Starting phenix.real_space_refine on Tue Sep 15 15:07:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7d58_30577/09_2026/7d58_30577.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d58_30577/09_2026/7d58_30577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d58_30577/09_2026/7d58_30577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d58_30577/09_2026/7d58_30577.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7d58_30577/09_2026/7d58_30577.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7d58_30577/09_2026/7d58_30577.cif" model { file = "/net/cci-nas-00/data/ceres_data/7d58_30577/09_2026/7d58_30577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d58_30577/09_2026/7d58_30577.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 7 6.06 5 P 46 5.49 5 S 275 5.16 5 C 25509 2.51 5 N 7040 2.21 5 O 7687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 312 residue(s): 0.23s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40568 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 10886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1387, 10886 Classifications: {'peptide': 1387} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 65, 'TRANS': 1321} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 8668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8668 Classifications: {'peptide': 1095} Link IDs: {'PTRANS': 49, 'TRANS': 1045} Chain breaks: 2 Chain: "C" Number of atoms: 2752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2752 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 17, 'TRANS': 327} Chain: "D" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1013 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "E" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1723 Classifications: {'peptide': 210} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 198} Chain: "F" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 636 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "G" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1493 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 12, 'TRANS': 174} Chain breaks: 2 Chain: "H" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1197 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain: "I" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 857 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "L" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 397 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "M" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1797 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 13, 'TRANS': 208} Chain breaks: 3 Chain: "N" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1038 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 126} Chain breaks: 2 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: "O" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3913 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 16, 'TRANS': 473} Chain breaks: 2 Chain: "P" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1103 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain breaks: 1 Chain: "Q" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 746 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain: "R" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 346 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "S" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 493 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "T" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 106 Classifications: {'RNAv2': 5} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna3p': 4} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 550 SG CYS A 69 57.001 104.140 88.635 1.00115.93 S ATOM 883 SG CYS A 112 70.501 81.767 133.873 1.00113.13 S ATOM 19132 SG CYS B1080 62.140 112.388 104.186 1.00 95.80 S ATOM 19217 SG CYS B1092 60.293 108.758 104.656 1.00 92.65 S ATOM 19245 SG CYS B1095 59.781 109.673 108.550 1.00 89.96 S ATOM 28409 SG CYS I 5 119.774 39.307 116.688 1.00149.63 S ATOM 28426 SG CYS I 8 116.432 37.978 114.229 1.00148.59 S ATOM 28557 SG CYS I 25 116.433 39.191 118.960 1.00157.61 S ATOM 28578 SG CYS I 28 116.546 35.626 116.951 1.00155.81 S ATOM 29139 SG CYS I 98 139.994 109.604 98.025 1.00194.05 S ATOM 29167 SG CYS I 102 138.811 111.223 100.950 1.00189.84 S ATOM 29280 SG CYS J 7 113.284 107.138 41.015 1.00 62.64 S ATOM 29304 SG CYS J 10 114.613 110.503 39.098 1.00 65.29 S ATOM 30681 SG CYS L 19 78.870 79.992 39.103 1.00101.80 S ATOM 30817 SG CYS L 36 75.449 77.944 36.933 1.00116.57 S ATOM 30843 SG CYS L 39 78.381 76.193 38.192 1.00118.15 S ATOM 38652 SG CYS P 290 47.344 88.635 116.075 1.00109.42 S ATOM 38699 SG CYS P 296 50.310 93.866 117.666 1.00109.09 S ATOM 38776 SG CYS P 307 43.703 92.773 115.963 1.00114.75 S ATOM 38634 SG CYS P 287 46.424 91.361 122.216 1.00111.08 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="ZN ZN I 202 " occ=0.75 Time building chain proxies: 8.13, per 1000 atoms: 0.20 Number of scatterers: 40568 At special positions: 0 Unit cell: (172.7, 173.8, 181.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 Fe 4 26.01 S 275 16.00 P 46 15.00 O 7687 8.00 N 7040 7.00 C 25509 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.43 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 P 400 " pdb="FE2 SF4 P 400 " - pdb=" SG CYS P 296 " pdb="FE1 SF4 P 400 " - pdb=" SG CYS P 290 " pdb="FE3 SF4 P 400 " - pdb=" SG CYS P 307 " pdb="FE4 SF4 P 400 " - pdb=" SG CYS P 287 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 82 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 69 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 112 " pdb=" ZN B2001 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1095 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1092 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1080 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 5 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 25 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 28 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 102 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 98 " pdb=" ZN J 100 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " Number of angles added : 6 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9376 Finding SS restraints... Secondary structure from input PDB file: 163 helices and 54 sheets defined 37.8% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 97 through 108 Processing helix chain 'A' and resid 118 through 130 removed outlier: 3.552A pdb=" N LYS A 123 " --> pdb=" O GLN A 119 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 153 removed outlier: 3.641A pdb=" N LYS A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 197 through 201 Processing helix chain 'A' and resid 210 through 214 removed outlier: 4.005A pdb=" N ARG A 213 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 227 Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.617A pdb=" N LEU A 239 " --> pdb=" O PRO A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 300 removed outlier: 3.683A pdb=" N ILE A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 319 removed outlier: 3.717A pdb=" N ASP A 309 " --> pdb=" O MET A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 346 removed outlier: 3.516A pdb=" N ARG A 344 " --> pdb=" O GLY A 340 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.673A pdb=" N ILE A 389 " --> pdb=" O HIS A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 411 removed outlier: 3.666A pdb=" N LYS A 406 " --> pdb=" O ASN A 402 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 407 " --> pdb=" O PHE A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 443 removed outlier: 3.915A pdb=" N MET A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN A 442 " --> pdb=" O GLU A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 492 through 497 removed outlier: 4.028A pdb=" N TYR A 496 " --> pdb=" O VAL A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 517 removed outlier: 3.671A pdb=" N ALA A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 522 removed outlier: 3.726A pdb=" N VAL A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 560 through 568 removed outlier: 3.509A pdb=" N CYS A 565 " --> pdb=" O ARG A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 602 removed outlier: 3.717A pdb=" N PHE A 601 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A 602 " --> pdb=" O LYS A 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 597 through 602' Processing helix chain 'A' and resid 662 through 671 Processing helix chain 'A' and resid 673 through 679 removed outlier: 3.734A pdb=" N ALA A 677 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 679 " --> pdb=" O GLU A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 695 removed outlier: 3.868A pdb=" N LEU A 683 " --> pdb=" O ALA A 679 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 684 " --> pdb=" O MET A 680 " (cutoff:3.500A) Proline residue: A 688 - end of helix Processing helix chain 'A' and resid 706 through 734 removed outlier: 4.002A pdb=" N LYS A 711 " --> pdb=" O GLN A 707 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA A 712 " --> pdb=" O GLY A 708 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 716 " --> pdb=" O ALA A 712 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU A 726 " --> pdb=" O LYS A 722 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR A 727 " --> pdb=" O LYS A 723 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE A 728 " --> pdb=" O CYS A 724 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLU A 729 " --> pdb=" O ASP A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 752 Processing helix chain 'A' and resid 752 through 769 removed outlier: 3.625A pdb=" N SER A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 758 " --> pdb=" O LYS A 754 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE A 759 " --> pdb=" O GLU A 755 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG A 769 " --> pdb=" O SER A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 784 Processing helix chain 'A' and resid 788 through 796 Processing helix chain 'A' and resid 827 through 832 Processing helix chain 'A' and resid 843 through 859 removed outlier: 3.822A pdb=" N ALA A 853 " --> pdb=" O PHE A 849 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 857 " --> pdb=" O ALA A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 877 removed outlier: 3.788A pdb=" N VAL A 863 " --> pdb=" O VAL A 859 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N THR A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ALA A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU A 867 " --> pdb=" O VAL A 863 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS A 877 " --> pdb=" O ARG A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 932 removed outlier: 3.559A pdb=" N VAL A 924 " --> pdb=" O GLU A 920 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA A 930 " --> pdb=" O ASP A 926 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 954 removed outlier: 3.781A pdb=" N LEU A 947 " --> pdb=" O ASN A 943 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A 954 " --> pdb=" O GLU A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 988 removed outlier: 3.555A pdb=" N LEU A 966 " --> pdb=" O GLN A 962 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 972 " --> pdb=" O GLU A 968 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER A 977 " --> pdb=" O ILE A 973 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 978 " --> pdb=" O LYS A 974 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A 982 " --> pdb=" O GLU A 978 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 983 " --> pdb=" O LYS A 979 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR A 987 " --> pdb=" O THR A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1002 removed outlier: 3.727A pdb=" N TYR A1001 " --> pdb=" O ARG A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1025 removed outlier: 3.816A pdb=" N GLU A1012 " --> pdb=" O PRO A1008 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1039 removed outlier: 3.633A pdb=" N GLN A1039 " --> pdb=" O ALA A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1047 Processing helix chain 'A' and resid 1066 through 1076 Processing helix chain 'A' and resid 1094 through 1105 removed outlier: 3.702A pdb=" N ALA A1098 " --> pdb=" O ASP A1094 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG A1104 " --> pdb=" O LEU A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1139 Processing helix chain 'A' and resid 1145 through 1155 Processing helix chain 'A' and resid 1184 through 1193 removed outlier: 3.530A pdb=" N VAL A1188 " --> pdb=" O SER A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1237 Processing helix chain 'A' and resid 1250 through 1258 Processing helix chain 'A' and resid 1262 through 1277 removed outlier: 3.737A pdb=" N THR A1266 " --> pdb=" O ALA A1262 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A1267 " --> pdb=" O ALA A1263 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE A1268 " --> pdb=" O ARG A1264 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASN A1277 " --> pdb=" O TYR A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1294 removed outlier: 3.765A pdb=" N VAL A1287 " --> pdb=" O ASP A1283 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET A1294 " --> pdb=" O LEU A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1312 Processing helix chain 'A' and resid 1314 through 1320 Processing helix chain 'A' and resid 1323 through 1335 removed outlier: 4.088A pdb=" N HIS A1327 " --> pdb=" O LYS A1323 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1350 Processing helix chain 'A' and resid 1356 through 1360 removed outlier: 3.514A pdb=" N LEU A1359 " --> pdb=" O GLY A1356 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHE A1360 " --> pdb=" O THR A1357 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1356 through 1360' Processing helix chain 'B' and resid 25 through 27 No H-bonds generated for 'chain 'B' and resid 25 through 27' Processing helix chain 'B' and resid 28 through 37 removed outlier: 3.693A pdb=" N ALA B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 51 removed outlier: 3.626A pdb=" N ILE B 44 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE B 47 " --> pdb=" O HIS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 98 through 105 Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 236 through 244 Processing helix chain 'B' and resid 247 through 256 removed outlier: 3.586A pdb=" N ILE B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 removed outlier: 3.744A pdb=" N ALA B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 275 Processing helix chain 'B' and resid 279 through 291 Processing helix chain 'B' and resid 304 through 316 removed outlier: 3.566A pdb=" N THR B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 346 Processing helix chain 'B' and resid 364 through 388 removed outlier: 4.419A pdb=" N LEU B 368 " --> pdb=" O LEU B 364 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 422 Processing helix chain 'B' and resid 444 through 453 removed outlier: 3.536A pdb=" N LEU B 449 " --> pdb=" O TYR B 445 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET B 452 " --> pdb=" O ALA B 448 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 519 removed outlier: 3.592A pdb=" N GLY B 519 " --> pdb=" O ALA B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 533 Processing helix chain 'B' and resid 551 through 566 removed outlier: 3.788A pdb=" N LEU B 555 " --> pdb=" O ASP B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 617 removed outlier: 3.510A pdb=" N MET B 611 " --> pdb=" O THR B 607 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU B 613 " --> pdb=" O LYS B 609 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU B 614 " --> pdb=" O HIS B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 627 Processing helix chain 'B' and resid 637 through 641 Processing helix chain 'B' and resid 661 through 665 removed outlier: 3.746A pdb=" N LEU B 664 " --> pdb=" O PRO B 661 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 665 " --> pdb=" O PHE B 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 661 through 665' Processing helix chain 'B' and resid 667 through 672 removed outlier: 3.526A pdb=" N GLY B 670 " --> pdb=" O VAL B 667 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU B 671 " --> pdb=" O CYS B 668 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE B 672 " --> pdb=" O ALA B 669 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 672' Processing helix chain 'B' and resid 679 through 690 Processing helix chain 'B' and resid 722 through 729 Processing helix chain 'B' and resid 730 through 733 Processing helix chain 'B' and resid 759 through 765 Processing helix chain 'B' and resid 933 through 938 removed outlier: 3.596A pdb=" N ARG B 937 " --> pdb=" O GLY B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 956 Processing helix chain 'B' and resid 974 through 980 removed outlier: 4.065A pdb=" N ARG B 978 " --> pdb=" O GLU B 974 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N HIS B 979 " --> pdb=" O ASP B 975 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY B 980 " --> pdb=" O LEU B 976 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 974 through 980' Processing helix chain 'B' and resid 1048 through 1059 removed outlier: 3.530A pdb=" N CYS B1054 " --> pdb=" O MET B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1061 through 1067 Processing helix chain 'B' and resid 1107 through 1118 Processing helix chain 'B' and resid 1119 through 1121 No H-bonds generated for 'chain 'B' and resid 1119 through 1121' Processing helix chain 'C' and resid 3 through 12 removed outlier: 3.733A pdb=" N ARG C 11 " --> pdb=" O VAL C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 49 removed outlier: 3.644A pdb=" N LYS C 47 " --> pdb=" O ASP C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 80 removed outlier: 3.976A pdb=" N ALA C 73 " --> pdb=" O ASP C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 112 Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 169 through 173 Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'C' and resid 246 through 257 Processing helix chain 'C' and resid 285 through 289 removed outlier: 3.950A pdb=" N PHE C 288 " --> pdb=" O ARG C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 346 removed outlier: 3.553A pdb=" N LEU C 321 " --> pdb=" O PRO C 317 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL C 322 " --> pdb=" O PRO C 318 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS C 327 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS C 332 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS C 333 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 337 " --> pdb=" O CYS C 333 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA C 342 " --> pdb=" O ASP C 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 26 removed outlier: 3.723A pdb=" N VAL D 16 " --> pdb=" O SER D 12 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP D 22 " --> pdb=" O GLN D 18 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS D 24 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU D 25 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN D 26 " --> pdb=" O ASP D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 35 through 56 removed outlier: 3.803A pdb=" N LEU D 42 " --> pdb=" O GLY D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 74 Processing helix chain 'D' and resid 79 through 89 removed outlier: 4.111A pdb=" N LEU D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N HIS D 89 " --> pdb=" O GLN D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 101 removed outlier: 3.737A pdb=" N ILE D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL D 101 " --> pdb=" O ILE D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 122 Processing helix chain 'E' and resid 2 through 25 removed outlier: 3.610A pdb=" N GLY E 25 " --> pdb=" O CYS E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 removed outlier: 3.923A pdb=" N GLN E 43 " --> pdb=" O GLU E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 95 removed outlier: 4.052A pdb=" N TYR E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET E 94 " --> pdb=" O TYR E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.622A pdb=" N MET E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 164 removed outlier: 3.881A pdb=" N GLU E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 74 Processing helix chain 'F' and resid 88 through 99 removed outlier: 3.882A pdb=" N ILE F 92 " --> pdb=" O ASP F 