Starting phenix.real_space_refine on Mon Mar 25 10:01:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnd_7532/03_2024/6cnd_7532.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnd_7532/03_2024/6cnd_7532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnd_7532/03_2024/6cnd_7532.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnd_7532/03_2024/6cnd_7532.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnd_7532/03_2024/6cnd_7532.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnd_7532/03_2024/6cnd_7532.pdb" } resolution = 4.8 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= 0.007 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 7 6.06 5 P 110 5.49 5 S 242 5.16 5 C 29976 2.51 5 N 8268 2.21 5 O 9233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1269": "OD1" <-> "OD2" Residue "B PHE 933": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 184": "NH1" <-> "NH2" Residue "P ARG 262": "NH1" <-> "NH2" Residue "R ARG 14": "NH1" <-> "NH2" Residue "R PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 294": "NH1" <-> "NH2" Residue "S TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 413": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 47836 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 11159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1428, 11159 Classifications: {'peptide': 1428} Link IDs: {'PCIS': 1, 'PTRANS': 65, 'TRANS': 1361} Chain breaks: 2 Chain: "B" Number of atoms: 8788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8788 Classifications: {'peptide': 1114} Link IDs: {'PTRANS': 43, '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: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1484 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 12, 'TRANS': 171} 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: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 549 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} 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: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 363 Classifications: {'peptide': 46} Link IDs: {'TRANS': 45} Chain: "M" Number of atoms: 1338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1338 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 8, 'TRANS': 155} Chain breaks: 1 Chain: "N" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 845 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain breaks: 1 Chain: "O" Number of atoms: 4329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4329 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 520} Chain breaks: 2 Chain: "P" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2242 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 7, 'TRANS': 269} Chain breaks: 2 Chain: "Q" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 368 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "R" Number of atoms: 4131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4131 Classifications: {'peptide': 522} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 502} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1649 Classifications: {'peptide': 217} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 42} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 43} Unresolved non-hydrogen planarities: 43 Chain: "X" Number of atoms: 1040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1040 Classifications: {'DNA': 51} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 50} Chain breaks: 1 Chain: "Y" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1249 Classifications: {'DNA': 61} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 60} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 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} Chain: "R" 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 492 SG CYS A 67 86.985 71.151 81.682 1.00 0.00 S ATOM 510 SG CYS A 70 89.988 72.658 78.472 1.00 0.00 S ATOM 557 SG CYS A 77 89.480 73.060 81.535 1.00 0.00 S ATOM 795 SG CYS A 107 71.042 115.693 88.580 1.00 0.00 S ATOM 818 SG CYS A 110 68.125 116.694 87.016 1.00 0.00 S ATOM 1184 SG CYS A 154 70.750 119.002 88.268 1.00 0.00 S ATOM 1208 SG CYS A 157 68.061 118.647 89.888 1.00 0.00 S ATOM 19520 SG CYS B1095 91.526 87.353 70.387 1.00 0.00 S ATOM 19543 SG CYS B1098 88.002 89.827 72.313 1.00 0.00 S ATOM 19609 SG CYS B1107 89.492 86.136 73.253 1.00 0.00 S ATOM 19629 SG CYS B1110 87.529 87.038 70.413 1.00 0.00 S ATOM 28652 SG CYS I 5 78.276 122.030 155.205 1.00 0.00 S ATOM 28671 SG CYS I 8 75.032 119.135 155.047 1.00 0.00 S ATOM 28799 SG CYS I 26 76.582 122.420 151.916 1.00 0.00 S ATOM 28822 SG CYS I 29 74.302 122.869 154.689 1.00 0.00 S ATOM 28988 SG CYS J 7 139.345 51.166 126.389 1.00 0.00 S ATOM 29011 SG CYS J 10 142.940 51.769 126.976 1.00 0.00 S ATOM 29291 SG CYS J 45 142.340 53.751 128.381 1.00 0.00 S ATOM 29297 SG CYS J 46 141.544 49.863 128.849 1.00 0.00 S ATOM 30330 SG CYS L 31 98.276 34.343 125.630 1.00 0.00 S ATOM 30350 SG CYS L 34 97.328 34.205 129.465 1.00 0.00 S ATOM 30454 SG CYS L 48 94.807 33.900 125.858 1.00 0.00 S ATOM 30477 SG CYS L 51 95.041 36.182 126.624 1.00 0.00 S ATOM 39788 SG CYS R 4 104.062 53.584 75.827 1.00 0.00 S ATOM 39811 SG CYS R 7 104.942 50.549 76.333 1.00 0.00 S ATOM 39952 SG CYS R 25 104.689 51.299 79.648 1.00 0.00 S ATOM 39972 SG CYS R 28 106.562 53.121 78.801 1.00 0.00 S Time building chain proxies: 23.08, per 1000 atoms: 0.48 Number of scatterers: 47836 At special positions: 0 Unit cell: (199.42, 169.92, 201.78, 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 7 29.99 S 242 16.00 P 110 15.00 O 9233 8.00 N 8268 7.00 C 29976 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: 19.33 Conformation dependent library (CDL) restraints added in 8.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 70 " pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 154 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 157 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1107 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1098 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1095 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1110 " pdb=" ZN I2000 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 26 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 8 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 29 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 5 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 46 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb=" ZN L2000 " pdb="ZN ZN L2000 " - pdb=" SG CYS L 51 " pdb="ZN ZN L2000 " - pdb=" SG CYS L 34 " pdb="ZN ZN L2000 " - pdb=" SG CYS L 48 " pdb="ZN ZN L2000 " - pdb=" SG CYS L 31 " pdb=" ZN R1001 " pdb="ZN ZN R1001 " - pdb=" SG CYS R 4 " pdb="ZN ZN R1001 " - pdb=" SG CYS R 25 " pdb="ZN ZN R1001 " - pdb=" SG CYS R 7 " pdb="ZN ZN R1001 " - pdb=" SG CYS R 28 " Number of angles added : 39 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10898 Finding SS restraints... Secondary structure from input PDB file: 215 helices and 53 sheets defined 42.5% alpha, 11.7% beta 46 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 15.86 Creating SS restraints... Processing helix chain 'A' and resid 22 through 30 removed outlier: 3.567A pdb=" N VAL A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 105 removed outlier: 3.784A pdb=" N GLN A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 128 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 146 through 151 removed outlier: 3.816A pdb=" N LYS A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 146 through 151' Processing helix chain 'A' and resid 191 through 208 removed outlier: 3.885A pdb=" N ASP A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N VAL A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 215 removed outlier: 3.946A pdb=" N TYR A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 283 through 302 removed outlier: 3.949A pdb=" N TRP A 294 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 328 removed outlier: 3.635A pdb=" N MET A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLU A 314 " --> pdb=" O ASN A 310 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS A 315 " --> pdb=" O ASN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 412 through 422 removed outlier: 3.528A pdb=" N GLU A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL A 421 " --> pdb=" O GLN A 417 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 456 removed outlier: 3.685A pdb=" N ASN A 455 " --> pdb=" O LYS A 451 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) 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 501 through 509 removed outlier: 3.530A pdb=" N VAL A 504 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR A 506 " --> pdb=" O CYS A 503 " (cutoff:3.500A) Proline residue: A 507 - end of helix Processing helix chain 'A' and resid 524 through 534 removed outlier: 3.593A pdb=" N ARG A 528 " --> pdb=" O THR A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 541 removed outlier: 3.753A pdb=" N ASN A 540 " --> pdb=" O GLY A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 566 removed outlier: 3.619A pdb=" N ILE A 564 " --> pdb=" O GLY A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 584 removed outlier: 3.647A pdb=" N SER A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 615 removed outlier: 3.810A pdb=" N ILE A 614 " --> pdb=" O PHE A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 686 Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.568A pdb=" N ALA A 690 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN A 692 " --> pdb=" O GLN A 688 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A 703 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN A 707 " --> pdb=" O ARG A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 718 Processing helix chain 'A' and resid 722 through 748 removed outlier: 4.236A pdb=" N ALA A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TYR A 735 " --> pdb=" O VAL A 731 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS A 737 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE A 745 " --> pdb=" O LEU A 741 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS A 747 " --> pdb=" O THR A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 784 removed outlier: 3.529A pdb=" N GLU A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 771 " --> pdb=" O GLY A 767 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A 784 " --> pdb=" O VAL A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 796 Processing helix chain 'A' and resid 802 through 811 removed outlier: 3.825A pdb=" N VAL A 806 " --> pdb=" O SER A 802 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET A 809 " --> pdb=" O ASN A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 894 removed outlier: 3.616A pdb=" N ILE A 866 " --> pdb=" O LEU A 862 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER A 867 " --> pdb=" O PHE A 863 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY A 868 " --> pdb=" O HIS A 864 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ARG A 869 " --> pdb=" O ALA A 865 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU A 881 " --> pdb=" O VAL A 877 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 891 " --> pdb=" O ARG A 887 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER A 892 " --> pdb=" O ARG A 888 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 893 " --> pdb=" O LEU A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 947 removed outlier: 3.605A pdb=" N ASP A 940 " --> pdb=" O ASN A 936 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE A 945 " --> pdb=" O HIS A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 975 removed outlier: 3.705A pdb=" N GLU A 961 " --> pdb=" O TYR A 957 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 966 " --> pdb=" O THR A 962 " (cutoff:3.500A) Proline residue: A 969 - end of helix removed outlier: 5.389A pdb=" N ARG A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 992 removed outlier: 3.820A pdb=" N LYS A 991 " --> pdb=" O GLU A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1026 removed outlier: 3.885A pdb=" N LEU A1019 " --> pdb=" O LYS A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1048 removed outlier: 3.850A pdb=" N THR A1047 " --> pdb=" O PRO A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1050 No H-bonds generated for 'chain 'A' and resid 1049 through 1050' Processing helix chain 'A' and resid 1051 through 1060 Processing helix chain 'A' and resid 1064 through 1081 removed outlier: 3.715A pdb=" N PHE A1070 " --> pdb=" O SER A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1098 removed outlier: 3.539A pdb=" N GLY A1098 " --> pdb=" O ALA A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1132 removed outlier: 3.607A pdb=" N ILE A1126 " --> pdb=" O GLY