 (ptt) REVERT: F 90 ARG cc_start: 0.7389 (tmm-80) cc_final: 0.7178 (ttp-170) REVERT: F 112 GLU cc_start: 0.6630 (tm-30) cc_final: 0.6135 (tm-30) REVERT: G 26 ILE cc_start: 0.8800 (mt) cc_final: 0.8529 (mt) REVERT: H 97 MET cc_start: -0.0736 (tpp) cc_final: -0.1936 (pmm) REVERT: H 102 TYR cc_start: 0.3179 (p90) cc_final: 0.1650 (p90) REVERT: H 123 MET cc_start: 0.6169 (ptp) cc_final: 0.5765 (ptp) REVERT: L 49 LYS cc_start: 0.7429 (mmmt) cc_final: 0.6887 (mttt) REVERT: M 77 LYS cc_start: 0.5940 (mtpp) cc_final: 0.5122 (tptp) REVERT: M 119 TRP cc_start: 0.4634 (OUTLIER) cc_final: 0.3928 (m-10) REVERT: M 262 GLU cc_start: 0.1964 (mm-30) cc_final: 0.1304 (mt-10) REVERT: O 38 GLU cc_start: 0.6508 (pm20) cc_final: 0.6004 (mm-30) REVERT: O 296 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6850 (mt) REVERT: O 368 ARG cc_start: 0.5679 (tpm170) cc_final: 0.5077 (tpt170) REVERT: O 585 MET cc_start: 0.5986 (mmt) cc_final: 0.5617 (mmt) REVERT: O 589 LEU cc_start: 0.5399 (OUTLIER) cc_final: 0.5179 (mp) REVERT: P 176 ASN cc_start: 0.6939 (t0) cc_final: 0.6273 (t0) outliers start: 109 outliers final: 72 residues processed: 572 average time/residue: 0.4922 time to fit residues: 472.7204 Evaluate side-chains 537 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 459 time to evaluate : 4.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 589 HIS Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1416 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 804 ASP Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 879 SER Chi-restraints excluded: chain B residue 898 VAL Chi-restraints excluded: chain B residue 919 LYS Chi-restraints excluded: chain B residue 933 PHE Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 281 ARG Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain G residue 140 PHE Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 134 ASN Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 60 PHE Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 119 TRP Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 162 PHE Chi-restraints excluded: chain N residue 286 ASP Chi-restraints excluded: chain N residue 411 ARG Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 296 LEU Chi-restraints excluded: chain O residue 460 LEU Chi-restraints excluded: chain O residue 496 ILE Chi-restraints excluded: chain O residue 589 LEU Chi-restraints excluded: chain P residue 215 TYR Chi-restraints excluded: chain P residue 312 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 417 optimal weight: 10.0000 chunk 439 optimal weight: 0.1980 chunk 401 optimal weight: 8.9990 chunk 427 optimal weight: 0.0030 chunk 257 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 335 optimal weight: 0.3980 chunk 131 optimal weight: 9.9990 chunk 386 optimal weight: 5.9990 chunk 404 optimal weight: 9.9990 chunk 426 optimal weight: 1.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 GLN ** A1354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN B 880 HIS ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 GLN E 5 ASN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 287 HIS O 207 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5170 moved from start: 1.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 39015 Z= 0.245 Angle : 0.805 23.965 52685 Z= 0.401 Chirality : 0.049 0.400 5960 Planarity : 0.006 0.275 6778 Dihedral : 6.049 72.549 5229 Min Nonbonded Distance : 1.460 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.34 % Allowed : 12.32 % Favored : 87.35 % Rotamer: Outliers : 2.32 % Allowed : 21.66 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.31 % 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: -2.80 (0.11), residues: 4765 helix: -0.77 (0.13), residues: 1563 sheet: -1.01 (0.24), residues: 485 loop : -2.83 (0.11), residues: 2717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 119 HIS 0.019 0.001 HIS A1354 PHE 0.033 0.002 PHE A 91 TYR 0.058 0.002 TYR B 715 ARG 0.014 0.001 ARG C 281 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 583 time to evaluate : 3.