88 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU F 97 " --> pdb=" O ALA F 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 34 Processing helix chain 'I' and resid 55 through 60 Processing helix chain 'J' and resid 17 through 25 Processing helix chain 'J' and resid 30 through 39 removed outlier: 3.883A pdb=" N GLY J 39 " --> pdb=" O LEU J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 51 Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 48 through 61 removed outlier: 3.592A pdb=" N GLY K 52 " --> pdb=" O ASP K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 130 removed outlier: 4.049A pdb=" N PHE K 96 " --> pdb=" O ALA K 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 7 removed outlier: 3.599A pdb=" N ASP M 6 " --> pdb=" O ASN M 3 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 83 Processing helix chain 'M' and resid 140 through 155 Processing helix chain 'M' and resid 192 through 203 removed outlier: 4.093A pdb=" N LEU M 196 " --> pdb=" O SER M 192 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU M 203 " --> pdb=" O LYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 215 through 227 Processing helix chain 'M' and resid 241 through 250 removed outlier: 3.962A pdb=" N MET M 247 " --> pdb=" O SER M 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 250 through 261 removed outlier: 3.532A pdb=" N THR N 261 " --> pdb=" O GLU N 257 " (cutoff:3.500A) Processing helix chain 'N' and resid 388 through 398 removed outlier: 3.736A pdb=" N LEU N 392 " --> pdb=" O ASP N 388 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 17 Processing helix chain 'O' and resid 18 through 31 removed outlier: 3.518A pdb=" N ILE O 29 " --> pdb=" O GLY O 25 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG O 30 " --> pdb=" O VAL O 26 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR O 31 " --> pdb=" O HIS O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 35 through 44 removed outlier: 3.701A pdb=" N GLY O 44 " --> pdb=" O ALA O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 60 Processing helix chain 'O' and resid 78 through 83 removed outlier: 3.633A pdb=" N VAL O 82 " --> pdb=" O GLN O 78 " (cutoff:3.500A) Processing helix chain 'O' and resid 84 through 86 No H-bonds generated for 'chain 'O' and resid 84 through 86' Processing helix chain 'O' and resid 87 through 99 removed outlier: 3.803A pdb=" N LEU O 98 " --> pdb=" O THR O 94 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 108 Processing helix chain 'O' and resid 109 through 114 Processing helix chain 'O' and resid 117 through 133 Processing helix chain 'O' and resid 140 through 154 removed outlier: 3.520A pdb=" N VAL O 144 " --> pdb=" O ASP O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 259 removed outlier: 3.854A pdb=" N PHE O 242 " --> pdb=" O ASN O 238 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET O 259 " --> pdb=" O VAL O 255 " (cutoff:3.500A) Processing helix chain 'O' and resid 261 through 271 removed outlier: 3.952A pdb=" N GLU O 265 " --> pdb=" O GLN O 261 " (cutoff:3.500A) Processing helix chain 'O' and resid 289 through 296 removed outlier: 3.510A pdb=" N SER O 296 " --> pdb=" O GLU O 292 " (cutoff:3.500A) Processing helix chain 'O' and resid 304 through 317 Processing helix chain 'O' and resid 338 through 358 removed outlier: 3.661A pdb=" N SER O 344 " --> pdb=" O LYS O 340 " (cutoff:3.500A) Processing helix chain 'O' and resid 359 through 372 Processing helix chain 'O' and resid 378 through 384 removed outlier: 4.233A pdb=" N ASP O 382 " --> pdb=" O LYS O 378 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE O 383 " --> pdb=" O GLN O 379 " (cutoff:3.500A) Processing helix chain 'O' and resid 387 through 400 Processing helix chain 'O' and resid 427 through 453 removed outlier: 3.541A pdb=" N ALA O 431 " --> pdb=" O ASN O 427 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR O 440 " --> pdb=" O LEU O 436 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS O 441 " --> pdb=" O HIS O 437 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU O 453 " --> pdb=" O ARG O 449 " (cutoff:3.500A) Processing helix chain 'O' and resid 454 through 456 No H-bonds generated for 'chain 'O' and resid 454 through 456' Processing helix chain 'O' and resid 457 through 478 removed outlier: 3.602A pdb=" N ALA O 469 " --> pdb=" O GLN O 465 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE O 470 " --> pdb=" O ARG O 466 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE O 471 " --> pdb=" O VAL O 467 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET O 474 " --> pdb=" O ILE O 470 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA O 476 " --> pdb=" O ALA O 472 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR O 477 " --> pdb=" O SER O 473 " (cutoff:3.500A) Processing helix chain 'O' and resid 480 through 491 removed outlier: 4.224A pdb=" N ILE O 491 " --> pdb=" O ILE O 487 " (cutoff:3.500A) Processing helix chain 'O' and resid 492 through 531 removed outlier: 3.607A pdb=" N GLN O 498 " --> pdb=" O PRO O 494 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LEU O 499 " --> pdb=" O GLU O 495 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU O 500 " --> pdb=" O ARG O 496 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR O 501 " --> pdb=" O GLN O 497 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG O 504 " --> pdb=" O GLU O 500 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE O 514 " --> pdb=" O ASP O 510 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR O 519 " --> pdb=" O GLN O 515 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER O 525 " --> pdb=" O PHE O 521 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYR O 526 " --> pdb=" O LEU O 522 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE O 527 " --> pdb=" O LEU O 523 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU O 528 " --> pdb=" O GLU O 524 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS O 529 " --> pdb=" O SER O 525 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR O 530 " --> pdb=" O TYR O 526 " (cutoff:3.500A) Processing helix chain 'P' and resid 173 through 199 Processing helix chain 'P' and resid 203 through 208 Processing helix chain 'P' and resid 213 through 224 removed outlier: 3.573A pdb=" N LYS P 218 " --> pdb=" O HIS P 214 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY P 224 " --> pdb=" O ILE P 220 " (cutoff:3.500A) Processing helix chain 'P' and resid 230 through 246 Processing helix chain 'P' and resid 285 through 290 removed outlier: 4.231A pdb=" N LEU P 289 " --> pdb=" O ALA P 285 " (cutoff:3.500A) Processing helix chain 'P' and resid 307 through 316 removed outlier: 3.619A pdb=" N PHE P 316 " --> pdb=" O GLU P 312 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 70 Processing helix chain 'Q' and resid 102 through 106 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.933A pdb=" N GLU A 4 " --> pdb=" O VAL G 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 1337 through 1338 removed outlier: 7.087A pdb=" N LYS B1127 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ILE A 18 " --> pdb=" O ARG B1125 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG B1125 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N PHE A 20 " --> pdb=" O ILE B1123 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE B1123 " --> pdb=" O PHE A 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 92 removed outlier: 11.637A pdb=" N LEU A 88 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 11.611A pdb=" N LEU A 256 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 11.373A pdb=" N LEU A 90 " --> pdb=" O ARG A 254 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ARG A 254 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 165 through 169 removed outlier: 3.726A pdb=" N LYS A 167 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE A 174 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU A 216 " --> pdb=" O HIS A 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 268 removed outlier: 3.798A pdb=" N GLY A 273 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1020 through 1023 removed outlier: 3.526A pdb=" N ARG A 487 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 488 " --> pdb=" O SER A 370 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 395 removed outlier: 3.619A pdb=" N ILE A 449 " --> pdb=" O GLN A 422 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE A 420 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N HIS A 453 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ALA A 418 " --> pdb=" O HIS A 453 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AA9, first strand: chain 'A' and resid 616 through 620 removed outlier: 3.711A pdb=" N SER A 647 " --> pdb=" O THR A 639 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLN A 641 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU A 645 " --> pdb=" O GLN A 641 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 800 through 801 removed outlier: 4.202A pdb=" N GLY A 800 " --> pdb=" O VAL A 834 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 883 through 884 removed outlier: 7.415A pdb=" N VAL A 890 " --> pdb=" O ILE A 898 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1209 through 1216 removed outlier: 3.898A pdb=" N ARG A1209 " --> pdb=" O GLU A1228 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N TYR A1223 " --> pdb=" O LEU A1089 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU A1089 " --> pdb=" O TYR A1223 " (cutoff:3.500A) removed outlier: 10.573A pdb=" N THR A1086 " --> pdb=" O THR A1244 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N THR A1244 " --> pdb=" O THR A1086 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLN A1088 " --> pdb=" O LYS A1242 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1108 through 1109 removed outlier: 6.893A pdb=" N THR A1108 " --> pdb=" O VAL A1201 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1165 through 1167 removed outlier: 3.992A pdb=" N TYR A1116 " --> pdb=" O LYS A1131 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU A1119 " --> pdb=" O ASN I 40 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASN I 40 " --> pdb=" O GLU A1119 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1361 through 1364 Processing sheet with id=AB7, first strand: chain 