A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1161 Processing helix chain 'A' and resid 1165 through 1170 Processing helix chain 'A' and resid 1190 through 1196 Processing helix chain 'A' and resid 1202 through 1213 removed outlier: 3.568A pdb=" N THR A1210 " --> pdb=" O ALA A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1214 through 1216 No H-bonds generated for 'chain 'A' and resid 1214 through 1216' Processing helix chain 'A' and resid 1254 through 1267 removed outlier: 3.746A pdb=" N TYR A1258 " --> pdb=" O ASN A1254 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN A1262 " --> pdb=" O TYR A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1306 Processing helix chain 'A' and resid 1318 through 1326 removed outlier: 3.888A pdb=" N VAL A1322 " --> pdb=" O HIS A1318 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER A1324 " --> pdb=" O LEU A1320 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL A1325 " --> pdb=" O GLU A1321 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1346 removed outlier: 3.904A pdb=" N ARG A1337 " --> pdb=" O TYR A1333 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS A1346 " --> pdb=" O THR A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1351 through 1364 removed outlier: 4.351A pdb=" N ILE A1355 " --> pdb=" O ASP A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1377 Processing helix chain 'A' and resid 1382 through 1387 Processing helix chain 'A' and resid 1391 through 1403 Processing helix chain 'A' and resid 1410 through 1418 removed outlier: 4.177A pdb=" N ILE A1416 " --> pdb=" O SER A1412 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A1417 " --> pdb=" O GLU A1413 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1428 removed outlier: 4.223A pdb=" N PHE A1428 " --> pdb=" O THR A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1442 removed outlier: 3.616A pdb=" N ASP A1440 " --> pdb=" O SER A1437 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1453 removed outlier: 3.547A pdb=" N LEU A1451 " --> pdb=" O LEU A1447 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER A1452 " --> pdb=" O PHE A1448 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN A1453 " --> pdb=" O GLU A1449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1447 through 1453' Processing helix chain 'A' and resid 1454 through 1456 No H-bonds generated for 'chain 'A' and resid 1454 through 1456' Processing helix chain 'B' and resid 39 through 44 removed outlier: 4.027A pdb=" N LYS B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.745A pdb=" N VAL B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS B 55 " --> pdb=" O PHE B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 80 removed outlier: 3.731A pdb=" N PHE B 65 " --> pdb=" O HIS B 61 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU B 73 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS B 74 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASN B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 122 Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 266 through 274 removed outlier: 3.660A pdb=" N GLY B 274 " --> pdb=" O GLN B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 292 removed outlier: 3.819A pdb=" N PHE B 283 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA B 284 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ASN B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 306 Processing helix chain 'B' and resid 323 through 331 removed outlier: 3.978A pdb=" N ALA B 328 " --> pdb=" O ILE B 324 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 331 " --> pdb=" O ILE B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 362 removed outlier: 3.712A pdb=" N ASN B 362 " --> pdb=" O MET B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 Processing helix chain 'B' and resid 379 through 409 removed outlier: 3.746A pdb=" N LEU B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS B 409 " --> pdb=" O LYS B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 426 removed outlier: 3.918A pdb=" N VAL B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 440 Processing helix chain 'B' and resid 463 through 470 removed outlier: 3.948A pdb=" N LEU B 467 " --> pdb=" O TYR B 463 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET B 470 " --> pdb=" O ALA B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 494 Processing helix chain 'B' and resid 526 through 537 Processing helix chain 'B' and resid 540 through 544 Processing helix chain 'B' and resid 567 through 582 removed outlier: 3.527A pdb=" N PHE B 571 " --> pdb=" O PHE B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 632 Processing helix chain 'B' and resid 638 through 643 Processing helix chain 'B' and resid 650 through 657 Processing helix chain 'B' and resid 676 through 680 removed outlier: 4.009A pdb=" N THR B 679 " --> pdb=" O GLU B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 688 Processing helix chain 'B' and resid 690 through 694 Processing helix chain 'B' and resid 695 through 707 removed outlier: 3.573A pdb=" N ASN B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR B 701 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS B 707 " --> pdb=" O CYS B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 720 Processing helix chain 'B' and resid 738 through 744 removed outlier: 3.899A pdb=" N GLU B 742 " --> pdb=" O THR B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 749 Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.959A pdb=" N ASN B 814 " --> pdb=" O VAL B 811 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 853 removed outlier: 3.649A pdb=" N ALA B 852 " --> pdb=" O THR B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 947 No H-bonds generated for 'chain 'B' and resid 945 through 947' Processing helix chain 'B' and resid 948 through 953 removed outlier: 3.724A pdb=" N ARG B 952 " --> pdb=" O GLY B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 971 removed outlier: 3.630A pdb=" N ILE B 962 " --> pdb=" O MET B 958 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B 969 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN B 970 " --> pdb=" O ALA B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 993 removed outlier: 4.433A pdb=" N MET B 987 " --> pdb=" O LYS B 983 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER B 988 " --> pdb=" O LEU B 984 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP B 993 " --> pdb=" O LYS B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1035 removed outlier: 3.800A pdb=" N LYS B1034 " --> pdb=" O MET B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1073 removed outlier: 3.753A pdb=" N CYS B1069 " --> pdb=" O MET B1065 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL B1070 " --> pdb=" O GLU B1066 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE B1071 " --> pdb=" O ARG B1067 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA B1072 " --> pdb=" O ASP B1068 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR B1073 " --> pdb=" O CYS B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1083 Processing helix chain 'B' and resid 1122 through 1135 Processing helix chain 'C' and resid 34 through 40 Processing helix chain 'C' and resid 60 through 73 removed outlier: 4.324A pdb=" N ALA C 64 " --> pdb=" O ASP C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 104 Processing helix chain 'C' and resid 121 through 125 Processing helix chain 'C' and resid 127 through 131 Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 174 through 180 removed outlier: 3.921A pdb=" N THR C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE C 179 " --> pdb=" O GLN C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 241 through 250 Processing helix chain 'C' and resid 278 through 282 Processing helix chain 'C' and resid 285 through 287 No H-bonds generated for 'chain 'C' and resid 285 through 287' Processing helix chain 'C' and resid 309 through 330 Processing helix chain 'D' and resid 15 through 27 Processing helix chain 'D' and resid 31 through 35 removed outlier: 3.894A pdb=" N LEU D 34 " --> pdb=" O GLN D 31 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 35 " --> pdb=" O LYS D 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 31 through 35' Processing helix chain 'D' and resid 55 through 72 removed outlier: 4.066A pdb=" N THR D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG D 60 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN D 61 " --> pdb=" O GLY D 57 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TYR D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU D 66 " --> pdb=" O VAL D 62 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 111 removed outlier: 3.807A pdb=" N MET D 107 " --> pdb=" O PHE D 103 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LYS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 123 Processing helix chain 'D' and resid 130 through 136 removed outlier: 3.759A pdb=" N TYR D 135 " --> pdb=" O MET D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 159 removed outlier: 3.824A pdb=" N MET D 153 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU D 154 " --> pdb=" O ILE D 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 25 removed outlier: 3.878A pdb=" N LYS E 24 " --> pdb=" O LYS E 20 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP E 25 " --> pdb=" O GLU E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 66 through 72 removed outlier: 3.833A pdb=" N SER E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 103 removed outlier: 3.946A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN E 101 " --> pdb=" O VAL E 97 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU E 102 " --> pdb=" O ILE E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 123 removed outlier: 3.508A pdb=" N MET E 121 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 140 No H-bonds generated for 'chain 'E' and resid 138 through 140' Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 168 removed outlier: 3.869A pdb=" N ARG E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 88 through 103 removed outlier: 3.841A pdb=" N LEU F 94 " --> pdb=" O ARG F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 126 removed outlier: 3.712A pdb=" N ALA F 126 " --> pdb=" O MET F 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 20 removed outlier: 3.648A pdb=" N GLN G 17 " --> pdb=" O PRO G 14 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N HIS G 19 " --> pdb=" O ASP G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 34 Processing helix chain 'H' and resid 130 through 134 removed outlier: 4.039A pdb=" N ASN H 133 " --> pdb=" O ARG H 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 27 removed outlier: 3.882A pdb=" N TRP J 18 " --> pdb=" O VAL J 14 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU J 19 " --> pdb=" O GLY J 15 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 40 Processing helix chain 'J' and resid 43 through 52 removed outlier: 4.542A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 Processing helix chain 'K' and resid 69 through 82 removed outlier: 3.537A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR K 78 " --> pdb=" O ASN K 74 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 142 removed outlier: 3.521A pdb=" N GLU K 137 " --> pdb=" O SER K 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 139 removed outlier: 3.946A pdb=" N GLU M 139 " --> pdb=" O LYS M 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 195 removed outlier: 4.118A pdb=" N ASP M 187 " --> pdb=" O PHE M 183 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ARG M 193 " --> pdb=" O ALA M 189 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN M 195 " --> pdb=" O VAL M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 229 through 241 removed outlier: 4.026A pdb=" N VAL M 236 " --> pdb=" O LEU M 232 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 261 removed outlier: 4.243A pdb=" N LYS M 256 " --> pdb=" O PHE M 252 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR M 258 " --> pdb=" O GLN M 254 " (cutoff:3.500A) Processing helix chain 'N' and resid 275 through 296 removed outlier: 4.446A pdb=" N GLU N 279 " --> pdb=" O GLU N 275 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS N 293 " --> pdb=" O HIS N 289 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 41 removed outlier: 3.564A pdb=" N THR O 41 " --> pdb=" O GLU O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 57 removed outlier: 3.985A pdb=" N GLU O 51 " --> pdb=" O PHE O 47 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 72 removed outlier: 4.522A pdb=" N SER O 63 " --> pdb=" O GLU O 59 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL O 64 " --> pdb=" O ARG O 60 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE O 65 " --> pdb=" O ALA O 61 