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 SER cc_start: 0.8097 (t) cc_final: 0.7698 (p) REVERT: A 219 MET cc_start: 0.0699 (ttt) cc_final: -0.0844 (mtp) REVERT: A 228 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8304 (tp) REVERT: A 325 MET cc_start: 0.4111 (ppp) cc_final: 0.1672 (tpp) REVERT: A 419 LEU cc_start: 0.8240 (tp) cc_final: 0.7468 (mp) REVERT: A 550 ILE cc_start: 0.4906 (tt) cc_final: 0.4681 (tt) REVERT: A 592 ILE cc_start: 0.5809 (mm) cc_final: 0.5528 (mm) REVERT: A 664 MET cc_start: 0.6141 (tmm) cc_final: 0.5794 (ttm) REVERT: A 794 MET cc_start: 0.0530 (pmm) cc_final: 0.0073 (pmm) REVERT: A 903 THR cc_start: 0.5760 (p) cc_final: 0.5542 (t) REVERT: B 217 GLN cc_start: 0.4849 (tt0) cc_final: 0.4617 (tt0) REVERT: B 269 MET cc_start: 0.2670 (tpt) cc_final: 0.0651 (ppp) REVERT: B 320 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6206 (tp) REVERT: B 565 ILE cc_start: 0.4731 (tt) cc_final: 0.4315 (tt) REVERT: B 931 MET cc_start: 0.7911 (mpp) cc_final: 0.7431 (mtm) REVERT: B 960 GLU cc_start: 0.5286 (tt0) cc_final: 0.4933 (tt0) REVERT: B 1067 ARG cc_start: 0.7154 (mmp80) cc_final: 0.6308 (mtm110) REVERT: B 1084 MET cc_start: 0.8626 (tmm) cc_final: 0.8365 (ttp) REVERT: B 1137 ILE cc_start: 0.8774 (mp) cc_final: 0.8508 (mt) REVERT: E 4 GLU cc_start: 0.5038 (mt-10) cc_final: 0.3969 (mm-30) REVERT: E 50 MET cc_start: 0.1065 (ppp) cc_final: -0.0198 (ptt) REVERT: F 85 MET cc_start: 0.5328 (tpt) cc_final: 0.4994 (tpt) REVERT: F 128 LYS cc_start: 0.7533 (mmtm) cc_final: 0.7255 (mmtm) REVERT: G 22 THR cc_start: 0.8028 (m) cc_final: 0.7658 (t) REVERT: G 26 ILE cc_start: 0.9054 (mt) cc_final: 0.8815 (mt) REVERT: H 102 TYR cc_start: 0.3071 (p90) cc_final: 0.1658 (p90) REVERT: H 123 MET cc_start: 0.6829 (ptp) cc_final: 0.6422 (ptp) REVERT: L 49 LYS cc_start: 0.7689 (mmmt) cc_final: 0.7174 (mttt) REVERT: M 119 TRP cc_start: 0.4976 (OUTLIER) cc_final: 0.4202 (m-10) REVERT: O 57 LEU cc_start: 0.7979 (mt) cc_final: 0.7557 (mt) REVERT: O 296 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6882 (mt) REVERT: O 368 ARG cc_start: 0.5714 (tpm170) cc_final: 0.5100 (tpt170) REVERT: O 528 MET cc_start: 0.4254 (pmm) cc_final: 0.3776 (pmm) REVERT: O 585 MET cc_start: 0.6455 (mmt) cc_final: 0.6136 (mmt) REVERT: O 589 LEU cc_start: 0.6247 (OUTLIER) cc_final: 0.5960 (mp) REVERT: O 605 LYS cc_start: 0.1951 (pttp) cc_final: 0.1491 (pttt) REVERT: P 176 ASN cc_start: 0.6932 (t0) cc_final: 0.6374 (t0) outliers start: 99 outliers final: 67 residues processed: 655 average time/residue: 0.4867 time to fit residues: 527.8227 Evaluate side-chains 574 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 502 time to evaluate : 4.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1416 ILE Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 804 ASP Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 879 SER Chi-restraints excluded: chain B residue 919 LYS Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 64 ASN Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 134 ASN Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 60 PHE Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 119 TRP Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain N residue 286 ASP Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 207 HIS Chi-restraints excluded: chain O residue 239 SER Chi-restraints excluded: chain O residue 296 LEU Chi-restraints excluded: chain O residue 460 LEU Chi-restraints excluded: chain O residue 493 GLU Chi-restraints excluded: chain O residue 589 LEU Chi-restraints excluded: chain P residue 197 ASN Chi-restraints excluded: chain P residue 215 TYR Chi-restraints excluded: chain P residue 312 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 280 optimal weight: 3.9990 chunk 452 optimal weight: 3.9990 chunk 275 optimal weight: 0.6980 chunk 214 optimal weight: 0.9990 chunk 314 optimal weight: 0.7980 chunk 474 optimal weight: 0.9990 chunk 436 optimal weight: 0.7980 chunk 377 optimal weight: 0.0570 chunk 39 optimal weight: 0.7980 chunk 291 optimal weight: 8.9990 chunk 231 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN A 608 GLN A 913 GLN A1058 GLN ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 HIS ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN E 5 ASN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 ASN M 89 GLN M 178 GLN O 161 GLN Q 44 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5256 moved from start: 1.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 39015 Z= 0.200 Angle : 0.758 24.830 52685 Z= 0.374 Chirality : 0.046 0.263 5960 Planarity : 0.005 0.069 6778 Dihedral : 5.835 71.391 5229 Min Nonbonded Distance : 1.560 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.33 % Favored : 88.35 % Rotamer: Outliers : 1.81 % Allowed : 23.02 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.28 % 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: -2.66 (0.12), residues: 4765 helix: -0.61 (0.13), residues: 1566 sheet: -1.06 (0.23), residues: 514 loop : -2.77 (0.11), residues: 2685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 788 HIS 0.010 0.001 HIS A1354 PHE 0.043 0.002 PHE O 287 TYR 0.045 0.002 TYR O 208 ARG 0.009 0.001 ARG J 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 545 time to evaluate : 4.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 SER cc_start: 0.8130 (t) cc_final: 0.7814 (p) REVERT: A 219 MET cc_start: 0.0680 (ttt) cc_final: -0.0954 (mtp) REVERT: A 228 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8208 (tp) REVERT: A 325 MET cc_start: 0.4162 (ppp) cc_final: 0.1733 (tpp) REVERT: A 374 ASP cc_start: 0.6888 (m-30) cc_final: 0.6668 (m-30) REVERT: A 419 LEU cc_start: 0.8319 (tp) cc_final: 0.7591 (mp) REVERT: A 450 MET cc_start: 0.6110 (ptt) cc_final: 0.5854 (ttp) REVERT: A 483 LEU cc_start: 0.8949 (mt) cc_final: 0.8701 (mp) REVERT: A 664 MET cc_start: 0.6080 (tmm) cc_final: 0.5807 (ttm) REVERT: A 794 MET cc_start: -0.0014 (pmm) cc_final: -0.0589 (pmm) REVERT: A 1104 MET cc_start: 0.0568 (mmt) cc_final: 0.0297 (mmt) REVERT: A 1379 MET cc_start: 0.3432 (ptm) cc_final: 0.3190 (ptp) REVERT: B 217 GLN cc_start: 0.4946 (tt0) cc_final: 0.4682 (tt0) REVERT: B 269 MET cc_start: 0.2665 (tpt) cc_final: 0.0843 (ppp) REVERT: B 320 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6224 (tp) REVERT: B 565 ILE cc_start: 0.5034 (tt) cc_final: 0.4650 (tt) REVERT: B 1067 ARG cc_start: 0.6914 (mmp80) cc_final: 0.6466 (mtm110) REVERT: B 1084 MET cc_start: 0.8739 (tmm) cc_final: 0.8171 (ttp) REVERT: C 319 ARG cc_start: 0.7687 (tpp80) cc_final: 0.7325 (tpt-90) REVERT: D 69 ASN cc_start: 0.5682 (OUTLIER) cc_final: 0.4960 (t0) REVERT: D 153 MET cc_start: 0.3188 (ppp) cc_final: 0.0961 (ttt) REVERT: E 4 GLU cc_start: 0.4741 (mt-10) cc_final: 0.3759 (mm-30) REVERT: E 50 MET cc_start: 0.1052 (ppp) cc_final: -0.0209 (ptt) REVERT: F 85 MET cc_start: 0.5315 (tpt) cc_final: 0.5016 (tpt) REVERT: F 112 GLU cc_start: 0.6536 (tm-30) cc_final: 0.6308 (pp20) REVERT: G 22 THR cc_start: 0.8072 (m) cc_final: 0.7680 (t) REVERT: G 26 ILE cc_start: 0.9085 (mt) cc_final: 0.8838 (mt) REVERT: G 190 LYS cc_start: 0.6005 (tppt) cc_final: 0.5274 (mmtm) REVERT: H 97 MET cc_start: -0.1558 (tpt) cc_final: -0.1810 (tpt) REVERT: H 102 TYR cc_start: 0.2770 (p90) cc_final: 0.1589 (p90) REVERT: H 123 MET cc_start: 