'B' and resid 64 through 66 removed outlier: 3.828A pdb=" N VAL B 65 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU B 75 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR B 120 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N TYR B 77 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N GLU B 118 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN B 79 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA B 111 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG B 135 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE B 113 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE B 117 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ASN B 129 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N TYR B 119 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ILE B 127 " --> pdb=" O TYR B 119 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG B 121 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ARG B 125 " --> pdb=" O ARG B 121 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 86 through 88 removed outlier: 3.880A pdb=" N VAL B 87 " --> pdb=" O ARG B 95 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG B 95 " --> pdb=" O VAL B 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AC1, first strand: chain 'B' and resid 361 through 363 removed outlier: 6.147A pdb=" N ILE B 180 " --> pdb=" O SER B 456 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 188 through 193 removed outlier: 3.996A pdb=" N ARG B 188 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL B 203 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ALA B 198 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL B 218 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 225 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE B 234 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 423 through 426 Processing sheet with id=AC4, first strand: chain 'B' and resid 501 through 502 removed outlier: 3.860A pdb=" N ARG B 594 " --> pdb=" O LEU B 633 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 633 " --> pdb=" O ARG B 594 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 501 through 502 Processing sheet with id=AC6, first strand: chain 'B' and resid 521 through 522 removed outlier: 5.539A pdb=" N ILE B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU B 541 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY B 547 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU B 538 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE B 585 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE B 540 " --> pdb=" O ILE B 585 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 708 through 712 removed outlier: 6.688A pdb=" N LEU B 880 " --> pdb=" O ILE B 871 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE B 871 " --> pdb=" O LEU B 880 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LYS B 882 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL B 869 " --> pdb=" O LYS B 882 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU B 884 " --> pdb=" O GLU B 867 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 708 through 712 removed outlier: 6.688A pdb=" N LEU B 880 " --> pdb=" O ILE B 871 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE B 871 " --> pdb=" O LEU B 880 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LYS B 882 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL B 869 " --> pdb=" O LYS B 882 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU B 884 " --> pdb=" O GLU B 867 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N VAL B 869 " --> pdb=" O LYS L 46 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS L 46 " --> pdb=" O VAL B 869 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 720 through 721 removed outlier: 6.172A pdb=" N HIS B 959 " --> pdb=" O LYS B 721 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 986 through 987 removed outlier: 3.778A pdb=" N ASP B 987 " --> pdb=" O ILE B1002 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE B1002 " --> pdb=" O ASP B 987 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN B1010 " --> pdb=" O SER B 898 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU B 755 " --> pdb=" O GLY B 908 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE B 910 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU B 757 " --> pdb=" O ILE B 910 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N ILE B 927 " --> pdb=" O ASN B 738 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR B 740 " --> pdb=" O ILE B 927 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N MET B 929 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ALA B 742 " --> pdb=" O MET B 929 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR B1003 " --> pdb=" O VAL B 743 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 794 through 795 Processing sheet with id=AD3, first strand: chain 'B' and resid 825 through 828 removed outlier: 3.829A pdb=" N GLN B 825 " --> pdb=" O TYR B 858 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE B 856 " --> pdb=" O LEU B 827 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 831 through 833 Processing sheet with id=AD5, first strand: chain 'B' and resid 1075 through 1079 Processing sheet with id=AD6, first strand: chain 'C' and resid 13 through 16 removed outlier: 4.716A pdb=" N LEU C 299 " --> pdb=" O LEU C 16 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 50 through 56 removed outlier: 5.638A pdb=" N VAL C 51 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL C 66 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N VAL C 53 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASP C 64 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER C 232 " --> pdb=" O SER C 309 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 174 through 175 removed outlier: 3.675A pdb=" N LYS C 91 " --> pdb=" O HIS C 213 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL C 215 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL C 89 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY C 217 " --> pdb=" O MET C 87 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N MET C 87 " --> pdb=" O GLY C 217 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL C 94 " --> pdb=" O VAL L 53 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL L 53 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 115 through 116 removed outlier: 3.978A pdb=" N ARG C 191 " --> pdb=" O HIS C 116 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 147 through 148 removed outlier: 3.931A pdb=" N THR C 147 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 167 through 168 removed outlier: 3.911A pdb=" N ALA C 200 " --> pdb=" O VAL C 168 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 262 through 267 Processing sheet with id=AE4, first strand: chain 'D' and resid 2 through 3 removed outlier: 3.682A pdb=" N ASP G 9 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL G 70 " --> pdb=" O ASP G 9 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER G 66 " --> pdb=" O ILE G 13 " (cutoff:3.500A) removed outlier: 12.499A pdb=" N HIS G 67 " --> pdb=" O LEU G 54 " (cutoff:3.500A) removed outlier: 11.405A pdb=" N LEU G 54 " --> pdb=" O HIS G 67 " (cutoff:3.500A) removed outlier: 12.289A pdb=" N LYS G 69 " --> pdb=" O THR G 52 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N THR G 52 " --> pdb=" O LYS G 69 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N HIS G 71 " --> pdb=" O ASP G 50 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ASP G 50 " --> pdb=" O HIS G 71 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ARG G 73 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU G 48 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU G 44 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 26 through 27 removed outlier: 4.863A pdb=" N ALA E 63 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA E 102 " --> pdb=" O ILE E 126 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU E 128 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 147 through 150 Processing sheet with id=AE7, first strand: chain 'G' and resid 107 through 109 removed outlier: 5.972A pdb=" N SER G 100 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ILE G 89 " --> pdb=" O SER G 100 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE G 89 " --> pdb=" O GLU G 146 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N GLU G 146 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ARG G 151 " --> pdb=" O ILE G 190 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE G 190 " --> pdb=" O ARG G 151 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL G 153 " --> pdb=" O GLY G 188 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N GLY G 188 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N GLU G 155 " --> pdb=" O LEU G 186 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU G 186 " --> pdb=" O GLU G 155 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N PHE G 157 " --> pdb=" O TYR G 184 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N TYR G 184 " --> pdb=" O PHE G 157 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 117 through 119 Processing sheet with id=AE9, first strand: chain 'H' and resid 4 through 15 removed outlier: 5.483A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER H 26 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL H 43 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU H 39 " --> pdb=" O CYS H 30 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP H 42 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU H 121 " --> pdb=" O TYR H 118 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 13 through 16 Processing sheet with id=AF2, first strand: chain 'I' and resid 64 through 66 removed outlier: 4.139A pdb=" N ALA I 77 " --> pdb=" O THR I 65 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE I 94 " --> pdb=" O ASP I 108 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP I 108 " --> pdb=" O PHE I 94 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 27 through 31 removed outlier: 7.483A pdb=" N LYS K 79 " --> pdb=" O THR K 72 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N THR K 72 " --> pdb=" O LYS K 79 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASN K 81 " --> pdb=" O TYR K 70 