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLY O 66 " --> pdb=" O ALA O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 81 removed outlier: 4.408A pdb=" N VAL O 80 " --> pdb=" O VAL O 76 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU O 81 " --> pdb=" O ARG O 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 101 removed outlier: 3.521A pdb=" N LEU O 101 " --> pdb=" O SER O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 126 through 133 removed outlier: 4.024A pdb=" N LEU O 130 " --> pdb=" O GLY O 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 133 through 144 removed outlier: 3.642A pdb=" N ILE O 137 " --> pdb=" O SER O 133 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE O 141 " --> pdb=" O ILE O 137 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR O 142 " --> pdb=" O ASP O 138 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN O 143 " --> pdb=" O GLU O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 167 Processing helix chain 'O' and resid 170 through 178 Processing helix chain 'O' and resid 189 through 194 removed outlier: 4.053A pdb=" N GLN O 193 " --> pdb=" O SER O 189 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 209 removed outlier: 4.093A pdb=" N TYR O 208 " --> pdb=" O LYS O 205 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 218 Processing helix chain 'O' and resid 233 through 258 removed outlier: 3.979A pdb=" N LYS O 237 " --> pdb=" O SER O 233 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN O 240 " --> pdb=" O LYS O 236 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS O 251 " --> pdb=" O THR O 247 " (cutoff:3.500A) Proline residue: O 256 - end of helix Processing helix chain 'O' and resid 259 through 264 removed outlier: 3.961A pdb=" N LEU O 263 " --> pdb=" O LEU O 259 " (cutoff:3.500A) Processing helix chain 'O' and resid 284 through 304 removed outlier: 3.530A pdb=" N GLN O 295 " --> pdb=" O ARG O 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 305 through 320 removed outlier: 4.129A pdb=" N ARG O 317 " --> pdb=" O LYS O 313 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LEU O 318 " --> pdb=" O ILE O 314 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR O 319 " --> pdb=" O ALA O 315 " (cutoff:3.500A) Processing helix chain 'O' and resid 324 through 328 Processing helix chain 'O' and resid 329 through 333 removed outlier: 3.572A pdb=" N THR O 333 " --> pdb=" O LEU O 330 " (cutoff:3.500A) Processing helix chain 'O' and resid 340 through 346 Processing helix chain 'O' and resid 346 through 356 removed outlier: 4.085A pdb=" N GLU O 353 " --> pdb=" O ALA O 349 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU O 354 " --> pdb=" O GLU O 350 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS O 355 " --> pdb=" O LEU O 351 " (cutoff:3.500A) Processing helix chain 'O' and resid 357 through 360 Processing helix chain 'O' and resid 454 through 461 Processing helix chain 'O' and resid 482 through 491 Processing helix chain 'O' and resid 492 through 497 removed outlier: 4.000A pdb=" N ILE O 496 " --> pdb=" O GLU O 493 " (cutoff:3.500A) Processing helix chain 'O' and resid 501 through 514 removed outlier: 3.864A pdb=" N MET O 505 " --> pdb=" O GLY O 501 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG O 506 " --> pdb=" O PRO O 502 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP O 513 " --> pdb=" O ARG O 509 " (cutoff:3.500A) Processing helix chain 'O' and resid 518 through 526 removed outlier: 3.508A pdb=" N ALA O 526 " --> pdb=" O ILE O 522 " (cutoff:3.500A) Processing helix chain 'O' and resid 529 through 542 removed outlier: 3.551A pdb=" N SER O 535 " --> pdb=" O LYS O 531 " (cutoff:3.500A) Processing helix chain 'O' and resid 569 through 577 removed outlier: 4.236A pdb=" N MET O 577 " --> pdb=" O SER O 573 " (cutoff:3.500A) Processing helix chain 'O' and resid 578 through 584 removed outlier: 3.508A pdb=" N GLU O 582 " --> pdb=" O ARG O 578 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASN O 584 " --> pdb=" O ASN O 580 " (cutoff:3.500A) Processing helix chain 'O' and resid 584 through 610 removed outlier: 4.467A pdb=" N GLN O 597 " --> pdb=" O GLU O 593 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU O 598 " --> pdb=" O LYS O 594 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN O 599 " --> pdb=" O LEU O 595 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR O 601 " --> pdb=" O GLN O 597 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LEU O 602 " --> pdb=" O GLU O 598 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS O 604 " --> pdb=" O SER O 600 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS O 605 " --> pdb=" O THR O 601 " (cutoff:3.500A) Processing helix chain 'O' and resid 620 through 649 removed outlier: 3.984A pdb=" N LYS O 628 " --> pdb=" O LEU O 624 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET O 629 " --> pdb=" O ASN O 625 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA O 639 " --> pdb=" O LEU O 635 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER O 646 " --> pdb=" O SER O 642 " (cutoff:3.500A) Processing helix chain 'P' and resid 11 through 25 Processing helix chain 'P' and resid 33 through 40 removed outlier: 3.857A pdb=" N GLN P 37 " --> pdb=" O GLN P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 58 Processing helix chain 'P' and resid 77 through 86 Processing helix chain 'P' and resid 87 through 101 removed outlier: 3.822A pdb=" N LEU P 92 " --> pdb=" O ALA P 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 115 Processing helix chain 'P' and resid 117 through 132 removed outlier: 4.176A pdb=" N CYS P 124 " --> pdb=" O VAL P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 175 through 191 removed outlier: 3.571A pdb=" N ARG P 184 " --> pdb=" O THR P 180 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE P 191 " --> pdb=" O SER P 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 209 through 213 Processing helix chain 'P' and resid 219 through 226 removed outlier: 4.395A pdb=" N GLU P 223 " --> pdb=" O GLN P 219 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 250 Processing helix chain 'P' and resid 266 through 271 Processing helix chain 'Q' and resid 48 through 67 Processing helix chain 'Q' and resid 1082 through 1087 Processing helix chain 'R' and resid 74 through 93 removed outlier: 3.765A pdb=" N ALA R 78 " --> pdb=" O GLU R 74 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR R 79 " --> pdb=" O SER R 75 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR R 92 " --> pdb=" O ARG R 88 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA R 93 " --> pdb=" O ALA R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 115 removed outlier: 3.650A pdb=" N GLN R 106 " --> pdb=" O ASP R 102 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP R 107 " --> pdb=" O ALA R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 138 removed outlier: 3.634A pdb=" N ALA R 133 " --> pdb=" O CYS R 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 142 through 148 removed outlier: 3.863A pdb=" N SER R 148 " --> pdb=" O ILE R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 167 Processing helix chain 'R' and resid 177 through 187 removed outlier: 4.314A pdb=" N PHE R 181 " --> pdb=" O ASP R 177 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLN R 183 " --> pdb=" O SER R 179 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N HIS R 184 " --> pdb=" O LEU R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 212 Processing helix chain 'R' and resid 219 through 235 Processing helix chain 'R' and resid 240 through 249 removed outlier: 4.110A pdb=" N VAL R 247 " --> pdb=" O GLU R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 264 Processing helix chain 'R' and resid 287 through 297 removed outlier: 4.190A pdb=" N VAL R 291 " --> pdb=" O PRO R 287 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN R 293 " --> pdb=" O SER R 289 " (cutoff:3.500A) Processing helix chain 'R' and resid 407 through 413 removed outlier: 3.505A pdb=" N VAL R 411 " --> pdb=" O ASP R 407 " (cutoff:3.500A) Processing helix chain 'R' and resid 454 through 472 removed outlier: 3.735A pdb=" N ALA R 466 " --> pdb=" O SER R 462 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE R 468 " --> pdb=" O LYS R 464 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE R 469 " --> pdb=" O TYR R 465 " (cutoff:3.500A) Processing helix chain 'R' and resid 497 through 506 removed outlier: 3.976A pdb=" N LEU R 501 " --> pdb=" O ARG R 497 " (cutoff:3.500A) Processing helix chain 'R' and resid 545 through 561 removed outlier: 3.727A pdb=" N ILE R 549 " --> pdb=" O GLN R 545 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR R 550 " --> pdb=" O ARG R 546 " (cutoff:3.500A) Proline residue: R 558 - end of helix Processing helix chain 'R' and resid 587 through 594 removed outlier: 3.744A pdb=" N TYR R 591 " --> pdb=" O THR R 587 " (cutoff:3.500A) Processing helix chain 'R' and resid 608 through 613 removed outlier: 3.727A pdb=" N ALA R 612 " --> pdb=" O GLU R 608 " (cutoff:3.500A) Processing helix chain 'R' and resid 616 through 632 Processing helix chain 'R' and resid 633 through 648 removed outlier: 3.951A pdb=" N GLU R 646 " --> pdb=" O ARG R 642 " (cutoff:3.500A) Processing helix chain 'S' and resid 293 through 318 removed outlier: 3.900A pdb=" N UNK S 317 " --> pdb=" O UNK S 313 " (cutoff:3.500A) Processing helix chain 'S' and resid 384 through 392 Processing helix chain 'S' and resid 421 through 435 removed outlier: 3.753A pdb=" N LYS S 427 " --> pdb=" O GLU S 423 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE S 428 " --> pdb=" O GLU S 424 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU S 432 " --> pdb=" O PHE S 428 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER S 433 " --> pdb=" O TYR S 429 " (cutoff:3.500A) Processing helix chain 'S' and resid 439 through 446 Processing helix chain 'S' and resid 450 through 465 removed outlier: 4.021A pdb=" N VAL S 454 " --> pdb=" O SER S 450 " (cutoff:3.500A) Processing helix chain 'S' and resid 465 through 475 Processing helix chain 'S' and resid 480 through 488 removed outlier: 3.741A pdb=" N TYR S 484 " --> pdb=" O ASN S 480 " (cutoff:3.500A) Processing helix chain 'S' and resid 494 through 531 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 19 removed outlier: 5.968A pdb=" N ILE A 13 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLU B1144 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLY A 15 " --> pdb=" O ARG B1142 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG B1142 " --> pdb=" O GLY A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 90 removed outlier: 11.583A pdb=" N LEU A 88 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N TYR A 260 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 180 removed outlier: 3.626A pdb=" N ASP A 220 " --> pdb=" O HIS A 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 373 Processing sheet with id=AA5, first strand: chain 'B' and resid 1036 through 1038 removed outlier: 3.888A pdb=" N THR A 379 " --> pdb=" O MET A 517 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP A 470 " --> pdb=" O ALA A 490 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG A 493 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE A 498 " --> pdb=" O ARG A 378 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL A 380 " --> pdb=" O PHE A 498 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU A 500 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N SER A 382 " --> pdb=" O LEU A 500 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 404 through 407 removed outlier: 4.980A pdb=" N TYR A 432 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 626 through 629 removed outlier: 6.668A pdb=" N ILE A 653 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 897 through 899 removed outlier: 7.394A pdb=" N VAL A 904 " --> pdb=" O VAL A 912 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1281 through 1285 removed outlier: 3.792A pdb=" N LEU A1293 " --> pdb=" O ALA A1143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1172 through 1174 removed outlier: 3.668A pdb=" N TYR A1172 " --> pdb=" O ARG A1187 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1430 through 1432 Processing sheet with id=AB3, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.514A pdb=" N ILE B 83 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASP B 132 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE B 98 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR B 130 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL B 100 " --> pdb=" O PRO B 128 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.514A pdb=" N ILE B 83 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASP B 132 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE B 98 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR B 130 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL B 100 " --> pdb=" O PRO B 128 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 133 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 145 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS B 144 " --> pdb=" O VAL S 397 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AB6, first strand: chain 'B' and resid 196 through 197 removed outlier: 7.048A pdb=" N VAL B 196 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 206 through 207 removed outlier: 3.872A pdb=" N LYS B 230 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ILE B 234 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N TYR B 241 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 441 through 444 Processing sheet with id=AB9, first strand: chain 'B' and resid 519 through 521 Processing sheet with id=AC1, first strand: chain 'B' and resid 590 through 593 removed outlier: 3.633A pdb=" N ALA B 598 " --> pdb=" O ASN B 593 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 619 through 620 removed outlier: 3.642A pdb=" N LEU B 612 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU B 647 " --> pdb=" O LEU B 612 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 619 through 620 Processing sheet with id=AC4, first strand: chain 'B' and resid 724 through 725 removed outlier: 7.702A pdb=" N LEU B 899 " --> pdb=" O ASP B 882 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASP B 882 " --> pdb=" O LEU B 899 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 724 through 725 Processing sheet with id=AC6, first strand: chain 'B' and resid 1001 through 1002 removed outlier: 6.699A pdb=" N LEU B 771 " --> pdb=" O GLY B 923 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE B 925 " --> pdb=" O LEU B 771 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU B 773 " --> pdb=" O ILE B 925 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B 772 " --> pdb=" O ILE B 943 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N ILE B 942 " --> pdb=" O ASN B 754 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N THR B 756 " --> pdb=" O ILE B 942 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N MET B 944 " --> pdb=" O THR B 756 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA B 758 " --> pdb=" O MET B 944 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL B 757 " --> pdb=" O GLY B1020 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 759 " --> pdb=" O PHE B1018 " (cutoff:3.500A) removed outlier: 5.159A 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: 4.639A 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 847 Processing sheet with id=AC9, first strand: chain 'B' and resid 1043 through 1044 removed outlier: 6.332A pdb=" N ARG B1043 " --> pdb=" O VAL R 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 1101 through 1102 removed outlier: 3.876A pdb=" N ASP B1093 " --> pdb=" O GLY B1102 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET B1119 " --> pdb=" O VAL B1092 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B1094 " --> pdb=" O ILE B1117 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 6 through 8 Processing sheet with id=AD3, first strand: chain 'C' and resid 41 through 47 removed outlier: 4.167A pdb=" N GLU C 41 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE C 57 " --> pdb=" O GLU C 41 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU C 47 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N GLU C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR C 224 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 41 through 47 removed outlier: 4.167A pdb=" N GLU C 41 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE C 57 " --> pdb=" O GLU C 41 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU C 47 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N GLU C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL C 294 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 168 through 169 removed outlier: 3.670A pdb=" N LYS C 168 " --> pdb=" O SER C 135 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER C 135 " --> pdb=" O LYS C 168 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLU C 201 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASN C 88 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR C 82 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE C 85 " --> pdb=" O VAL L 65 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL L 65 " --> pdb=" O PHE C 85 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 141 through 142 removed outlier: 4.152A pdb=" N THR C 141 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AD8, first strand: chain 'D' and resid 5 through 9 removed outlier: 5.422A pdb=" N ARG D 7 " --> pdb=" O LEU G 4 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N LEU G 4 " --> pdb=" O ARG D 7 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER G 5 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR G 71 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG G 73 " --> pdb=" O ASP G 50 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL G 75 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ILE G 48 " --> pdb=" O VAL G 75 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 60 through 62 removed outlier: 3.523A pdb=" N GLY E 108 " --> pdb=" O THR E 131 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AE2, first strand: chain 'G' and resid 83 through 85 Processing sheet with id=AE3, first strand: chain 'G' and resid 153 through 155 Processing sheet with id=AE4, first strand: chain 'H' and resid 95 through 96 removed outlier: 4.852A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU H 27 " --> pdb=" O GLU H 14 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP H 16 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG H 25 " --> pdb=" O ASP H 16 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU H 111 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU H 106 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA H 113 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N PHE H 104 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR H 102 " --> pdb=" O TYR H 115 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 25 through 26 removed outlier: 5.287A pdb=" N TYR I 31 " --> pdb=" O CYS I 26 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 61 through 66 Processing sheet with id=AE7, first strand: chain 'N' and resid 362 through 363 removed outlier: 7.520A pdb=" N LEU M 170 " --> pdb=" O PRO M 75 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LYS M 77 " --> pdb=" O LEU M 170 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N MET N 305 " --> pdb=" O ALA M 161 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 119 through 121 removed outlier: 3.917A pdb=" N TRP M 119 " --> pdb=" O GLY M 150 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY M 150 " --> pdb=" O TRP M 119 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 119 through 121 removed outlier: 3.917A pdb=" N TRP M 119 " --> pdb=" O GLY M 150 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY M 150 " --> pdb=" O TRP M 119 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL M 87 " --> pdb=" O ALA M 177 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LEU M 179 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLN M 89 " --> pdb=" O LEU M 179 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR M 90 " --> pdb=" O ASP N 393 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP N 393 " --> pdb=" O TYR M 90 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ALA M 248 " --> pdb=" O LEU N 408 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 104 through 109 Processing sheet with id=AF2, first strand: chain 'O' and resid 549 through 551 Processing sheet with id=AF3, first strand: chain 'P' and resid 61 through 64 Processing sheet with id=AF4, first strand: chain 'P' and resid 134 through 137 removed outlier: 3.750A pdb=" N MET P 149 " --> pdb=" O LYS P 135 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'P' and resid 255 through 256 Processing sheet with id=AF6, first strand: chain 'R' and resid 12 through 15 Processing sheet with id=AF7, first strand: chain 'R' and resid 446 through 452 removed outlier: 4.575A pdb=" N GLY R 451 " --> pdb=" O ILE R 396 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE R 396 " --> pdb=" O GLY R 451 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LEU R 393 " --> pdb=" O SER R 489 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N SER R 489 " --> pdb=" O LEU R 393 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN R 395 " --> pdb=" O VAL R 487 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR R 399 " --> pdb=" O ILE R 483 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ILE R 483 " --> pdb=" O THR R 399 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N THR R 401 " --> pdb=" O PHE R 481 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE R 481 " --> pdb=" O THR R 401 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR R 541 " --> pdb=" O VAL R 529 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL R 529 " --> pdb=" O THR R 541 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'R' and resid 420 through 421 removed outlier: 3.701A pdb=" N ASN R 421 " --> pdb=" O PHE R 425 " (cutoff:3.500A) 1682 hydrogen bonds defined for protein. 4662 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 180 hydrogen bond angles 0 basepair planarities 46 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 22.02 Time building geometry restraints manager: 20.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 15151 1.34 - 1.46: 10894 1.46 - 1.58: 22254 1.58 - 1.71: 220 1.71 - 1.83: 393 Bond restraints: 48912 Sorted by residual: bond pdb=" CA GLU O 125 " pdb=" C GLU O 125 " ideal model delta sigma weight residual 1.522 1.636 -0.115 1.31e-02 5.83e+03 7.65e+01 bond pdb=" CA MET B 517 " pdb=" CB MET B 517 " ideal model delta sigma weight residual 1.525 1.456 0.068 1.25e-02 6.40e+03 2.97e+01 bond pdb=" CA LYS A 348 " pdb=" C LYS A 348 " ideal model delta sigma weight residual 1.524 1.588 -0.064 1.26e-02 6.30e+03 2.57e+01 bond pdb=" N PRO A 791 " pdb=" CD PRO A 791 " ideal model delta sigma weight residual 1.473 1.538 -0.065 1.40e-02 5.10e+03 2.17e+01 bond pdb=" CA PRO A 791 " pdb=" C PRO A 791 " ideal model delta sigma weight residual 1.520 1.585 -0.066 1.42e-02 4.96e+03 2.16e+01 ... (remaining 48907 not shown) Histogram of bond angle deviations from ideal: 97.55 - 104.86: 1403 104.86 - 112.16: 24068 112.16 - 119.47: 17032 119.47 - 126.77: 23219 126.77 - 134.08: 794 Bond angle restraints: 66516 Sorted by residual: angle pdb=" C ASP R 190 " pdb=" CA ASP R 190 " pdb=" CB ASP R 190 " ideal model delta sigma weight residual 116.54 103.50 13.04 1.15e+00 7.56e-01 1.28e+02 angle pdb=" C GLU R 512 " pdb=" N PRO R 513 " pdb=" CA PRO R 513 " ideal model delta sigma weight residual 119.84 132.19 -12.35 1.25e+00 6.40e-01 9.76e+01 angle pdb=" N ASP R 190 " pdb=" CA ASP R 190 " pdb=" C ASP R 190 " ideal model delta sigma weight residual 108.31 122.80 -14.49 1.52e+00 4.33e-01 9.09e+01 angle pdb=" N LYS R 211 " pdb=" CA LYS R 211 " pdb=" C LYS R 211 " ideal model delta sigma weight residual 111.28 121.48 -10.20 1.09e+00 8.42e-01 8.76e+01 angle pdb=" N VAL A 347 " pdb=" CA VAL A 347 " pdb=" C VAL A 347 " ideal model delta sigma weight residual 111.05 122.37 -11.32 1.25e+00 6.40e-01 8.20e+01 ... (remaining 66511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.50: 28878 34.50 - 69.01: 814 69.01 - 103.51: 71 103.51 - 138.02: 1 138.02 - 172.52: 3 Dihedral angle restraints: 29767 sinusoidal: 12955 harmonic: 16812 Sorted by residual: dihedral pdb=" CA THR I 23 " pdb=" C THR I 23 " pdb=" N LEU I 24 " pdb=" CA LEU I 24 " ideal model delta harmonic sigma weight residual 180.00 150.47 29.53 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA HIS B 334 " pdb=" C HIS B 334 " pdb=" N LEU B 335 " pdb=" CA LEU B 335 " ideal model delta harmonic sigma weight residual 180.00 150.48 29.52 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA GLU A1033 " pdb=" C GLU A1033 " pdb=" N PRO A1034 " pdb=" CA PRO A1034 " ideal model delta harmonic sigma weight residual 180.00 150.50 29.50 0 5.00e+00 4.00e-02 3.48e+01 ... (remaining 29764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 7063 0.107 - 0.215: 420 0.215 - 0.322: 31 0.322 - 0.429: 12 0.429 - 0.537: 3 Chirality restraints: 7529 Sorted by residual: chirality pdb=" CA VAL A 347 " pdb=" N VAL A 347 " pdb=" C VAL A 347 " pdb=" CB VAL A 347 " both_signs ideal model delta sigma weight residual False 2.44 1.90 0.54 2.00e-01 2.50e+01 7.20e+00 chirality pdb=" CA GLU O 125 " pdb=" N GLU O 125 " pdb=" C GLU O 125 " pdb=" CB GLU O 