0.6804 (ptp) cc_final: 0.6462 (ptp) REVERT: L 49 LYS cc_start: 0.7572 (mmmt) cc_final: 0.7217 (mttt) REVERT: M 119 TRP cc_start: 0.4823 (OUTLIER) cc_final: 0.4084 (m-10) REVERT: M 262 GLU cc_start: 0.1688 (mp0) cc_final: 0.0557 (mm-30) REVERT: O 296 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6763 (mt) REVERT: O 368 ARG cc_start: 0.5692 (tpm170) cc_final: 0.5079 (tpt170) REVERT: O 528 MET cc_start: 0.4513 (pmm) cc_final: 0.4096 (pmm) REVERT: O 585 MET cc_start: 0.6624 (mmt) cc_final: 0.6318 (mmt) REVERT: O 589 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6486 (mp) REVERT: O 605 LYS cc_start: 0.2164 (pttp) cc_final: 0.1793 (pttt) REVERT: P 176 ASN cc_start: 0.6916 (t0) cc_final: 0.6378 (t0) REVERT: P 188 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: P 241 ARG cc_start: 0.3748 (mmp80) cc_final: 0.3371 (ttt90) outliers start: 77 outliers final: 56 residues processed: 600 average time/residue: 0.4736 time to fit residues: 477.6208 Evaluate side-chains 561 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 498 time to evaluate : 4.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1416 ILE Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 804 ASP Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 919 LYS Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 115 TRP Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 134 ASN Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 60 PHE Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 119 TRP Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain N residue 286 ASP Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 296 LEU Chi-restraints excluded: chain O residue 460 LEU Chi-restraints excluded: chain O residue 589 LEU Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain P residue 197 ASN Chi-restraints excluded: chain P residue 215 TYR Chi-restraints excluded: chain P residue 312 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 299 optimal weight: 0.9980 chunk 402 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 348 optimal weight: 9.9990 chunk 55 optimal weight: 0.2980 chunk 104 optimal weight: 1.9990 chunk 378 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 chunk 388 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 69 optimal weight: 0.3980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 716 ASN B 800 ASN B 822 GLN B1130 GLN ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN E 5 ASN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 161 GLN ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.237263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.213269 restraints weight = 65503.779| |-----------------------------------------------------------------------------| r_work (start): 0.4454 rms_B_bonded: 2.23 r_work: 0.4291 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5669 moved from start: 1.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.330 39015 Z= 0.344 Angle : 0.919 59.200 52685 Z= 0.487 Chirality : 0.051 1.524 5960 Planarity : 0.005 0.116 6778 Dihedral : 5.838 71.344 5229 Min Nonbonded Distance : 1.559 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.88 % Favored : 87.83 % Rotamer: Outliers : 1.95 % Allowed : 23.19 % Favored : 74.87 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.28 % 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: -2.67 (0.12), residues: 4765 helix: -0.61 (0.13), residues: 1568 sheet: -1.06 (0.23), residues: 514 loop : -2.77 (0.11), residues: 2683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 788 HIS 0.007 0.001 HIS A 92 PHE 0.048 0.002 PHE E 96 TYR 0.043 0.002 TYR M 169 ARG 0.017 0.001 ARG M 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9605.32 seconds wall clock time: 175 minutes 3.12 seconds (10503.12 seconds total)