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR K 70 " --> pdb=" O ASN K 81 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ARG K 83 " --> pdb=" O CYS K 68 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N CYS K 68 " --> pdb=" O ARG K 83 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLN K 85 " --> pdb=" O GLU K 66 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 370 through 386 removed outlier: 6.925A pdb=" N HIS M 207 " --> pdb=" O GLY N 371 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N MET N 373 " --> pdb=" O HIS M 207 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N HIS M 209 " --> pdb=" O MET N 373 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL N 375 " --> pdb=" O HIS M 209 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR M 211 " --> pdb=" O VAL N 375 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N GLY N 377 " --> pdb=" O TYR M 211 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA M 47 " --> pdb=" O LEU M 208 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N TYR M 210 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N LEU M 45 " --> pdb=" O TYR M 210 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N HIS M 44 " --> pdb=" O ALA M 61 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ALA M 61 " --> pdb=" O HIS M 44 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER M 46 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU M 59 " --> pdb=" O SER M 46 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL M 56 " --> pdb=" O SER M 104 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN M 134 " --> pdb=" O SER M 105 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR M 107 " --> pdb=" O ILE M 132 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE M 132 " --> pdb=" O THR M 107 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU M 27 " --> pdb=" O LEU M 133 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU M 135 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLN M 29 " --> pdb=" O LEU M 135 " (cutoff:3.500A) removed outlier: 10.999A pdb=" N PHE N 356 " --> pdb=" O HIS N 381 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N HIS N 381 " --> pdb=" O PHE N 356 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN N 358 " --> pdb=" O VAL N 379 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N SER N 362 " --> pdb=" O VAL N 375 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VAL N 375 " --> pdb=" O SER N 362 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLY N 364 " --> pdb=" O MET N 373 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N MET N 373 " --> pdb=" O GLY N 364 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N LEU N 266 " --> pdb=" O HIS N 381 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N LEU N 383 " --> pdb=" O LEU N 266 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N PHE N 268 " --> pdb=" O LEU N 383 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N CYS N 385 " --> pdb=" O PHE N 268 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLN N 270 " --> pdb=" O CYS N 385 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU N 265 " --> pdb=" O TYR M 119 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N LEU M 124 " --> pdb=" O GLU M 12 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ASP M 14 " --> pdb=" O LEU M 124 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU M 126 " --> pdb=" O ASP M 14 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TYR M 16 " --> pdb=" O LEU M 126 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN M 11 " --> pdb=" O ILE N 331 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL M 15 " --> pdb=" O GLY N 327 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY N 327 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LEU M 17 " --> pdb=" O GLN N 325 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLN N 325 " --> pdb=" O LEU M 17 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL N 337 " --> pdb=" O VAL N 348 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 63 through 68 Processing sheet with id=AF6, first strand: chain 'O' and resid 157 through 159 Processing sheet with id=AF7, first strand: chain 'O' and resid 323 through 327 Processing sheet with id=AF8, first strand: chain 'O' and resid 405 through 410 Processing sheet with id=AF9, first strand: chain 'P' and resid 211 through 212 removed outlier: 3.542A pdb=" N TYR P 270 " --> pdb=" O ALA P 211 " (cutoff:3.500A) 1505 hydrogen bonds defined for protein. 4293 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.28 Time building geometry restraints manager: 4.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.44: 17215 1.44 - 1.66: 23763 1.66 - 1.88: 427 1.88 - 2.10: 0 2.10 - 2.32: 12 Bond restraints: 41417 Sorted by residual: bond pdb=" C1' DC S 18 " pdb=" N1 DC S 18 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 8.09e+00 bond pdb=" C3' DG S 12 " pdb=" C2' DG S 12 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.06e+00 bond pdb=" C GLU A 996 " pdb=" N PRO A 997 " ideal model delta sigma weight residual 1.332 1.360 -0.028 1.12e-02 7.97e+03 6.43e+00 bond pdb=" C1' DC S 23 " pdb=" N1 DC S 23 " ideal model delta sigma weight residual 1.468 1.501 -0.033 1.40e-02 5.10e+03 5.47e+00 bond pdb=" C1' DT S 17 " pdb=" N1 DT S 17 " ideal model delta sigma weight residual 1.468 1.499 -0.031 1.40e-02 5.10e+03 4.87e+00 ... (remaining 41412 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 54892 1.95 - 3.90: 1078 3.90 - 5.84: 114 5.84 - 7.79: 20 7.79 - 9.74: 4 Bond angle restraints: 56108 Sorted by residual: angle pdb=" N ASN A1180 " pdb=" CA ASN A1180 " pdb=" C ASN A1180 " ideal model delta sigma weight residual 108.52 116.23 -7.71 1.52e+00 4.33e-01 2.57e+01 angle pdb=" C GLY A 914 " pdb=" N LYS A 915 " pdb=" CA LYS A 915 " ideal model delta sigma weight residual 121.54 131.16 -9.62 1.91e+00 2.74e-01 2.54e+01 angle pdb=" N VAL A 37 " pdb=" CA VAL A 37 " pdb=" C VAL A 37 " ideal model delta sigma weight residual 113.71 109.03 4.68 9.50e-01 1.11e+00 2.43e+01 angle pdb=" N THR A 111 " pdb=" CA THR A 111 " pdb=" C THR A 111 " ideal model delta sigma weight residual 114.56 108.99 5.57 1.27e+00 6.20e-01 1.92e+01 angle pdb=" N ILE A1378 " pdb=" CA ILE A1378 " pdb=" C ILE A1378 " ideal model delta sigma weight residual 113.10 108.87 4.23 9.70e-01 1.06e+00 1.90e+01 ... (remaining 56103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 22822 17.35 - 34.71: 1908 34.71 - 52.06: 473 52.06 - 69.42: 91 69.42 - 86.77: 39 Dihedral angle restraints: 25333 sinusoidal: 10831 harmonic: 14502 Sorted by residual: dihedral pdb=" CA LYS D 77 " pdb=" C LYS D 77 " pdb=" N LEU D 78 " pdb=" CA LEU D 78 " ideal model delta harmonic sigma weight residual -180.00 -130.90 -49.10 0 5.00e+00 4.00e-02 9.64e+01 dihedral pdb=" CA HIS O 68 " pdb=" C HIS O 68 " pdb=" N LYS O 69 " pdb=" CA LYS O 69 " ideal model delta harmonic sigma weight residual -180.00 -136.74 -43.26 0 5.00e+00 4.00e-02 7.49e+01 dihedral pdb=" CA ILE B 751 " pdb=" C ILE B 751 " pdb=" N GLU B 752 " pdb=" CA GLU B 752 " ideal model delta harmonic sigma weight residual -180.00 -141.93 -38.07 0 5.00e+00 4.00e-02 5.80e+01 ... (remaining 25330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.276: 6301 4.276 - 8.553: 0 8.553 - 12.829: 0 12.829 - 17.105: 0 17.105 - 21.381: 4 Chirality restraints: 6305 Sorted by residual: chirality pdb="FE4 SF4 P 400 " pdb=" S1 SF4 P 400 " pdb=" S2 SF4 P 400 " pdb=" S3 SF4 P 400 " both_signs ideal model delta sigma weight residual False 10.55 -10.83 21.38 2.00e-01 2.50e+01 1.14e+04 chirality pdb="FE3 SF4 P 400 " pdb=" S1 SF4 P 400 " pdb=" S2 SF4 P 400 " pdb=" S4 SF4 P 400 " both_signs ideal model delta sigma weight residual False -10.55 10.75 -21.31 2.00e-01 2.50e+01 1.14e+04 chirality pdb="FE2 SF4 P 400 " pdb=" S1 SF4 P 400 " pdb=" S3 SF4 P 400 " pdb=" S4 SF4 P 400 " both_signs ideal model delta sigma weight residual False 10.55 -10.72 21.28 2.00e-01 2.50e+01 1.13e+04 ... (remaining 6302 not shown) Planarity restraints: 7071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS O 68 " -0.012 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C HIS O 68 " 0.044 2.00e-02 2.50e+03 pdb=" O HIS O 68 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS O 69 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 208 " 0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO A 209 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 209 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 209 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO G 110 " -0.028 5.00e-02 4.00e+02 4.30e-02 2.95e+00 pdb=" N PRO G 111 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO G 111 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 111 " -0.024 5.00e-02 4.00e+02 ... (remaining 7068 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 785 2.69 - 3.24: 37573 3.24 - 3.80: 60219 3.80 - 4.35: 79352 4.35 - 4.90: 130237 Nonbonded interactions: 308166 Sorted by model distance: nonbonded pdb=" OG1 THR O 2 " pdb=" OE1 GLU O 5 " model vdw 2.139 3.040 nonbonded pdb=" OH TYR P 309 " pdb=" O PRO Q 39 " model vdw 2.140 3.040 nonbonded pdb=" O THR P 194 " pdb=" OG SER P 198 " model vdw 2.224 3.040 nonbonded pdb=" OG1 THR B 66 " pdb=" O TRP B 73 " model vdw 2.225 3.040 nonbonded pdb=" O LEU D 78 " pdb=" OG1 THR D 79 " model vdw 2.240 3.040 ... (remaining 308161 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 49.140 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2414 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 : 0.010 0.639 41438 Z= 0.352 Angle : 0.784 40.391 56126 Z= 0.425 Chirality : 0.536 21.381 6305 Planarity : 0.003 0.055 7071 Dihedral : 13.996 86.770 15957 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.77 % Favored : 94.19 % Rotamer: Outliers : 0.09 % Allowed : 4.09 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.64 (0.10), residues: 4922 helix: -1.99 (0.10), residues: 1734 sheet: -1.40 (0.17), residues: 774 loop : -3.14 (0.10), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 226 TYR 0.016 0.001 TYR B1003 PHE 0.015 0.001 PHE G 104 TRP 0.007 0.001 TRP B 27 HIS 0.008 0.001 HIS D 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.17 (41417) covalent geometry : angle 0.66879 / 0.42 (56108) hydrogen bonds : bond 0.20508 / 13.92 ( 1484) hydrogen bonds : angle 7.06966 / 4.90 ( 4293) metal