125 " both_signs ideal model delta sigma weight residual False 2.51 3.00 -0.49 2.00e-01 2.50e+01 5.91e+00 chirality pdb=" CA ALA O 526 " pdb=" N ALA O 526 " pdb=" C ALA O 526 " pdb=" CB ALA O 526 " both_signs ideal model delta sigma weight residual False 2.48 2.02 0.46 2.00e-01 2.50e+01 5.39e+00 ... (remaining 7526 not shown) Planarity restraints: 8164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 790 " 0.070 5.00e-02 4.00e+02 1.05e-01 1.76e+01 pdb=" N PRO A 791 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO A 791 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 791 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 116 " 0.065 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO F 117 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO F 117 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO F 117 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP O 328 " 0.057 5.00e-02 4.00e+02 8.77e-02 1.23e+01 pdb=" N PRO O 329 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO O 329 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO O 329 " 0.050 5.00e-02 4.00e+02 ... (remaining 8161 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 1100 2.60 - 3.17: 49760 3.17 - 3.75: 76907 3.75 - 4.32: 106363 4.32 - 4.90: 156905 Nonbonded interactions: 391035 Sorted by model distance: nonbonded pdb=" O SER A 250 " pdb=" N ARG A 252 " model vdw 2.023 2.520 nonbonded pdb=" CG1 VAL C 83 " pdb=" CE2 PHE C 85 " model vdw 2.064 3.760 nonbonded pdb=" OD1 ASN A 715 " pdb=" N ASP A 716 " model vdw 2.069 2.520 nonbonded pdb=" NH2 ARG O 40 " pdb=" O GLU P 314 " model vdw 2.070 2.520 nonbonded pdb=" O ALA F 80 " pdb=" OG1 THR F 81 " model vdw 2.072 2.440 ... (remaining 391030 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.040 Extract box with map and model: 7.670 Check model and map are aligned: 0.750 Set scattering table: 0.440 Process input model: 142.110 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.170 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 48912 Z= 0.393 Angle : 1.135 14.488 66516 Z= 0.691 Chirality : 0.059 0.537 7529 Planarity : 0.006 0.105 8164 Dihedral : 14.380 172.520 18869 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 38.71 Ramachandran Plot: Outliers : 1.56 % Allowed : 17.99 % Favored : 80.44 % Rotamer: Outliers : 0.72 % Allowed : 1.77 % Favored : 97.51 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.18 (0.08), residues: 5625 helix: -4.09 (0.07), residues: 1712 sheet: -2.51 (0.16), residues: 646 loop : -3.39 (0.09), residues: 3267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP C 31 HIS 0.013 0.002 HIS A 675 PHE 0.053 0.003 PHE O 576 TYR 0.032 0.003 TYR B 416 ARG 0.014 0.001 ARG S 449 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1048 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1012 time to evaluate : 5.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.8303 (tt) cc_final: 0.7947 (tt) REVERT: A 103 LEU cc_start: 0.8981 (tt) cc_final: 0.8594 (tt) REVERT: A 141 LEU cc_start: 0.9107 (mt) cc_final: 0.8850 (tt) REVERT: A 303 LEU cc_start: 0.8481 (tt) cc_final: 0.8141 (tt) REVERT: A 374 ASP cc_start: 0.8901 (t70) cc_final: 0.8309 (p0) REVERT: A 375 PHE cc_start: 0.8288 (m-80) cc_final: 0.8008 (m-10) REVERT: A 384 ASP cc_start: 0.8402 (t0) cc_final: 0.8134 (t0) REVERT: A 463 GLU cc_start: 0.6143 (mt-10) cc_final: 0.5746 (mt-10) REVERT: A 470 ASP cc_start: 0.6510 (m-30) cc_final: 0.6144 (m-30) REVERT: A 486 LEU cc_start: 0.9522 (mp) cc_final: 0.9295 (mm) REVERT: A 524 THR cc_start: 0.7610 (t) cc_final: 0.7354 (p) REVERT: A 535 MET cc_start: 0.7755 (ttt) cc_final: 0.7340 (ttt) REVERT: A 554 THR cc_start: 0.9281 (p) cc_final: 0.8657 (m) REVERT: A 558 ILE cc_start: 0.9553 (mt) cc_final: 0.9229 (mt) REVERT: A 800 LYS cc_start: 0.7794 (mmmt) cc_final: 0.7520 (tptm) REVERT: A 828 GLN cc_start: 0.6715 (tt0) cc_final: 0.6240 (mm-40) REVERT: A 885 MET cc_start: 0.7539 (ttt) cc_final: 0.7171 (ttp) REVERT: A 898 CYS cc_start: 0.8473 (t) cc_final: 0.7818 (t) REVERT: A 1421 MET cc_start: 0.9123 (ttm) cc_final: 0.8837 (ttp) REVERT: B 347 LEU cc_start: 0.8521 (tt) cc_final: 0.8284 (tt) REVERT: B 384 ILE cc_start: 0.9246 (mt) cc_final: 0.9038 (mt) REVERT: B 390 ASP cc_start: 0.8220 (m-30) cc_final: 0.7135 (m-30) REVERT: B 492 SER cc_start: 0.8865 (p) cc_final: 0.8661 (t) REVERT: B 516 LEU cc_start: 0.8582 (mp) cc_final: 0.7752 (tp) REVERT: B 517 MET cc_start: 0.7661 (mtp) cc_final: 0.7033 (mtp) REVERT: B 687 LEU cc_start: 0.8586 (mt) cc_final: 0.8356 (tp) REVERT: B 721 ILE cc_start: 0.9466 (mt) cc_final: 0.9167 (mp) REVERT: B 763 SER cc_start: 0.8457 (t) cc_final: 0.8005 (p) REVERT: B 790 LYS cc_start: 0.7987 (pttp) cc_final: 0.7727 (ptmt) REVERT: B 931 MET cc_start: 0.8493 (ptp) cc_final: 0.8184 (ptp) REVERT: B 961 LEU cc_start: 0.9006 (tt) cc_final: 0.8747 (tt) REVERT: B 1004 LEU cc_start: 0.8400 (mt) cc_final: 0.6938 (mp) REVERT: B 1013 LEU cc_start: 0.9104 (mt) cc_final: 0.8826 (mm) REVERT: B 1087 SER cc_start: 0.8783 (m) cc_final: 0.8390 (p) REVERT: C 101 ILE cc_start: 0.9369 (mp) cc_final: 0.8878 (tp) REVERT: C 320 ILE cc_start: 0.9477 (mt) cc_final: 0.9167 (mm) REVERT: D 131 MET cc_start: 0.7254 (ptp) cc_final: 0.6845 (ptp) REVERT: E 22 MET cc_start: 0.7844 (ttt) cc_final: 0.7559 (ttt) REVERT: E 136 ASN cc_start: 0.7464 (t0) cc_final: 0.6861 (t0) REVERT: E 187 TYR cc_start: 0.6605 (t80) cc_final: 0.6007 (t80) REVERT: F 85 MET cc_start: 0.6904 (mtt) cc_final: 0.6615 (mtt) REVERT: H 137 GLN cc_start: 0.6777 (mt0) cc_final: 0.6572 (mt0) REVERT: I 2 LEU cc_start: 0.8623 (tp) cc_final: 0.8385 (tp) REVERT: K 76 LEU cc_start: 0.9028 (tp) cc_final: 0.8354 (tt) REVERT: K 77 ARG cc_start: 0.8369 (ptm-80) cc_final: 0.8040 (tmm160) REVERT: K 91 TYR cc_start: 0.8584 (p90) cc_final: 0.8363 (p90) REVERT: K 124 LEU cc_start: 0.8821 (tt) cc_final: 0.8615 (tt) REVERT: N 309 LEU cc_start: 0.7567 (mp) cc_final: 0.7304 (mt) REVERT: O 81 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6828 (mm-30) REVERT: O 96 VAL cc_start: 0.8605 (m) cc_final: 0.8394 (p) REVERT: O 123 ASN cc_start: 0.5790 (t0) cc_final: 0.5216 (t0) REVERT: O 144 MET cc_start: 0.6586 (tpt) cc_final: 0.6283 (tpp) REVERT: O 577 MET cc_start: 0.6558 (mmm) cc_final: 0.4576 (tpp) REVERT: O 590 PHE cc_start: 0.6921 (m-80) cc_final: 0.5940 (m-80) REVERT: O 642 SER cc_start: 0.8476 (m) cc_final: 0.8269 (p) REVERT: R 227 CYS cc_start: 0.8803 (m) cc_final: 0.8497 (m) outliers start: 36 outliers final: 13 residues processed: 1038 average time/residue: 0.6004 time to fit residues: 1010.1919 Evaluate side-chains 568 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 555 time to evaluate : 5.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 483 optimal weight: 4.9990 chunk 434 optimal weight: 5.9990 chunk 240 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 292 optimal weight: 30.0000 chunk 232 optimal weight: 1.9990 chunk 449 optimal weight: 9.9990 chunk 173 optimal weight: 0.9990 chunk 273 optimal weight: 10.0000 chunk 334 optimal weight: 7.9990 chunk 520 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN A 180 HIS ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN A 643 ASN A 675 HIS ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 ASN ** A1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1356 GLN ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN B 298 GLN B 396 ASN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 ASN B 441 ASN B 626 HIS ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 902 GLN ** B1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 ASN B1148 GLN ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 ASN C 99 HIS ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** D 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN E 3 GLN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN F 78 GLN H 133 ASN K 64 GLN ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 144 ASN M 254 GLN ** N 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 288 GLN N 377 ASN ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 162 ASN ** O 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 222 HIS O 310 GLN ** O 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 626 GLN P 19 HIS P 53 GLN P 239 ASN P 305 HIS ** R 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 613 HIS S 384 HIS S 440 ASN ** S 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 506 GLN S 509 HIS Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 48912 Z= 0.317 Angle : 0.885 14.614 66516 Z= 0.467 Chirality : 0.049 0.380 7529 Planarity : 0.006 0.081 8164 Dihedral : 17.266 173.122 7491 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 28.25 Ramachandran Plot: Outliers : 0.76 % Allowed : 13.17 % Favored : 86.06 % Rotamer: Outliers : 0.16 % Allowed : 3.94 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -4.03 (0.09), residues: 5625 helix: -2.54 (0.09), residues: 1908 sheet: -2.22 (0.18), residues: 607 loop : -2.92 (0.10), residues: 3110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 146 HIS 0.014 0.002 HIS A1318 PHE 0.032 0.002 PHE A 364 TYR 0.031 0.003 TYR A 602 ARG 0.013 0.001 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 784 time to evaluate : 5.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.7212 (ptp) cc_final: 0.6821 (ptp) REVERT: A 365 ARG cc_start: 0.6753 (pmt-80) cc_final: 0.6372 (pmt170) REVERT: A 374 ASP cc_start: 0.8770 (t70) cc_final: 0.8508 (p0) REVERT: A 384 ASP cc_start: 0.8603 (t0) cc_final: 0.8135 (t0) REVERT: A 456 LEU cc_start: 0.8561 (tp) cc_final: 0.8207 (tp) REVERT: A 470 ASP cc_start: 0.7058 (m-30) cc_final: 0.6495 (m-30) REVERT: A 563 LEU cc_start: 0.8370 (mm) cc_final: 0.8088 (mm) REVERT: A 716 ASP cc_start: 0.8703 (m-30) cc_final: 0.8426 (m-30) REVERT: A 793 ILE cc_start: 0.7830 (mt) cc_final: 0.7365 (mm) REVERT: A 828 GLN cc_start: 0.7103 (tt0) cc_final: 0.6670 (mm-40) REVERT: A 885 MET cc_start: 0.7310 (ttt) cc_final: 0.6964 (ttp) REVERT: A 890 MET cc_start: 0.6914 (tpp) cc_final: 0.6505 (tpp) REVERT: A 1336 ILE cc_start: 0.9566 (pt) cc_final: 0.9214 (tt) REVERT: A 1421 MET cc_start: 0.9100 (ttm) cc_final: 0.8731 (ttp) REVERT: B 281 ASP cc_start: 0.7495 (p0) cc_final: 0.6769 (p0) REVERT: B 332 ILE cc_start: 0.8259 (pt) cc_final: 0.8046 (mt) REVERT: B 347 LEU cc_start: 0.8313 (tt) cc_final: 0.8086 (tt) REVERT: B 371 TYR cc_start: 0.7072 (p90) cc_final: 0.6773 (p90) REVERT: B 422 ILE cc_start: 0.9274 (pt) cc_final: 0.9064 (pt) REVERT: B 469 MET cc_start: 0.9195 (ptm) cc_final: 0.8782 (tmm) REVERT: B 492 SER cc_start: 0.9126 (p) cc_final: 0.8881 (t) REVERT: B 516 LEU cc_start: 0.8522 (mp) cc_final: 0.7777 (tp) REVERT: B 517 MET cc_start: 0.7432 (mtp) cc_final: 0.6903 (mtp) REVERT: B 523 ASP cc_start: 0.8261 (t0) cc_final: 0.8013 (p0) REVERT: B 524 ASP cc_start: 0.7690 (t70) cc_final: 0.7259 (t70) REVERT: B 649 LEU cc_start: 0.7808 (mp) cc_final: 0.7295 (mp) REVERT: B 942 ILE cc_start: 0.9058 (mt) cc_final: 0.8636 (tt) REVERT: B 953 MET cc_start: 0.6789 (ppp) cc_final: 0.6521 (ppp) REVERT: B 958 MET cc_start: 0.7148 (mtm) cc_final: 0.6907 (mtm) REVERT: B 1068 ASP cc_start: 0.6331 (t70) cc_final: 0.4611 (t70) REVERT: B 1087 SER cc_start: 0.8687 (m) cc_final: 0.8425 (p) REVERT: C 75 VAL cc_start: 0.9101 (m) cc_final: 0.8835 (m) REVERT: C 101 ILE cc_start: 0.9428 (mp) cc_final: 0.8885 (tp) REVERT: C 248 GLN cc_start: 0.8768 (pt0) cc_final: 0.8433 (pp30) REVERT: D 98 MET cc_start: 0.6119 (mmp) cc_final: 0.5241 (mmt) REVERT: E 22 MET cc_start: 0.8014 (ttt) cc_final: 0.7767 (ttt) REVERT: E 136 ASN cc_start: 0.7267 (t0) cc_final: 0.6704 (t0) REVERT: F 86 THR cc_start: 0.7938 (m) cc_final: 0.7736 (m) REVERT: H 122 LEU cc_start: 0.7955 (mm) cc_final: 0.7569 (tt) REVERT: H 137 GLN cc_start: 0.6730 (mt0) cc_final: 0.6464 (mt0) REVERT: I 1 MET cc_start: 0.5770 (ttt) cc_final: 0.4925 (ttt) REVERT: K 103 ILE cc_start: 0.8957 (tt) cc_final: 0.8663 (tt) REVERT: K 124 LEU cc_start: 0.9189 (tt) cc_final: 0.8723 (tt) REVERT: K 128 CYS cc_start: 0.8872 (m) cc_final: 0.8663 (m) REVERT: M 181 PRO cc_start: 0.7393 (Cg_endo) cc_final: 0.7109 (Cg_exo) REVERT: O 81 GLU cc_start: 0.6817 (mm-30) cc_final: 0.6560 (mm-30) REVERT: O 144 MET cc_start: 0.6020 (tpt) cc_final: 0.5346 (tmm) REVERT: O 484 MET cc_start: 0.7816 (mpp) cc_final: 0.7210 (mpp) REVERT: O 580 ASN cc_start: 0.6592 (m110) cc_final: 0.6350 (m110) REVERT: Q 61 PHE cc_start: 0.6491 (t80) cc_final: 0.5702 (t80) outliers start: 8 outliers final: 2 residues processed: 790 average time/residue: 0.5563 time to fit residues: 741.3935 Evaluate side-chains 547 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 545 time to evaluate : 5.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 289 optimal weight: 40.0000 chunk 161 optimal weight: 9.9990 chunk 433 optimal weight: 10.0000 chunk 354 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 521 optimal weight: 7.9990 chunk 563 optimal weight: 10.0000 chunk 464 optimal weight: 50.0000 chunk 516 optimal weight: 50.0000 chunk 177 optimal weight: 10.0000 chunk 418 optimal weight: 10.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 GLN ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN A 688 GLN ** A 707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 HIS ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 ASN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN G 31 ASN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 254 GLN ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 367 ASN ** S 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 440 ASN ** S 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 528 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.141 48912 Z= 0.467 Angle : 0.916 17.251 66516 Z= 0.483 Chirality : 0.049 0.424 7529 Planarity : 0.007 0.088 8164 Dihedral : 17.151 170.108 7491 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 33.75 Ramachandran Plot: Outliers : 0.91 % Allowed : 15.06 % Favored : 84.04 % Rotamer: Outliers : 0.18 % Allowed : 4.66 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.69 (0.10), residues: 5625 helix: -1.93 (0.10), residues: 1942 sheet: -2.30 (0.18), residues: 609 loop : -2.90 (0.10), residues: 3074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 31 HIS 0.016 0.002 HIS A1318 PHE 0.034 0.002 PHE I 33 TYR 0.033 0.003 TYR C 157 ARG 0.044 0.001 ARG A1152 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 652 time to evaluate : 5.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 84 LEU cc_start: 0.8611 (tt) cc_final: 0.8156 (tt) REVERT: A 95 TYR cc_start: 0.7729 (m-10) cc_final: 0.7293 (m-10) REVERT: A 176 LEU cc_start: 0.9400 (mp) cc_final: 0.8830 (mp) REVERT: A 219 MET cc_start: 0.7358 (ptp) cc_final: 0.7133 (ptp) REVERT: A 365 ARG cc_start: 0.6664 (pmt-80) cc_final: 0.5959 (pmt170) REVERT: A 384 ASP cc_start: 0.8929 (t0) cc_final: 0.8599 (t0) REVERT: A 456 LEU cc_start: 0.8672 (tp) cc_final: 0.8433 (tp) REVERT: A 470 ASP cc_start: 0.6950 (m-30) cc_final: 0.6226 (m-30) REVERT: A 694 MET cc_start: 0.7428 (mmt) cc_final: 0.7153 (tpp) REVERT: A 716 ASP cc_start: 0.8913 (m-30) cc_final: 0.8528 (m-30) REVERT: A 828 GLN cc_start: 0.6961 (tt0) cc_final: 0.6314 (mm-40) REVERT: A 885 MET cc_start: 0.7482 (ttt) cc_final: 0.7126 (ttp) REVERT: A 1336 ILE cc_start: 0.9534 (pt) cc_final: 0.9277 (tt) REVERT: A 1348 MET cc_start: 0.8047 (pmm) cc_final: 0.7779 (pmm) REVERT: A 1362 MET cc_start: 0.8801 (tpp) cc_final: 0.8547 (tpt) REVERT: A 1421 MET cc_start: 0.9082 (ttm) cc_final: 0.8143 (ttp) REVERT: B 281 ASP cc_start: 0.7703 (p0) cc_final: 0.7366 (p0) REVERT: B 469 MET cc_start: 0.9142 (ptm) cc_final: 0.8853 (tmm) REVERT: B 492 SER cc_start: 0.9174 (p) cc_final: 0.8885 (t) REVERT: B 538 VAL cc_start: 0.7229 (p) cc_final: 0.6895 (p) REVERT: B 649 LEU cc_start: 0.7739 (mp) cc_final: 0.7483 (mp) REVERT: B 698 ARG cc_start: 0.8928 (mmt90) cc_final: 0.8257 (tpp80) REVERT: B 942 ILE cc_start: 0.8842 (mt) cc_final: 0.8571 (tt) REVERT: B 1018 PHE cc_start: 0.7778 (t80) cc_final: 0.7154 (t80) REVERT: B 1087 SER cc_start: 0.8523 (m) cc_final: 0.8275 (p) REVERT: B 1137 ILE cc_start: 0.9208 (mt) cc_final: 0.8906 (mm) REVERT: C 75 VAL cc_start: 0.9237 (m) cc_final: 0.8944 (m) REVERT: C 101 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.8885 (tp) REVERT: D 98 MET cc_start: 0.6090 (mmp) cc_final: 0.5172 (mmt) REVERT: E 18 THR cc_start: 0.9370 (m) cc_final: 0.9115 (m) REVERT: E 114 ASN cc_start: 0.7289 (m110) cc_final: 0.7013 (m-40) REVERT: E 136 ASN cc_start: 0.7209 (t0) cc_final: 0.6475 (t0) REVERT: F 114 GLU cc_start: 0.8671 (pp20) cc_final: 0.7649 (pm20) REVERT: H 122 LEU cc_start: 0.8179 (mm) cc_final: 0.7716 (tt) REVERT: H 137 GLN cc_start: 0.6989 (mt0) cc_final: 0.6706 (mt0) REVERT: I 1 MET cc_start: 0.5965 (ttt) cc_final: 0.5163 (ttt) REVERT: K 91 TYR cc_start: 0.8759 (p90) cc_final: 0.8553 (p90) REVERT: K 124 LEU cc_start: 0.9138 (tt) cc_final: 0.8907 (tt) REVERT: K 129 ASP cc_start: 0.8245 (m-30) cc_final: 0.7926 (m-30) REVERT: L 56 LEU cc_start: 0.8826 (pp) cc_final: 0.8507 (pp) REVERT: O 32 MET cc_start: 0.4910 (tmm) cc_final: 0.4147 (mmp) REVERT: O 71 LEU cc_start: 0.7756 (tt) cc_final: 0.7531 (tp) REVERT: O 81 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6802 (mm-30) REVERT: O 138 ASP cc_start: 0.6818 (t70) cc_final: 0.6588 (t0) REVERT: O 144 MET cc_start: 0.6183 (tpt) cc_final: 0.5679 (tmm) REVERT: P 148 TYR cc_start: 0.5075 (m-80) cc_final: 0.4822 (m-10) REVERT: Q 61 PHE cc_start: 0.6293 (t80) cc_final: 0.5593 (t80) outliers start: 9 outliers final: 1 residues processed: 659 average time/residue: 0.5687 time to fit residues: 633.0770 Evaluate side-chains 483 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 481 time to evaluate : 5.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 515 optimal weight: 0.7980 chunk 391 optimal weight: 5.9990 chunk 270 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 248 optimal weight: 10.0000 chunk 350 optimal weight: 10.0000 chunk 523 optimal weight: 30.0000 chunk 553 optimal weight: 30.0000 chunk 273 optimal weight: 10.0000 chunk 495 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 707 ASN ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 801 HIS B 821 HIS B 883 GLN ** B1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN G 31 ASN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN ** M 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 178 GLN M 254 GLN O 43 ASN O 332 GLN ** O 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 440 ASN ** S 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 528 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 48912 Z= 0.270 Angle : 0.785 15.390 66516 Z= 0.412 Chirality : 0.046 0.436 7529 Planarity : 0.005 0.085 8164 Dihedral : 16.915 169.148 7491 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 26.02 Ramachandran Plot: Outliers : 0.94 % Allowed : 13.23 % Favored : 85.83 % Rotamer: Outliers : 0.02 % Allowed : 3.54 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.10), residues: 5625 helix: -1.31 (0.11), residues: 1956 sheet: -2.08 (0.18), residues: 609 loop : -2.69 (0.11), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 13 HIS 0.011 0.001 HIS A1318 PHE 0.034 0.002 PHE I 33 TYR 0.022 0.002 TYR O 199 ARG 0.022 0.001 ARG O 534 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 701 time to evaluate : 5.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 84 LEU cc_start: 0.8451 (tt) cc_final: 0.8057 (tt) REVERT: A 95 TYR cc_start: 0.7263 (m-10) cc_final: 0.6794 (m-10) REVERT: A 219 MET cc_start: 0.7286 (ptp) cc_final: 0.7049 (ptp) REVERT: A 365 ARG cc_start: 0.6141 (pmt-80) cc_final: 0.5445 (pmt170) REVERT: A 384 ASP cc_start: 0.8585 (t0) cc_final: 0.7981 (t0) REVERT: A 419 LEU cc_start: 0.8900 (tp) cc_final: 0.8620 (tp) REVERT: A 456 LEU cc_start: 0.8654 (tp) cc_final: 0.8426 (tp) REVERT: A 470 ASP cc_start: 0.7108 (m-30) cc_final: 0.6461 (m-30) REVERT: A 563 LEU cc_start: 0.8485 (mm) cc_final: 0.8205 (mm) REVERT: A 694 MET cc_start: 0.7509 (mmt) cc_final: 0.7251 (tpp) REVERT: A 828 GLN cc_start: 0.7076 (tt0) cc_final: 0.6576 (mm-40) REVERT: A 885 MET cc_start: 0.7469 (ttt) cc_final: 0.6968 (ttp) REVERT: A 1348 MET cc_start: 0.8300 (pmm) cc_final: 0.7964 (pmm) REVERT: A 1362 MET cc_start: 0.8862 (tpp) cc_final: 0.8462 (tpp) REVERT: A 1421 MET cc_start: 0.8956 (ttm) cc_final: 0.8407 (ttp) REVERT: B 193 VAL cc_start: 0.8869 (t) cc_final: 0.8557 (p) REVERT: B 469 MET cc_start: 0.9127 (ptm) cc_final: 0.8687 (tmm) REVERT: B 492 SER cc_start: 0.9172 (p) cc_final: 0.8829 (t) REVERT: B 516 LEU cc_start: 0.8170 (mp) cc_final: 0.7813 (tp) REVERT: B 942 ILE cc_start: 0.8869 (mt) cc_final: 0.8560 (tt) REVERT: B 961 LEU cc_start: 0.8550 (tt) cc_final: 0.8256 (tt) REVERT: B 984 LEU cc_start: 0.8112 (tt) cc_final: 0.7840 (tt) REVERT: B 990 ILE cc_start: 0.8991 (mt) cc_final: 0.8699 (mm) REVERT: B 1018 PHE cc_start: 0.7585 (t80) cc_final: 0.7062 (t80) REVERT: B 1137 ILE cc_start: 0.9273 (mt) cc_final: 0.9002 (mm) REVERT: C 70 ILE cc_start: 0.8704 (tt) cc_final: 0.8452 (tt) REVERT: C 75 VAL cc_start: 0.9128 (m) cc_final: 0.8855 (m) REVERT: C 101 ILE cc_start: 0.9326 (mp) cc_final: 0.8891 (tp) REVERT: C 248 GLN cc_start: 0.8739 (pt0) cc_final: 0.8116 (pp30) REVERT: D 98 MET cc_start: 0.5837 (mmp) cc_final: 0.4866 (mmt) REVERT: F 85 MET cc_start: 0.8316 (mmp) cc_final: 0.8104 (mmm) REVERT: F 114 GLU cc_start: 0.8509 (pp20) cc_final: 0.7792 (pm20) REVERT: H 122 LEU cc_start: 0.8308 (mm) cc_final: 0.7703 (tt) REVERT: H 137 GLN cc_start: 0.6954 (mt0) cc_final: 0.6425 (mt0) REVERT: I 1 MET cc_start: 0.5897 (ttt) cc_final: 0.5106 (ttt) REVERT: I 9 ASN cc_start: 0.8313 (m110) cc_final: 0.8081 (m110) REVERT: K 124 LEU cc_start: 0.9056 (tt) cc_final: 0.8490 (tt) REVERT: K 128 CYS cc_start: 0.8940 (m) cc_final: 0.8362 (t) REVERT: K 129 ASP cc_start: 0.8299 (m-30) cc_final: 0.7750 (m-30) REVERT: N 417 VAL cc_start: 0.7373 (m) cc_final: 0.7142 (m) REVERT: O 81 GLU cc_start: 0.6897 (mm-30) cc_final: 0.6498 (mm-30) REVERT: O 144 MET cc_start: 0.6022 (tpt) cc_final: 0.5583 (tmm) REVERT: O 197 MET cc_start: 0.7256 (ppp) cc_final: 0.6973 (ppp) REVERT: O 286 ARG cc_start: 0.5125 (mmp80) cc_final: 0.4881 (mmp80) REVERT: O 484 MET cc_start: 0.7655 (mpp) cc_final: 0.7361 (mpp) REVERT: Q 43 ILE cc_start: 0.7209 (pt) cc_final: 0.6972 (pt) REVERT: Q 49 ASN cc_start: 0.6932 (t0) cc_final: 0.6697 (t0) REVERT: Q 61 PHE cc_start: 0.6042 (t80) cc_final: 0.5464 (t80) outliers start: 1 outliers final: 0 residues processed: 701 average time/residue: 0.5902 time to fit residues: 707.9430 Evaluate side-chains 503 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 503 time to evaluate : 5.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 461 optimal weight: 4.9990 chunk 314 optimal weight: 9.9990 chunk 8 optimal weight: 0.8980 chunk 412 optimal weight: 0.9980 chunk 228 optimal weight: 3.9990 chunk 472 optimal weight: 20.0000 chunk 382 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 282 optimal weight: 4.9990 chunk 497 optimal weight: 20.0000 chunk 139 optimal weight: 8.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 707 ASN ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 ASN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 883 GLN B1029 HIS ** B1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN H 139 ASN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 178 GLN M 254 GLN ** O 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 575 ASN ** O 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 444 GLN S 528 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 48912 Z= 0.269 Angle : 0.769 16.293 66516 Z= 0.402 Chirality : 0.046 0.465 7529 Planarity : 0.005 0.089 8164 Dihedral : 16.742 165.320 7491 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 24.95 Ramachandran Plot: Outliers : 1.01 % Allowed : 13.26 % Favored : 85.72 % Rotamer: Outliers : 0.02 % Allowed : 3.82 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.10), residues: 5625 helix: -0.97 (0.11), residues: 1969 sheet: -2.06 (0.18), residues: 634 loop : -2.64 (0.11), residues: 3022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 31 HIS 0.011 0.001 HIS A1318 PHE 0.034 0.002 PHE I 33 TYR 0.024 0.002 TYR C 157 ARG 0.013 0.001 ARG O 534 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 671 time to evaluate : 5.