coordination : bond 0.41105 / 23.11 ( 21) metal coordination : angle 22.89953 / 11.47 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 977 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 973 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 ASN cc_start: 0.3266 (t0) cc_final: 0.3018 (m-40) REVERT: A 671 TRP cc_start: 0.1532 (m100) cc_final: 0.0931 (m-90) REVERT: A 751 LEU cc_start: 0.3395 (mt) cc_final: 0.3085 (mp) REVERT: B 97 VAL cc_start: 0.3052 (p) cc_final: 0.2744 (m) REVERT: B 279 THR cc_start: 0.5932 (p) cc_final: 0.4512 (p) REVERT: B 910 ILE cc_start: 0.6149 (mt) cc_final: 0.5851 (mt) REVERT: C 251 GLU cc_start: 0.7061 (mp0) cc_final: 0.6549 (tp30) REVERT: D 11 LEU cc_start: 0.3699 (pt) cc_final: 0.3401 (pt) REVERT: E 85 LYS cc_start: 0.8171 (tptt) cc_final: 0.7494 (mptt) REVERT: G 98 HIS cc_start: 0.6441 (m-70) cc_final: 0.6031 (m170) REVERT: G 142 MET cc_start: 0.0923 (mmt) cc_final: 0.0594 (mmt) REVERT: M 33 ARG cc_start: 0.0326 (tpt170) cc_final: -0.0024 (tpt-90) REVERT: M 80 ASN cc_start: 0.5966 (m-40) cc_final: 0.4578 (t0) REVERT: M 97 MET cc_start: 0.3616 (mpp) cc_final: 0.3184 (tmt) REVERT: M 244 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6728 (mm-30) REVERT: M 248 MET cc_start: 0.3502 (ttm) cc_final: 0.2994 (ppp) REVERT: N 339 LEU cc_start: 0.5170 (tt) cc_final: 0.4712 (mm) REVERT: O 28 LEU cc_start: 0.2974 (mt) cc_final: 0.2618 (mt) REVERT: O 298 PRO cc_start: 0.4668 (Cg_exo) cc_final: 0.3214 (Cg_endo) REVERT: P 179 VAL cc_start: 0.8529 (m) cc_final: 0.8254 (m) REVERT: Q 67 THR cc_start: 0.4601 (p) cc_final: 0.3620 (t) REVERT: Q 110 MET cc_start: 0.1801 (tmm) cc_final: 0.1289 (ttp) REVERT: Q 111 MET cc_start: -0.0252 (tpt) cc_final: -0.0761 (tmt) outliers start: 4 outliers final: 2 residues processed: 976 average time/residue: 0.7616 time to fit residues: 902.9554 Evaluate side-chains 539 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 537 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain I residue 36 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 8.9990 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 470 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 40 ASN A 47 GLN A 114 HIS A 157 HIS A 225 ASN A 400 ASN ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 GLN A 566 GLN A 673 GLN A 693 ASN A 738 GLN ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN A 885 GLN A1039 GLN A1202 GLN ** A1231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1385 HIS ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN B 280 GLN B 381 ASN B 399 GLN ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 GLN B 569 ASN B 648 HIS B 678 ASN ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 HIS B1010 GLN B1021 HIS B1034 GLN C 32 ASN C 55 HIS C 172 HIS C 194 HIS ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 HIS ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN E 35 GLN ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN G 17 GLN G 115 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 GLN I 74 HIS I 99 ASN I 104 HIS K 38 HIS K 45 HIS L 23 HIS M 66 ASN M 106 GLN ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 197 GLN M 200 HIS M 235 ASN M 707 GLN O 16 HIS ** O 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 60 HIS O 68 HIS ** O 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 62 GLN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.147610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.118791 restraints weight = 96076.419| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 3.64 r_work: 0.3780 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3784 r_free = 0.3784 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3784 r_free = 0.3784 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3803 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.361 41438 Z= 0.347 Angle : 1.370 51.126 56126 Z= 0.735 Chirality : 0.166 6.609 6305 Planarity : 0.008 0.145 7071 Dihedral : 9.921 67.543 5926 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 4.34 % Allowed : 16.39 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.10), residues: 4922 helix: -1.53 (0.11), residues: 1772 sheet: -1.15 (0.17), residues: 753 loop : -2.80 (0.11), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG Q 108 TYR 0.043 0.004 TYR H 90 PHE 0.048 0.004 PHE A 420 TRP 0.024 0.003 TRP B 476 HIS 0.021 0.003 HIS M 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00827 / 0.35 (41417) covalent geometry : angle 1.28146 / 0.73 (56108) hydrogen bonds : bond 0.05819 / 3.90 ( 1484) hydrogen bonds : angle 5.95331 / 4.14 ( 4293) metal coordination : bond 0.05247 / 3.57 ( 21) metal coordination : angle 27.15471 / 15.21 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 694 time to evaluate : 1.498 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: A 194 LEU cc_start: 0.7305 (mt) cc_final: 0.6828 (mt) REVERT: A 211 LEU cc_start: 0.2692 (OUTLIER) cc_final: 0.2372 (mp) REVERT: A 260 LEU cc_start: 0.3891 (OUTLIER) cc_final: 0.3093 (tp) REVERT: A 332 MET cc_start: 0.1183 (ttt) cc_final: 0.0980 (ttm) REVERT: A 425 HIS cc_start: 0.6549 (m-70) cc_final: 0.6213 (m90) REVERT: A 440 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6941 (ttp) REVERT: A 804 ILE cc_start: 0.5617 (mp) cc_final: 0.4988 (mp) REVERT: A 808 ARG cc_start: 0.4427 (OUTLIER) cc_final: 0.3849 (ttm170) REVERT: A 1041 ILE cc_start: 0.4219 (mp) cc_final: 0.2601 (tp) REVERT: A 1085 ILE cc_start: 0.3860 (mt) cc_final: 0.3595 (mt) REVERT: A 1129 LEU cc_start: 0.5120 (OUTLIER) cc_final: 0.4804 (pt) REVERT: A 1131 LYS cc_start: 0.5396 (tptt) cc_final: 0.5076 (tptt) REVERT: A 1353 MET cc_start: 0.5605 (OUTLIER) cc_final: 0.5061 (mtp) REVERT: B 77 TYR cc_start: 0.5349 (m-80) cc_final: 0.4248 (m-10) REVERT: B 90 SER cc_start: 0.7867 (m) cc_final: 0.7598 (p) REVERT: B 109 TYR cc_start: 0.0114 (OUTLIER) cc_final: -0.0701 (t80) REVERT: B 254 MET cc_start: 0.2447 (mtt) cc_final: 0.0270 (tpt) REVERT: B 340 ARG cc_start: 0.5360 (tpt170) cc_final: 0.5117 (tpt90) REVERT: B 349 ASN cc_start: 0.6556 (p0) cc_final: 0.5977 (m-40) REVERT: B 384 MET cc_start: 0.5617 (ppp) cc_final: 0.4879 (mmt) REVERT: B 415 MET cc_start: 0.3764 (ptp) cc_final: 0.3135 (tpt) REVERT: B 916 MET cc_start: -0.0261 (mmm) cc_final: -0.0575 (mmp) REVERT: B 987 ASP cc_start: 0.3037 (m-30) cc_final: 0.2794 (m-30) REVERT: B 1032 THR cc_start: 0.0770 (t) cc_final: -0.0730 (p) REVERT: C 33 TYR cc_start: 0.3635 (m-80) cc_final: 0.3429 (p90) REVERT: C 233 TYR cc_start: 0.4778 (OUTLIER) cc_final: 0.2104 (p90) REVERT: C 251 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.6975 (tp30) REVERT: C 324 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.5264 (tp30) REVERT: E 72 MET cc_start: 0.4215 (OUTLIER) cc_final: 0.3722 (tmt) REVERT: E 85 LYS cc_start: 0.8554 (tptt) cc_final: 0.8089 (mmtm) REVERT: E 110 MET cc_start: 0.1081 (tpt) cc_final: -0.3575 (ppp) REVERT: F 107 ARG cc_start: 0.2448 (OUTLIER) cc_final: 0.2024 (tpp-160) REVERT: G 48 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6857 (tm) REVERT: G 89 ILE cc_start: 0.8452 (mt) cc_final: 0.8209 (tp) REVERT: H 47 ILE cc_start: 0.6286 (OUTLIER) cc_final: 0.5715 (tp) REVERT: H 126 GLN cc_start: 0.4716 (OUTLIER) cc_final: 0.4490 (mm110) REVERT: K 28 GLU cc_start: 0.5389 (mt-10) cc_final: 0.4823 (mp0) REVERT: K 29 MET cc_start: 0.5873 (tmm) cc_final: 0.5665 (tmm) REVERT: K 80 ILE cc_start: 0.4806 (mt) cc_final: 0.4472 (mt) REVERT: M 73 LYS cc_start: 0.6924 (tttt) cc_final: 0.6355 (pttt) REVERT: M 80 ASN cc_start: 0.6507 (m-40) cc_final: 0.4901 (t0) REVERT: M 97 MET cc_start: 0.3926 (mpp) cc_final: 0.3448 (tmt) REVERT: M 244 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7098 (mm-30) REVERT: M 248 MET cc_start: 0.3395 (ttm) cc_final: 0.2514 (ptm) REVERT: M 250 MET cc_start: 0.3916 (OUTLIER) cc_final: 0.3554 (mmm) REVERT: N 330 LEU cc_start: 0.5680 (mp) cc_final: 0.5405 (mp) REVERT: N 350 MET cc_start: 0.4280 (pmm) cc_final: 0.4046 (pmm) REVERT: O 1 MET cc_start: 0.7154 (mtm) cc_final: 0.6606 (mtm) REVERT: O 85 MET cc_start: 0.5424 (mpt) cc_final: 0.5124 (mmp) REVERT: O 360 SER cc_start: 0.6558 (p) cc_final: 0.6210 (t) REVERT: O 468 GLU cc_start: 0.7641 (pt0) cc_final: 0.7389 (pt0) REVERT: O 526 TYR cc_start: 0.4635 (t80) cc_final: 0.3931 (t80) REVERT: P 301 GLU cc_start: 0.5851 (pt0) cc_final: 0.4438 (mt-10) REVERT: Q 57 MET cc_start: 0.7016 (mpp) cc_final: 0.6483 (mmm) REVERT: Q 110 MET cc_start: 0.2364 (tmm) cc_final: 0.1319 (ttp) REVERT: Q 111 MET cc_start: 0.0033 (tpt) cc_final: -0.1185 (tmt) outliers start: 191 outliers final: 46 residues processed: 813 average time/residue: 0.6936 time to fit residues: 694.8521 Evaluate side-chains 574 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 512 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 808 ARG Chi-restraints excluded: chain A residue 921 PHE Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain A residue 1049 THR Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 109 TYR Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 769 CYS Chi-restraints excluded: chain B residue 881 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 233 TYR Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain F residue 107 ARG Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 126 GLN Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 75 GLU Chi-restraints excluded: chain M residue 214 ARG Chi-restraints excluded: chain M residue 217 ARG Chi-restraints excluded: chain M residue 250 MET Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 84 ARG Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain P residue 311 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 288 optimal weight: 7.9990 chunk 272 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 258 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 229 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 ASN A 215 GLN A 241 ASN A 290 ASN A 343 GLN A 400 ASN A 422 GLN A 623 GLN A 794 GLN ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1180 ASN ** A1231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1286 HIS B 159 ASN B 273 GLN B 475 GLN ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 959 HIS B1082 GLN ** B1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 HIS F 72 GLN ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 GLN H 76 ASN H 87 