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 84 LEU cc_start: 0.8512 (tt) cc_final: 0.8296 (tt) REVERT: A 219 MET cc_start: 0.7323 (ptp) cc_final: 0.6986 (ptp) REVERT: A 384 ASP cc_start: 0.8574 (t0) cc_final: 0.8132 (t0) REVERT: A 456 LEU cc_start: 0.8763 (tp) cc_final: 0.8499 (tp) REVERT: A 470 ASP cc_start: 0.7200 (m-30) cc_final: 0.6551 (m-30) REVERT: A 501 ASN cc_start: 0.8938 (t0) cc_final: 0.8646 (t0) REVERT: A 568 ASP cc_start: 0.8885 (m-30) cc_final: 0.8504 (m-30) REVERT: A 571 TYR cc_start: 0.8165 (m-80) cc_final: 0.7762 (m-80) REVERT: A 694 MET cc_start: 0.7599 (mmt) cc_final: 0.7306 (tpp) REVERT: A 828 GLN cc_start: 0.7054 (tt0) cc_final: 0.6505 (mm-40) REVERT: A 885 MET cc_start: 0.7376 (ttt) cc_final: 0.6965 (ttp) REVERT: A 926 MET cc_start: 0.8439 (tpp) cc_final: 0.8181 (tpp) REVERT: A 1362 MET cc_start: 0.8858 (tpp) cc_final: 0.8513 (tpp) REVERT: A 1409 GLU cc_start: 0.6331 (tm-30) cc_final: 0.5853 (tm-30) REVERT: A 1421 MET cc_start: 0.8992 (ttm) cc_final: 0.8250 (ttp) REVERT: B 193 VAL cc_start: 0.8927 (t) cc_final: 0.8677 (p) REVERT: B 332 ILE cc_start: 0.8415 (pt) cc_final: 0.8172 (pt) REVERT: B 469 MET cc_start: 0.9129 (ptm) cc_final: 0.8711 (tmm) REVERT: B 492 SER cc_start: 0.9208 (p) cc_final: 0.8905 (t) REVERT: B 523 ASP cc_start: 0.8072 (t0) cc_final: 0.7801 (p0) REVERT: B 531 LYS cc_start: 0.8501 (ptpt) cc_final: 0.7973 (ttpt) REVERT: B 961 LEU cc_start: 0.8584 (tt) cc_final: 0.8348 (tt) REVERT: B 987 MET cc_start: 0.8060 (mmp) cc_final: 0.7838 (mmp) REVERT: B 1018 PHE cc_start: 0.7368 (t80) cc_final: 0.7077 (t80) REVERT: C 75 VAL cc_start: 0.9067 (m) cc_final: 0.8810 (p) REVERT: C 101 ILE cc_start: 0.9349 (mp) cc_final: 0.8846 (tp) REVERT: C 248 GLN cc_start: 0.8644 (pt0) cc_final: 0.8116 (pp30) REVERT: C 320 ILE cc_start: 0.9110 (mt) cc_final: 0.8674 (tp) REVERT: D 98 MET cc_start: 0.5665 (mmp) cc_final: 0.4653 (mmt) REVERT: E 136 ASN cc_start: 0.6877 (t0) cc_final: 0.6407 (t0) REVERT: F 85 MET cc_start: 0.8215 (mmp) cc_final: 0.7833 (mmm) REVERT: F 114 GLU cc_start: 0.8581 (pp20) cc_final: 0.7701 (pm20) REVERT: H 122 LEU cc_start: 0.8103 (mm) cc_final: 0.7752 (tt) REVERT: I 1 MET cc_start: 0.5651 (ttt) cc_final: 0.4893 (ttt) REVERT: K 91 TYR cc_start: 0.8498 (p90) cc_final: 0.8238 (p90) REVERT: K 124 LEU cc_start: 0.9067 (tt) cc_final: 0.8763 (tt) REVERT: K 129 ASP cc_start: 0.8240 (m-30) cc_final: 0.7811 (m-30) REVERT: O 81 GLU cc_start: 0.6938 (mm-30) cc_final: 0.6495 (mm-30) REVERT: O 144 MET cc_start: 0.6066 (tpt) cc_final: 0.5467 (tmm) REVERT: Q 49 ASN cc_start: 0.7107 (t0) cc_final: 0.6810 (t0) REVERT: Q 61 PHE cc_start: 0.5818 (t80) cc_final: 0.5407 (t80) outliers start: 1 outliers final: 0 residues processed: 671 average time/residue: 0.5472 time to fit residues: 624.1387 Evaluate side-chains 483 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 483 time to evaluate : 5.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 186 optimal weight: 0.0020 chunk 498 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 325 optimal weight: 0.0670 chunk 136 optimal weight: 2.9990 chunk 554 optimal weight: 7.9990 chunk 460 optimal weight: 10.0000 chunk 256 optimal weight: 10.0000 chunk 46 optimal weight: 0.3980 chunk 183 optimal weight: 0.0270 chunk 291 optimal weight: 40.0000 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 ASN ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 HIS ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 ASN ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 ASN H 139 ASN K 64 GLN ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 178 GLN M 254 GLN N 308 GLN O 161 GLN ** O 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 124 ASN ** S 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 528 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 48912 Z= 0.203 Angle : 0.756 12.874 66516 Z= 0.389 Chirality : 0.046 0.350 7529 Planarity : 0.005 0.081 8164 Dihedral : 16.537 167.474 7491 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 20.99 Ramachandran Plot: Outliers : 1.05 % Allowed : 11.91 % Favored : 87.04 % Rotamer: Outliers : 0.06 % Allowed : 2.15 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.11), residues: 5625 helix: -0.68 (0.11), residues: 1983 sheet: -1.82 (0.19), residues: 623 loop : -2.54 (0.11), residues: 3019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 13 HIS 0.012 0.001 HIS C 297 PHE 0.036 0.002 PHE I 33 TYR 0.027 0.002 TYR A 508 ARG 0.011 0.000 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 729 time to evaluate : 5.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 93 ILE cc_start: 0.7504 (tt) cc_final: 0.7134 (tt) REVERT: A 95 TYR cc_start: 0.7062 (m-10) cc_final: 0.6386 (m-10) REVERT: A 219 MET cc_start: 0.7418 (ptp) cc_final: 0.7175 (ptp) REVERT: A 289 LEU cc_start: 0.9235 (pp) cc_final: 0.8966 (tt) REVERT: A 384 ASP cc_start: 0.8340 (t0) cc_final: 0.7576 (t0) REVERT: A 419 LEU cc_start: 0.8712 (tp) cc_final: 0.8442 (tp) REVERT: A 456 LEU cc_start: 0.8857 (tp) cc_final: 0.8560 (tp) REVERT: A 542 LEU cc_start: 0.8398 (mt) cc_final: 0.8054 (mt) REVERT: A 551 ILE cc_start: 0.9005 (pt) cc_final: 0.8627 (pt) REVERT: A 563 LEU cc_start: 0.8174 (mm) cc_final: 0.7820 (mm) REVERT: A 568 ASP cc_start: 0.8596 (m-30) cc_final: 0.8292 (m-30) REVERT: A 571 TYR cc_start: 0.8181 (m-80) cc_final: 0.7858 (m-80) REVERT: A 694 MET cc_start: 0.7477 (mmt) cc_final: 0.7255 (tpp) REVERT: A 885 MET cc_start: 0.7450 (ttt) cc_final: 0.6867 (ttp) REVERT: A 926 MET cc_start: 0.8380 (tpp) cc_final: 0.8050 (tpp) REVERT: A 1304 MET cc_start: 0.5925 (mmm) cc_final: 0.5607 (mmm) REVERT: A 1362 MET cc_start: 0.8873 (tpp) cc_final: 0.8328 (tpp) REVERT: A 1421 MET cc_start: 0.8747 (ttm) cc_final: 0.8355 (ttp) REVERT: B 193 VAL cc_start: 0.8803 (t) cc_final: 0.8510 (p) REVERT: B 281 ASP cc_start: 0.7161 (p0) cc_final: 0.6924 (p0) REVERT: B 351 MET cc_start: 0.7498 (tpt) cc_final: 0.7097 (tpt) REVERT: B 469 MET cc_start: 0.9106 (ptm) cc_final: 0.8884 (tmm) REVERT: B 531 LYS cc_start: 0.8358 (ptpt) cc_final: 0.7976 (ttpt) REVERT: B 727 LEU cc_start: 0.8932 (pp) cc_final: 0.8492 (pp) REVERT: B 728 MET cc_start: 0.8112 (mtp) cc_final: 0.7879 (mtp) REVERT: B 961 LEU cc_start: 0.8571 (tt) cc_final: 0.8296 (tt) REVERT: B 1065 MET cc_start: 0.7269 (tpp) cc_final: 0.6976 (tpp) REVERT: B 1136 ASN cc_start: 0.7889 (t0) cc_final: 0.6095 (m-40) REVERT: B 1137 ILE cc_start: 0.9351 (mt) cc_final: 0.9132 (mm) REVERT: C 70 ILE cc_start: 0.8422 (tt) cc_final: 0.7851 (tt) REVERT: C 75 VAL cc_start: 0.8946 (m) cc_final: 0.8673 (p) REVERT: C 101 ILE cc_start: 0.9285 (mp) cc_final: 0.8730 (tp) REVERT: C 320 ILE cc_start: 0.8991 (mt) cc_final: 0.8633 (tp) REVERT: D 98 MET cc_start: 0.5427 (mmp) cc_final: 0.4400 (mmt) REVERT: E 136 ASN cc_start: 0.6778 (t0) cc_final: 0.6206 (t0) REVERT: F 89 GLU cc_start: 0.5595 (tm-30) cc_final: 0.4908 (tm-30) REVERT: F 114 GLU cc_start: 0.8281 (pp20) cc_final: 0.8049 (pm20) REVERT: H 122 LEU cc_start: 0.8078 (mm) cc_final: 0.7774 (tt) REVERT: I 1 MET cc_start: 0.5457 (ttt) cc_final: 0.4641 (ttt) REVERT: K 47 ILE cc_start: 0.7665 (pt) cc_final: 0.7337 (pt) REVERT: K 60 SER cc_start: 0.6864 (m) cc_final: 0.6622 (m) REVERT: K 126 ASP cc_start: 0.8144 (m-30) cc_final: 0.7877 (m-30) REVERT: K 129 ASP cc_start: 0.8175 (m-30) cc_final: 0.7777 (m-30) REVERT: N 388 THR cc_start: 0.9177 (m) cc_final: 0.8708 (p) REVERT: O 81 GLU cc_start: 0.6804 (mm-30) cc_final: 0.6369 (mm-30) REVERT: O 144 MET cc_start: 0.5928 (tpt) cc_final: 0.5384 (tmm) REVERT: Q 49 ASN cc_start: 0.7110 (t0) cc_final: 0.6862 (t0) REVERT: Q 61 PHE cc_start: 0.5763 (t80) cc_final: 0.5461 (t80) outliers start: 3 outliers final: 0 residues processed: 730 average time/residue: 0.5385 time to fit residues: 672.7863 Evaluate side-chains 511 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 511 time to evaluate : 5.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 534 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 315 optimal weight: 3.9990 chunk 404 optimal weight: 5.9990 chunk 313 optimal weight: 3.9990 chunk 466 optimal weight: 0.5980 chunk 309 optimal weight: 9.9990 chunk 552 optimal weight: 20.0000 chunk 345 optimal weight: 10.0000 chunk 336 optimal weight: 0.8980 chunk 254 optimal weight: 0.9980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 ASN ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 754 ASN ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 821 HIS ** B1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN G 69 ASN H 139 ASN K 64 GLN ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 178 GLN M 254 GLN ** N 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 369 HIS ** O 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 184 HIS ** S 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 528 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 48912 Z= 0.229 Angle : 0.750 12.815 66516 Z= 0.388 Chirality : 0.046 0.471 7529 Planarity : 0.005 0.083 8164 Dihedral : 16.395 170.175 7491 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 22.07 Ramachandran Plot: Outliers : 1.00 % Allowed : 12.55 % Favored : 86.45 % Rotamer: Outliers : 0.06 % Allowed : 1.61 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.54 (0.11), residues: 5625 helix: -0.52 (0.11), residues: 2004 sheet: -1.88 (0.18), residues: 665 loop : -2.55 (0.11), residues: 2956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 315 HIS 0.021 0.001 HIS E 146 PHE 0.032 0.002 PHE I 33 TYR 0.033 0.002 TYR F 84 ARG 0.016 0.001 ARG O 291 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 666 time to evaluate : 6.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 95 TYR cc_start: 0.6837 (m-10) cc_final: 0.6614 (m-10) REVERT: A 219 MET cc_start: 0.7428 (ptp) cc_final: 0.7159 (ptp) REVERT: A 289 LEU cc_start: 0.9250 (pp) cc_final: 0.9009 (tt) REVERT: A 384 ASP cc_start: 0.8305 (t0) cc_final: 0.7730 (t0) REVERT: A 456 LEU cc_start: 0.8822 (tp) cc_final: 0.8534 (tp) REVERT: A 501 ASN cc_start: 0.8731 (t0) cc_final: 0.8479 (t0) REVERT: A 568 ASP cc_start: 0.8718 (m-30) cc_final: 0.8261 (m-30) REVERT: A 694 MET cc_start: 0.7459 (mmt) cc_final: 0.7231 (tpp) REVERT: A 885 MET cc_start: 0.7382 (ttt) cc_final: 0.7002 (ttp) REVERT: A 894 GLU cc_start: 0.7275 (tt0) cc_final: 0.6964 (tt0) REVERT: A 926 MET cc_start: 0.8416 (tpp) cc_final: 0.8118 (tpp) REVERT: A 1304 MET cc_start: 0.5927 (mmm) cc_final: 0.5684 (mmm) REVERT: A 1362 MET cc_start: 0.8884 (tpp) cc_final: 0.8399 (tpp) REVERT: A 1421 MET cc_start: 0.8774 (ttm) cc_final: 0.8108 (ttp) REVERT: B 193 VAL cc_start: 0.9026 (t) cc_final: 0.8614 (p) REVERT: B 351 MET cc_start: 0.7410 (tpt) cc_final: 0.7024 (tpt) REVERT: B 390 ASP cc_start: 0.8372 (p0) cc_final: 0.8136 (p0) REVERT: B 469 MET cc_start: 0.9117 (ptm) cc_final: 0.8834 (tmm) REVERT: B 531 LYS cc_start: 0.8493 (ptpt) cc_final: 0.8155 (ttpt) REVERT: B 746 TYR cc_start: 0.8476 (t80) cc_final: 0.8205 (t80) REVERT: B 961 LEU cc_start: 0.8614 (tt) cc_final: 0.8108 (tt) REVERT: B 987 MET cc_start: 0.7933 (mmp) cc_final: 0.7613 (mmp) REVERT: B 1065 MET cc_start: 0.7131 (tpp) cc_final: 0.6853 (tpp) REVERT: B 1068 ASP cc_start: 0.6361 (t0) cc_final: 0.5041 (t70) REVERT: B 1136 ASN cc_start: 0.6755 (t0) cc_final: 0.6121 (m-40) REVERT: C 70 ILE cc_start: 0.8477 (tt) cc_final: 0.8034 (tt) REVERT: C 93 GLN cc_start: 0.7226 (mp10) cc_final: 0.7019 (mt0) REVERT: C 101 ILE cc_start: 0.9233 (mp) cc_final: 0.8732 (tp) REVERT: C 320 ILE cc_start: 0.8934 (mt) cc_final: 0.8676 (tp) REVERT: D 98 MET cc_start: 0.5422 (mmp) cc_final: 0.4381 (mmt) REVERT: E 215 MET cc_start: 0.5830 (tmm) cc_final: 0.5476 (tmm) REVERT: F 89 GLU cc_start: 0.5589 (tm-30) cc_final: 0.5325 (tm-30) REVERT: I 1 MET cc_start: 0.5421 (ttt) cc_final: 0.4394 (ttt) REVERT: J 49 MET cc_start: 0.8876 (mmm) cc_final: 0.8427 (mmt) REVERT: M 166 MET cc_start: 0.7135 (tpp) cc_final: 0.6925 (tpt) REVERT: N 388 THR cc_start: 0.9099 (m) cc_final: 0.8799 (p) REVERT: O 81 GLU cc_start: 0.6803 (mm-30) cc_final: 0.6465 (mm-30) REVERT: O 144 MET cc_start: 0.5972 (tpt) cc_final: 0.5419 (tmm) REVERT: Q 49 ASN cc_start: 0.7150 (t0) cc_final: 0.6860 (t0) REVERT: Q 61 PHE cc_start: 0.5776 (t80) cc_final: 0.5511 (t80) outliers start: 3 outliers final: 1 residues processed: 667 average time/residue: 0.5234 time to fit residues: 602.0645 Evaluate side-chains 489 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 488 time to evaluate : 5.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 341 optimal weight: 0.2980 chunk 220 optimal weight: 10.0000 chunk 329 optimal weight: 10.0000 chunk 166 optimal weight: 0.5980 chunk 108 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 chunk 351 optimal weight: 9.9990 chunk 376 optimal weight: 0.9980 chunk 273 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 434 optimal weight: 8.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 HIS ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 936 GLN ** B1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 ASN ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN M 86 HIS M 178 GLN M 254 GLN ** O 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 528 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 48912 Z= 0.203 Angle : 0.740 12.148 66516 Z= 0.379 Chirality : 0.045 0.443 7529 Planarity : 0.005 0.103 8164 Dihedral : 16.249 171.006 7491 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 1.01 % Allowed : 11.77 % Favored : 87.22 % Rotamer: Outliers : 0.02 % Allowed : 1.08 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.11), residues: 5625 helix: -0.33 (0.12), residues: 2000 sheet: -1.80 (0.18), residues: 665 loop : -2.48 (0.11), residues: 2960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 315 HIS 0.018 0.001 HIS E 146 PHE 0.038 0.002 PHE A 610 TYR 0.024 0.002 TYR O 199 ARG 0.019 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 692 time to evaluate : 5.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.9445 (pp) cc_final: 0.8202 (tt) REVERT: A 219 MET cc_start: 0.7341 (ptp) cc_final: 0.7085 (ptp) REVERT: A 289 LEU cc_start: 0.9195 (pp) cc_final: 0.8968 (tt) REVERT: A 384 ASP cc_start: 0.8012 (t0) cc_final: 0.7427 (t0) REVERT: A 456 LEU cc_start: 0.8849 (tp) cc_final: 0.8579 (tp) REVERT: A 568 ASP cc_start: 0.8649 (m-30) cc_final: 0.8282 (m-30) REVERT: A 694 MET cc_start: 0.7501 (mmt) cc_final: 0.7134 (tpp) REVERT: A 885 MET cc_start: 0.7443 (ttt) cc_final: 0.6949 (tmm) REVERT: A 891 LYS cc_start: 0.8758 (mmtp) cc_final: 0.8444 (tppt) REVERT: A 926 MET cc_start: 0.8240 (tpp) cc_final: 0.7976 (tpp) REVERT: A 1059 LEU cc_start: 0.8555 (tt) cc_final: 0.8336 (tt) REVERT: A 1362 MET cc_start: 0.8797 (tpp) cc_final: 0.8264 (tpp) REVERT: A 1417 LEU cc_start: 0.9158 (mm) cc_final: 0.8929 (mm) REVERT: A 1421 MET cc_start: 0.8733 (ttm) cc_final: 0.8369 (ttp) REVERT: B 193 VAL cc_start: 0.8969 (t) cc_final: 0.8620 (p) REVERT: B 267 GLU cc_start: 0.7905 (tp30) cc_final: 0.7604 (tp30) REVERT: B 351 MET cc_start: 0.7399 (tpt) cc_final: 0.6986 (tpt) REVERT: B 390 ASP cc_start: 0.8289 (p0) cc_final: 0.8062 (p0) REVERT: B 469 MET cc_start: 0.9078 (ptm) cc_final: 0.8817 (tmm) REVERT: B 716 ASN cc_start: 0.9038 (p0) cc_final: 0.8600 (p0) REVERT: B 746 TYR cc_start: 0.8366 (t80) cc_final: 0.8072 (t80) REVERT: B 961 LEU cc_start: 0.8529 (tt) cc_final: 0.8141 (tt) REVERT: B 962 ILE cc_start: 0.8991 (mp) cc_final: 0.8784 (mm) REVERT: B 987 MET cc_start: 0.7937 (mmp) cc_final: 0.7608 (mmp) REVERT: B 1065 MET cc_start: 0.7062 (tpp) cc_final: 0.6849 (tpp) REVERT: B 1136 ASN cc_start: 0.6943 (t0) cc_final: 0.6657 (m-40) REVERT: C 70 ILE cc_start: 0.8310 (tt) cc_final: 0.8020 (tt) REVERT: C 93 GLN cc_start: 0.7110 (mp10) cc_final: 0.6871 (mt0) REVERT: C 101 ILE cc_start: 0.9161 (mp) cc_final: 0.8769 (mm) REVERT: D 98 MET cc_start: 0.5319 (mmp) cc_final: 0.4326 (mmt) REVERT: E 215 MET cc_start: 0.5970 (tmm) cc_final: 0.5680 (tmm) REVERT: F 120 ILE cc_start: 0.8884 (pt) cc_final: 0.8683 (pt) REVERT: I 1 MET cc_start: 0.5379 (ttt) cc_final: 0.4394 (ttt) REVERT: J 49 MET cc_start: 0.8907 (mmm) cc_final: 0.8375 (mmt) REVERT: K 47 ILE cc_start: 0.7492 (pt) cc_final: 0.7288 (pt) REVERT: K 60 SER cc_start: 0.7353 (p) cc_final: 0.6384 (m) REVERT: K 126 ASP cc_start: 0.8040 (m-30) cc_final: 0.7798 (m-30) REVERT: L 64 LEU cc_start: 0.9152 (tp) cc_final: 0.8623 (mt) REVERT: N 388 THR cc_start: 0.9204 (m) cc_final: 0.8961 (p) REVERT: O 81 GLU cc_start: 0.6726 (mm-30) cc_final: 0.6373 (mm-30) REVERT: O 144 MET cc_start: 0.5950 (tpt) cc_final: 0.5392 (tmm) REVERT: Q 49 ASN cc_start: 0.7092 (t0) cc_final: 0.6811 (t0) REVERT: Q 61 PHE cc_start: 0.5870 (t80) cc_final: 0.5522 (t80) REVERT: R 520 ILE cc_start: 0.8398 (mp) cc_final: 0.8168 (mt) outliers start: 1 outliers final: 0 residues processed: 692 average time/residue: 0.5177 time to fit residues: 620.4692 Evaluate side-chains 504 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 5.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 502 optimal weight: 5.9990 chunk 529 optimal weight: 8.9990 chunk 482 optimal weight: 1.9990 chunk 514 optimal weight: 8.9990 chunk 528 optimal weight: 10.0000 chunk 309 optimal weight: 10.0000 chunk 224 optimal weight: 0.6980 chunk 404 optimal weight: 0.2980 chunk 157 optimal weight: 0.9990 chunk 465 optimal weight: 0.0570 chunk 486 optimal weight: 6.9990 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 ASN ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 GLN ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 821 HIS ** B1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN G 69 ASN H 139 ASN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 178 GLN M 254 GLN ** O 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.5212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 48912 Z= 0.195 Angle : 0.731 11.930 66516 Z= 0.374 Chirality : 0.045 0.390 7529 Planarity : 0.005 0.076 8164 Dihedral : 16.100 172.099 7491 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.98 % Allowed : 11.63 % Favored : 87.40 % Rotamer: Outliers : 0.06 % Allowed : 0.74 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.11), residues: 5625 helix: -0.27 (0.12), residues: 2011 sheet: -1.71 (0.19), residues: 668 loop : -2.45 (0.11), residues: 2946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 315 HIS 0.011 0.001 HIS B1036 PHE 0.033 0.002 PHE A 610 TYR 0.022 0.001 TYR O 199 ARG 0.013 0.000 ARG O 534 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 685 time to evaluate : 5.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.6650 (t80) cc_final: 0.6267 (t80) REVERT: A 115 LEU cc_start: 0.7201 (mt) cc_final: 0.6982 (mp) REVERT: A 141 LEU cc_start: 0.8565 (tt) cc_final: 0.8290 (tt) REVERT: A 219 MET cc_start: 0.7387 (ptp) cc_final: 0.7114 (ptp) REVERT: A 274 MET cc_start: 0.7509 (mmp) cc_final: 0.6942 (mmp) REVERT: A 384 ASP cc_start: 0.7829 (t0) cc_final: 0.7208 (t0) REVERT: A 456 LEU cc_start: 0.8898 (tp) cc_final: 0.8627 (tp) REVERT: A 559 THR cc_start: 0.8687 (t) cc_final: 0.8433 (t) REVERT: A 568 ASP cc_start: 0.8535 (m-30) cc_final: 0.8094 (m-30) REVERT: A 624 ILE cc_start: 0.9070 (mp) cc_final: 0.8694 (tt) REVERT: A 694 MET cc_start: 0.7448 (mmt) cc_final: 0.7092 (tpp) REVERT: A 926 MET cc_start: 0.8081 (tpp) cc_final: 0.7801 (tpp) REVERT: A 1059 LEU cc_start: 0.8495 (tt) cc_final: 0.8287 (tt) REVERT: A 1202 ILE cc_start: 0.5340 (tt) cc_final: 0.5062 (tt) REVERT: A 1304 MET cc_start: 0.6099 (mmm) cc_final: 0.5695 (tpt) REVERT: A 1362 MET cc_start: 0.8740 (tpp) cc_final: 0.8148 (tpp) REVERT: A 1403 MET cc_start: 0.8154 (mtm) cc_final: 0.7857 (tmm) REVERT: A 1421 MET cc_start: 0.8606 (ttm) cc_final: 0.8005 (ttp) REVERT: B 193 VAL cc_start: 0.9011 (t) cc_final: 0.8590 (p) REVERT: B 351 MET cc_start: 0.7376 (tpt) cc_final: 0.6950 (tpt) REVERT: B 469 MET cc_start: 0.9002 (ptm) cc_final: 0.8789 (tmm) REVERT: B 961 LEU cc_start: 0.8429 (tt) cc_final: 0.8067 (tt) REVERT: B 987 MET cc_start: 0.7851 (mmp) cc_final: 0.7461 (mmp) REVERT: B 1068 ASP cc_start: 0.6319 (t0) cc_final: 0.4372 (t70) REVERT: C 70 ILE cc_start: 0.8152 (tt) cc_final: 0.7907 (tt) REVERT: C 101 ILE cc_start: 0.9081 (mp) cc_final: 0.8648 (mm) REVERT: C 196 LEU cc_start: 0.8796 (pp) cc_final: 0.7830 (tt) REVERT: D 98 MET cc_start: 0.5230 (mmp) cc_final: 0.4225 (mmt) REVERT: I 1 MET cc_start: 0.5668 (ttt) cc_final: 0.4463 (ttt) REVERT: J 49 MET cc_start: 0.8877 (mmm) cc_final: 0.8370 (mmt) REVERT: J 63 TYR cc_start: 0.7744 (m-80) cc_final: 0.7541 (m-10) REVERT: K 80 ILE cc_start: 0.8410 (tp) cc_final: 0.8176 (tp) REVERT: K 89 CYS cc_start: 0.7703 (p) cc_final: 0.6783 (p) REVERT: L 56 LEU cc_start: 0.8377 (pp) cc_final: 0.8143 (pp) REVERT: L 64 LEU cc_start: 0.9101 (tp) cc_final: 0.8570 (mt) REVERT: N 388 THR cc_start: 0.9032 (m) cc_final: 0.8745 (p) REVERT: O 81 GLU cc_start: 0.6735 (mm-30) cc_final: 0.6313 (mm-30) REVERT: O 138 ASP cc_start: 0.6721 (t70) cc_final: 0.6517 (t0) REVERT: O 144 MET cc_start: 0.5845 (tpt) cc_final: 0.5273 (tmm) REVERT: Q 61 PHE cc_start: 0.5850 (t80) cc_final: 0.5542 (t80) outliers start: 3 outliers final: 1 residues processed: 686 average time/residue: 0.5229 time to fit residues: 624.3905 Evaluate side-chains 508 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 507 time to evaluate : 6.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 512 optimal weight: 8.9990 chunk 337 optimal weight: 0.0070 chunk 544 optimal weight: 30.0000 chunk 332 optimal weight: 0.7980 chunk 258 optimal weight: 10.0000 chunk 378 optimal weight: 10.0000 chunk 570 optimal weight: 10.0000 chunk 525 optimal weight: 40.0000 chunk 454 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 351 optimal weight: 9.9990 overall best weight: 4.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 ASN ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 ASN ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 ASN H 139 ASN ** I 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 254 GLN ** N 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 216 GLN ** O 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 626 GLN S 528 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 48912 Z= 0.305 Angle : 0.772 13.792 66516 Z= 0.400 Chirality : 0.046 0.449 7529 Planarity : 0.005 0.072 8164 Dihedral : 16.128 172.810 7491 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 24.40 Ramachandran Plot: Outliers : 0.96 % Allowed : 12.92 % Favored : 86.12 % Rotamer: Outliers : 0.04 % Allowed : 0.44 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.28 (0.11), residues: 5625 helix: -0.23 (0.12), residues: 2022 sheet: -1.68 (0.18), residues: 695 loop : -2.48 (0.11), residues: 2908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 258 HIS 0.012 0.001 HIS A1318 PHE 0.024 0.002 PHE I 33 TYR 0.019 0.002 TYR A1364 ARG 0.011 0.001 ARG O 534 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 640 time to evaluate : 5.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.7407 (ptp) cc_final: 0.7171 (ptp) REVERT: A 274 MET cc_start: 0.7522 (mmp) cc_final: 0.6992 (mmp) REVERT: A 384 ASP cc_start: 0.8438 (t0) cc_final: 0.7800 (t0) REVERT: A 456 LEU cc_start: 0.8877 (tp) cc_final: 0.8545 (tp) REVERT: A 568 ASP cc_start: 0.8633 (m-30) cc_final: 0.8214 (m-30) REVERT: A 694 MET cc_start: 0.7595 (mmt) cc_final: 0.7141 (tpp) REVERT: A 926 MET cc_start: 0.8318 (tpp) cc_final: 0.7961 (tpp) REVERT: A 1304 MET cc_start: 0.6092 (mmm) cc_final: 0.5708 (tpt) REVERT: A 1362 MET cc_start: 0.8813 (tpp) cc_final: 0.8443 (tpp) REVERT: A 1403 MET cc_start: 0.8311 (mtm) cc_final: 0.7774 (tmm) REVERT: A 1421 MET cc_start: 0.8741 (ttm) cc_final: 0.7973 (ttp) REVERT: B 193 VAL cc_start: 0.9101 (t) cc_final: 0.8755 (p) REVERT: B 267 GLU cc_start: 0.7624 (tp30) cc_final: 0.6987 (tp30) REVERT: B 469 MET cc_start: 0.9091 (ptm) cc_final: 0.8791 (tmm) REVERT: B 524 ASP cc_start: 0.6186 (t70) cc_final: 0.5602 (t0) REVERT: B 698 ARG cc_start: 0.8853 (mmt90) cc_final: 0.8089 (tpp80) REVERT: B 961 LEU cc_start: 0.8563 (tt) cc_final: 0.8034 (tt) REVERT: B 987 MET cc_start: 0.7979 (mmp) cc_final: 0.7729 (mmp) REVERT: B 1135 MET cc_start: 0.7613 (tmm) cc_final: 0.7242 (ttp) REVERT: C 93 GLN cc_start: 0.6941 (mp10) cc_final: 0.6610 (mt0) REVERT: C 101 ILE cc_start: 0.9191 (mp) cc_final: 0.8788 (mm) REVERT: D 98 MET cc_start: 0.5525 (mmp) cc_final: 0.4409 (mmt) REVERT: F 103 MET cc_start: 0.8514 (mmm) cc_final: 0.8182 (mmm) REVERT: I 1 MET cc_start: 0.5558 (ttt) cc_final: 0.4492 (ttt) REVERT: J 49 MET cc_start: 0.9006 (mmm) cc_final: 0.8579 (mmt) REVERT: L 56 LEU cc_start: 0.8573 (pp) cc_final: 0.8164 (pp) REVERT: L 64 LEU cc_start: 0.9084 (tp) cc_final: 0.8565 (mt) REVERT: N 388 THR cc_start: 0.9177 (m) cc_final: 0.8896 (p) REVERT: O 81 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6411 (mm-30) REVERT: O 144 MET cc_start: 0.5987 (tpt) cc_final: 0.5325 (tmm) REVERT: O 547 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7224 (tp30) REVERT: Q 61 PHE cc_start: 0.5946 (t80) cc_final: 0.5606 (t80) outliers start: 2 outliers final: 0 residues processed: 640 average time/residue: 0.5276 time to fit residues: 587.0689 Evaluate side-chains 477 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 477 time to evaluate : 5.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 278 optimal weight: 0.3980 chunk 361 optimal weight: 9.9990 chunk 484 optimal weight: 0.5980 chunk 139 optimal weight: 1.9990 chunk 419 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 126 optimal weight: 10.0000 chunk 455 optimal weight: 20.0000 chunk 190 optimal weight: 10.0000 chunk 467 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 HIS ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 ASN ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 821 HIS B1029 HIS ** B1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 ASN H 139 ASN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 178 GLN M 254 GLN ** O 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.072212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.050984 restraints weight = 243734.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.052734 restraints weight = 150900.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.053452 restraints weight = 100196.959| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.5500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 48912 Z= 0.192 Angle : 0.738 11.706 66516 Z= 0.376 Chirality : 0.045 0.415 7529 Planarity : 0.005 0.070 8164 Dihedral : 16.025 172.416 7491 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.92 % Allowed : 11.41 % Favored : 87.66 % Rotamer: Outliers : 0.04 % Allowed : 0.28 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.13 (0.11), residues: 5625 helix: -0.09 (0.12), residues: 2008 sheet: -1.44 (0.19), residues: 683 loop : -2.44 (0.11), residues: 2934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 258 HIS 0.011 0.001 HIS B1036 PHE 0.027 0.002 PHE E 96 TYR 0.030 0.002 TYR B 463 ARG 0.034 0.001 ARG A1280 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11384.27 seconds wall clock time: 206 minutes 38.03 seconds (12398.03 seconds total)