GLN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 HIS ** K 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 GLN ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 374 HIS O 377 GLN P 200 GLN P 240 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.149128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.120782 restraints weight = 98006.019| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 3.53 r_work: 0.3824 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3820 r_free = 0.3820 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3820 r_free = 0.3820 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4239 moved from start: 0.6211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.277 41438 Z= 0.255 Angle : 1.218 50.577 56126 Z= 0.661 Chirality : 0.166 6.441 6305 Planarity : 0.006 0.091 7071 Dihedral : 9.717 70.746 5920 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.81 % Favored : 94.15 % Rotamer: Outliers : 4.41 % Allowed : 20.58 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.11), residues: 4922 helix: -0.95 (0.11), residues: 1792 sheet: -0.87 (0.18), residues: 719 loop : -2.65 (0.11), residues: 2411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG M 150 TYR 0.051 0.003 TYR H 97 PHE 0.068 0.003 PHE A 849 TRP 0.028 0.002 TRP B 476 HIS 0.021 0.002 HIS B1093 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.25 (41417) covalent geometry : angle 1.12862 / 0.66 (56108) hydrogen bonds : bond 0.04873 / 3.25 ( 1484) hydrogen bonds : angle 5.40121 / 3.75 ( 4293) metal coordination : bond 0.02467 / 1.66 ( 21) metal coordination : angle 25.55509 / 13.75 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 614 time to evaluate : 1.584 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 116 MET cc_start: 0.3535 (mpt) cc_final: 0.3282 (mpp) REVERT: A 211 LEU cc_start: 0.2659 (OUTLIER) cc_final: 0.2254 (mt) REVERT: A 223 VAL cc_start: 0.5638 (t) cc_final: 0.5396 (p) REVERT: A 332 MET cc_start: 0.1447 (ttt) cc_final: 0.1107 (ttp) REVERT: A 423 GLN cc_start: 0.5795 (OUTLIER) cc_final: 0.5225 (tm-30) REVERT: A 425 HIS cc_start: 0.6588 (m-70) cc_final: 0.6030 (m90) REVERT: A 448 ASP cc_start: 0.4623 (m-30) cc_final: 0.4304 (m-30) REVERT: A 578 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7661 (pptt) REVERT: A 650 MET cc_start: 0.2382 (ptt) cc_final: 0.1449 (ttt) REVERT: A 651 ASP cc_start: 0.4159 (OUTLIER) cc_final: -0.0284 (t0) REVERT: A 716 LEU cc_start: 0.4789 (OUTLIER) cc_final: 0.4403 (mp) REVERT: A 770 GLU cc_start: -0.0321 (OUTLIER) cc_final: -0.0529 (tt0) REVERT: A 808 ARG cc_start: 0.4654 (ppt170) cc_final: 0.4146 (mtp85) REVERT: A 1048 MET cc_start: 0.0334 (OUTLIER) cc_final: -0.1140 (mpt) REVERT: A 1085 ILE cc_start: 0.3739 (mt) cc_final: 0.3441 (mt) REVERT: A 1131 LYS cc_start: 0.5384 (tptt) cc_final: 0.4937 (tptt) REVERT: A 1294 MET cc_start: 0.2421 (OUTLIER) cc_final: 0.1158 (pp-130) REVERT: A 1353 MET cc_start: 0.5705 (OUTLIER) cc_final: 0.5350 (mpt) REVERT: B 90 SER cc_start: 0.7912 (m) cc_final: 0.7687 (p) REVERT: B 254 MET cc_start: 0.2404 (mtt) cc_final: 0.0386 (tpt) REVERT: B 340 ARG cc_start: 0.5680 (tpt170) cc_final: 0.5139 (tpm-80) REVERT: B 349 ASN cc_start: 0.6591 (p0) cc_final: 0.6014 (m-40) REVERT: B 384 MET cc_start: 0.5632 (ppp) cc_final: 0.5112 (mmt) REVERT: B 578 LEU cc_start: 0.4694 (OUTLIER) cc_final: 0.4494 (tt) REVERT: B 694 MET cc_start: 0.3131 (ttp) cc_final: 0.2832 (ptp) REVERT: B 719 MET cc_start: 0.1097 (pmm) cc_final: 0.0530 (ptm) REVERT: B 725 ILE cc_start: 0.2936 (mt) cc_final: 0.2715 (mp) REVERT: B 808 ILE cc_start: 0.6567 (mm) cc_final: 0.6251 (mt) REVERT: B 817 PRO cc_start: 0.4890 (Cg_endo) cc_final: 0.4423 (Cg_exo) REVERT: B 996 GLU cc_start: 0.4628 (mm-30) cc_final: 0.4213 (mp0) REVERT: B 1032 THR cc_start: 0.1148 (t) cc_final: -0.0541 (p) REVERT: B 1088 TYR cc_start: 0.5764 (p90) cc_final: 0.4001 (t80) REVERT: B 1089 SER cc_start: 0.5327 (m) cc_final: 0.4809 (m) REVERT: C 95 TYR cc_start: 0.5460 (m-10) cc_final: 0.5127 (m-10) REVERT: C 141 ARG cc_start: 0.6995 (mmm-85) cc_final: 0.6706 (mtp85) REVERT: C 251 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7027 (tp30) REVERT: E 72 MET cc_start: 0.3767 (OUTLIER) cc_final: 0.2992 (mmt) REVERT: E 85 LYS cc_start: 0.8491 (tptt) cc_final: 0.7826 (mmtm) REVERT: E 110 MET cc_start: 0.0718 (OUTLIER) cc_final: -0.1139 (tpp) REVERT: F 107 ARG cc_start: 0.2397 (OUTLIER) cc_final: 0.1544 (tpp-160) REVERT: G 89 ILE cc_start: 0.8590 (mt) cc_final: 0.8337 (tp) REVERT: H 47 ILE cc_start: 0.6356 (OUTLIER) cc_final: 0.6010 (tp) REVERT: K 27 LEU cc_start: 0.3186 (OUTLIER) cc_final: 0.2847 (tt) REVERT: K 28 GLU cc_start: 0.5520 (mt-10) cc_final: 0.5117 (mp0) REVERT: K 80 ILE cc_start: 0.4767 (mt) cc_final: 0.4551 (mt) REVERT: M 73 LYS cc_start: 0.7105 (tttt) cc_final: 0.6483 (pttt) REVERT: M 97 MET cc_start: 0.3587 (mpp) cc_final: 0.3117 (tmt) REVERT: M 221 GLU cc_start: 0.6509 (mm-30) cc_final: 0.6050 (pt0) REVERT: M 248 MET cc_start: 0.3852 (ttm) cc_final: 0.3086 (ppp) REVERT: M 250 MET cc_start: 0.4011 (mmt) cc_final: 0.3737 (mmm) REVERT: N 376 LEU cc_start: 0.5273 (mm) cc_final: 0.4872 (mm) REVERT: O 85 MET cc_start: 0.5997 (mpt) cc_final: 0.5572 (mpp) REVERT: O 526 TYR cc_start: 0.4442 (t80) cc_final: 0.3903 (t80) REVERT: P 175 GLU cc_start: 0.7443 (tm-30) cc_final: 0.7170 (tm-30) REVERT: P 203 MET cc_start: 0.6785 (mpt) cc_final: 0.6540 (mpp) REVERT: P 301 GLU cc_start: 0.6092 (pt0) cc_final: 0.4916 (mt-10) REVERT: Q 110 MET cc_start: 0.2306 (tmm) cc_final: 0.1038 (ttp) REVERT: Q 111 MET cc_start: -0.0079 (tpt) cc_final: -0.1439 (tmt) outliers start: 194 outliers final: 56 residues processed: 751 average time/residue: 0.6407 time to fit residues: 602.2978 Evaluate side-chains 585 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 513 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 578 LYS Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 921 PHE Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain A residue 1215 ASP Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 49 TYR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 789 LYS Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 919 CYS Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 1013 LYS Chi-restraints excluded: chain B residue 1021 HIS Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 107 ARG Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 214 ARG Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 304 SER Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 403 PHE Chi-restraints excluded: chain P residue 295 ASP Chi-restraints excluded: chain Q residue 58 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 230 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 437 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 481 optimal weight: 2.9990 chunk 406 optimal weight: 6.9990 chunk 482 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 198 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 HIS A 566 GLN ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 820 HIS A1239 HIS ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 HIS B 692 GLN ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 982 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 GLN D 18 GLN ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN ** G 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 GLN J 61 ASN ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 29 GLN M 106 GLN M 121 GLN M 134 GLN O 16 HIS O 27 HIS O 60 HIS O 68 HIS O 155 HIS O 291 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.153454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.126745 restraints weight = 103314.915| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 3.65 r_work: 0.3909 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3909 r_free = 0.3909 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3909 r_free = 0.3909 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5663 moved from start: 0.9933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.249 41438 Z= 0.407 Angle : 1.537 50.594 56126 Z= 0.817 Chirality : 0.171 6.356 6305 Planarity : 0.010 0.225 7071 Dihedral : 10.471 77.299 5920 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 23.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.76 % Favored : 91.10 % Rotamer: Outliers : 7.28 % Allowed : 20.96 % Favored : 71.76 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.10), residues: 4922 helix: -1.50 (0.11), residues: 1771 sheet: -1.22 (0.19), residues: 694 loop : -2.87 (0.11), residues: 2457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.054 0.002 ARG A1019 TYR 0.069 0.004 TYR E 26 PHE 0.094 0.005 PHE H 56 TRP 0.038 0.004 TRP A 671 HIS 0.017 0.003 HIS B 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00961 / 0.41 (41417) covalent geometry : angle 1.46380 / 0.82 (56108) hydrogen bonds : bond 0.06454 / 4.37 ( 1484) hydrogen bonds : angle 6.52885 / 4.51 ( 4293) metal coordination : bond 0.01556 / 0.91 ( 21) metal coordination : angle 26.26464 / 14.03 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1069 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 320 poor density : 749 time to evaluate : 1.728 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: A 34 ILE cc_start: 0.2937 (mm) cc_final: 0.1434 (mt) REVERT: A 211 LEU cc_start: 0.3412 (OUTLIER) cc_final: 0.2875 (mt) REVERT: A 260 LEU cc_start: 0.6270 (OUTLIER) cc_final: 0.6054 (tt) REVERT: A 543 GLN cc_start: 0.5805 (OUTLIER) cc_final: 0.4559 (pp30) REVERT: A 662 ASN cc_start: 0.7002 (m-40) cc_final: 0.6758 (t0) REVERT: A 758 VAL cc_start: 0.5486 (OUTLIER) cc_final: 0.4600 (p) REVERT: A 767 CYS cc_start: 0.8146 (t) cc_final: 0.7796 (t) REVERT: A 770 GLU cc_start: 0.1669 (OUTLIER) cc_final: 0.1364 (tp30) REVERT: A 804 ILE cc_start: 0.6648 (OUTLIER) cc_final: 0.6443 (mp) REVERT: A 808 ARG cc_start: 0.4921 (OUTLIER) cc_final: 0.4616 (mmt90) REVERT: A 916 ASP cc_start: 0.1094 (OUTLIER) cc_final: 0.0523 (m-30) REVERT: A 987 TYR cc_start: 0.3082 (m-10) cc_final: 0.2844 (m-80) REVERT: A 1047 GLN cc_start: 0.5113 (OUTLIER) cc_final: 0.4640 (pp30) REVERT: A 1048 MET cc_start: 0.1521 (OUTLIER) cc_final: -0.0604 (mpt) REVERT: A 1085 ILE cc_start: 0.3864 (mt) cc_final: 0.3517 (mt) REVERT: A 1294 MET cc_start: 0.5353 (ttm) cc_final: 0.4889 (ppp) REVERT: A 1305 ARG cc_start: 0.5816 (ptp-170) cc_final: 0.3007 (tpt170) REVERT: B 106 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7741 (t0) REVERT: B 136 MET cc_start: 0.7403 (tpt) cc_final: 0.7177 (tpp) REVERT: B 199 VAL cc_start: 0.5351 (OUTLIER) cc_final: 0.4926 (m) REVERT: B 254 MET cc_start: 0.2790 (mtt) cc_final: 0.1312 (ttm) REVERT: B 349 ASN cc_start: 0.6567 (p0) cc_final: 0.6258 (m-40) REVERT: B 384 MET cc_start: 0.6267 (ppp) cc_final: 0.5619 (mmt) REVERT: B 660 GLU cc_start: 0.5271 (mm-30) cc_final: 0.4683 (tp30) REVERT: B 673 PRO cc_start: 0.7151 (Cg_exo) cc_final: 0.5798 (Cg_endo) REVERT: B 709 MET cc_start: 0.8108 (tmm) cc_final: 0.7906 (tmm) REVERT: B 711 LEU cc_start: 0.8006 (mt) cc_final: 0.7268 (mt) REVERT: B 719 MET cc_start: 0.5028 (pmm) cc_final: 0.4501 (mtp) REVERT: B 892 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6908 (tm-30) REVERT: B 895 ASP cc_start: 0.7787 (m-30) cc_final: 0.7054 (m-30) REVERT: B 907 CYS cc_start: 0.6437 (m) cc_final: 0.5250 (m) REVERT: B 1062 MET cc_start: 0.7114 (mmm) cc_final: 0.6857 (mpp) REVERT: B 1069 MET cc_start: 0.3295 (ppp) cc_final: 0.2644 (ppp) REVERT: B 1089 SER cc_start: 0.6449 (m) cc_final: 0.6072 (p) REVERT: C 87 MET cc_start: 0.8643 (mmm) cc_final: 0.8368 (mmm) REVERT: C 135 ILE cc_start: 0.6940 (tt) cc_final: 0.6703 (mm) REVERT: C 233 TYR cc_start: 0.7675 (OUTLIER) cc_final: 0.7284 (p90) REVERT: C 251 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7440 (tp30) REVERT: C 286 GLU cc_start: 0.7485 (tt0) cc_final: 0.6910 (tm-30) REVERT: C 345 MET cc_start: 0.5796 (mmt) cc_final: 0.5232 (tmt) REVERT: D 1 MET cc_start: 0.4724 (OUTLIER) cc_final: 0.2172 (mmt) REVERT: E 85 LYS cc_start: 0.8609 (tptt) cc_final: 0.7953 (mmtm) REVERT: E 108 GLN cc_start: 0.6451 (mp10) cc_final: 0.5978 (mp10) REVERT: E 110 MET cc_start: 0.1621 (OUTLIER) cc_final: 0.0986 (tpt) REVERT: E 142 HIS cc_start: 0.6636 (t-90) cc_final: 0.6316 (t-90) REVERT: E 151 MET cc_start: 0.0359 (pp-130) cc_final: 0.0033 (ttp) REVERT: F 107 ARG cc_start: 0.2372 (OUTLIER) cc_final: 0.1503 (tpt170) REVERT: F 121 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8123 (t0) REVERT: G 48 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8197 (tm) REVERT: G 142 MET cc_start: 0.0331 (OUTLIER) cc_final: -0.0357 (mtp) REVERT: H 92 MET cc_start: 0.5314 (OUTLIER) cc_final: 0.5016 (ptp) REVERT: H 133 HIS cc_start: 0.6834 (OUTLIER) cc_final: 0.6508 (m-70) REVERT: I 1 MET cc_start: 0.4699 (pmm) cc_final: 0.3976 (pp-130) REVERT: I 60 GLU cc_start: 0.5857 (mm-30) cc_final: 0.5555 (mm-30) REVERT: I 101 GLN cc_start: 0.5141 (pp30) cc_final: 0.4193 (mm-40) REVERT: J 33 ASP cc_start: 0.7730 (m-30) cc_final: 0.7507 (m-30) REVERT: J 41 LYS cc_start: 0.8665 (tmmt) cc_final: 0.8339 (tppp) REVERT: K 29 MET cc_start: 0.7156 (tmm) cc_final: 0.6895 (tmm) REVERT: K 44 LEU cc_start: 0.6451 (mm) cc_final: 0.6076 (mp) REVERT: K 80 ILE cc_start: 0.5434 (mt) cc_final: 0.5125 (mt) REVERT: K 111 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7709 (pp) REVERT: K 128 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6647 (tpp-160) REVERT: L 51 ARG cc_start: 0.8555 (ppp80) cc_final: 0.8270 (ptp-170) REVERT: M 73 LYS cc_start: 0.7229 (tttt) cc_final: 0.6729 (ttpt) REVERT: M 129 LEU cc_start: 0.0073 (OUTLIER) cc_final: -0.0241 (mp) REVERT: M 248 MET cc_start: 0.4100 (ttm) cc_final: 0.3323 (ppp) REVERT: M 250 MET cc_start: 0.4485 (mmt) cc_final: 0.4235 (mmm) REVERT: N 262 LYS cc_start: 0.4798 (OUTLIER) cc_final: 0.4421 (pptt) REVERT: O 7 LYS cc_start: 0.6749 (tptp) cc_final: 0.6304 (pttm) REVERT: O 85 MET cc_start: 0.6936 (mpt) cc_final: 0.6539 (mpp) REVERT: O 118 MET cc_start: 0.3065 (ttt) cc_final: 0.0878 (pp-130) REVERT: P 175 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7133 (tm-30) REVERT: P 220 ILE cc_start: 0.8195 (mm) cc_final: 0.7985 (pp) REVERT: Q 110 MET cc_start: 0.3722 (tmm) cc_final: 0.3172 (ttt) outliers start: 320 outliers final: 89 residues processed: 962 average time/residue: 0.6210 time to fit residues: 751.6954 Evaluate side-chains 676 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 560 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 72 CYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 543 GLN Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 808 ARG Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain A residue 1047 GLN Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1049 THR Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain B residue 49 TYR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 892 GLU Chi-restraints excluded: chain B residue 1021 HIS Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 233 TYR Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 107 ARG Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 56 PHE Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain K residue 128 ARG Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 75 GLU Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 262 LYS Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain O residue 5 GLU Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 137 LYS Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 377 GLN Chi-restraints excluded: chain O residue 404 MET Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 295 ASP Chi-restraints excluded: chain Q residue 46 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 234 optimal weight: 2.9990 chunk 238 optimal weight: 6.9990 chunk 306 optimal weight: 3.9990 chunk 386 optimal weight: 0.9990 chunk 443 optimal weight: 0.0980 chunk 29 optimal weight: 0.8980 chunk 204 optimal weight: 0.7980 chunk 243 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 410 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 ASN B 159 ASN ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** B 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 806 HIS ** B 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 959 HIS B 982 ASN ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 HIS C 32 ASN C 96 ASN D 60 HIS ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN M 29 GLN M 80 ASN M 125 HIS M 134 GLN ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 291 ASN O 437 HIS O 451 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.153369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.125945 restraints weight = 101941.358| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 3.67 r_work: 0.3893 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3894 r_free = 0.3894 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3894 r_free = 0.3894 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5738 moved from start: 1.0490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.246 41438 Z= 0.219 Angle : 1.247 50.613 56126 Z= 0.669 Chirality : 0.166 6.322 6305 Planarity : 0.006 0.063 7071 Dihedral : 9.957 76.345 5920 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.77 % Favored : 94.17 % Rotamer: Outliers : 4.80 % Allowed : 27.19 % Favored : 68.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.11), residues: 4922 helix: -0.93 (0.11), residues: 1778 sheet: -0.97 (0.19), residues: 692 loop : -2.62 (0.11), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 121 TYR 0.043 0.002 TYR B1003 PHE 0.030 0.002 PHE H 10 TRP 0.030 0.002 TRP B1091 HIS 0.012 0.002 HIS D 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.22 (41417) covalent geometry : angle 1.15649 / 0.67 (56108) hydrogen bonds : bond 0.04384 / 2.90 ( 1484) hydrogen bonds : angle 5.59038 / 3.86 ( 4293) metal coordination : bond 0.01478 / 0.73 ( 21) metal coordination : angle 26.02921 / 13.65 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 623 time to evaluate : 1.521 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: A 116 MET cc_start: 0.5818 (ttm) cc_final: 0.4541 (mpp) REVERT: A 211 LEU cc_start: 0.2949 (OUTLIER) cc_final: 0.2133 (mt) REVERT: A 371 PRO cc_start: 0.7240 (Cg_endo) cc_final: 0.6760 (Cg_exo) REVERT: A 389 ILE cc_start: 0.8503 (mp) cc_final: 0.8223 (mp) REVERT: A 451 GLU cc_start: 0.6868 (mt-10) cc_final: 0.6645 (mm-30) REVERT: A 577 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7225 (pm20) REVERT: A 596 THR cc_start: 0.2368 (OUTLIER) cc_final: 0.1786 (p) REVERT: A 767 CYS cc_start: 0.7994 (t) cc_final: 0.7104 (p) REVERT: A 770 GLU cc_start: 0.1569 (OUTLIER) cc_final: 0.0898 (tt0) REVERT: A 1048 MET cc_start: 0.1203 (OUTLIER) cc_final: -0.0764 (mpt) REVERT: A 1085 ILE cc_start: 0.4013 (mt) cc_final: 0.3615 (mt) REVERT: A 1158 LEU cc_start: 0.2876 (OUTLIER) cc_final: 0.2667 (pt) REVERT: A 1275 MET cc_start: 0.6986 (mmt) cc_final: 0.6602 (mmt) REVERT: B 90 SER cc_start: 0.8023 (m) cc_final: 0.7755 (p) REVERT: B 106 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7571 (t0) REVERT: B 139 MET cc_start: 0.1413 (mtt) cc_final: 0.1158 (tmm) REVERT: B 199 VAL cc_start: 0.5431 (OUTLIER) cc_final: 0.4994 (m) REVERT: B 254 MET cc_start: 0.2575 (mtt) cc_final: 0.1731 (ptm) REVERT: B 349 ASN cc_start: 0.6800 (p0) cc_final: 0.6502 (m-40) REVERT: B 384 MET cc_start: 0.6274 (ppp) cc_final: 0.5532 (mmt) REVERT: B 478 MET cc_start: 0.3700 (ppp) cc_final: 0.3431 (pmm) REVERT: B 660 GLU cc_start: 0.5321 (mm-30) cc_final: 0.4906 (tp30) REVERT: B 729 GLU cc_start: 0.7139 (tp30) cc_final: 0.6784 (tm-30) REVERT: B 803 ILE cc_start: 0.4995 (mp) cc_final: 0.4759 (mp) REVERT: B 1015 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.6922 (mtm) REVERT: B 1050 MET cc_start: 0.7914 (tpp) cc_final: 0.7141 (mtm) REVERT: B 1051 GLU cc_start: 0.6862 (mp0) cc_final: 0.6627 (mp0) REVERT: B 1069 MET cc_start: 0.3452 (OUTLIER) cc_final: 0.3129 (ppp) REVERT: B 1089 SER cc_start: 0.6121 (m) cc_final: 0.5669 (p) REVERT: C 29 PHE cc_start: 0.6474 (m-80) cc_final: 0.6236 (m-80) REVERT: C 125 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7819 (ttm170) REVERT: C 251 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7477 (tp30) REVERT: C 345 MET cc_start: 0.6298 (mmt) cc_final: 0.5606 (tmm) REVERT: D 1 MET cc_start: 0.4879 (OUTLIER) cc_final: 0.4456 (mtt) REVERT: E 110 MET cc_start: 0.1326 (OUTLIER) cc_final: -0.0167 (tpp) REVERT: F 96 GLU cc_start: 0.6214 (tp30) cc_final: 0.5963 (tp30) REVERT: F 107 ARG cc_start: 0.2396 (OUTLIER) cc_final: 0.2001 (mmt90) REVERT: G 142 MET cc_start: 0.0484 (OUTLIER) cc_final: 0.0087 (mmm) REVERT: H 47 ILE cc_start: 0.7145 (OUTLIER) cc_final: 0.6606 (pp) REVERT: I 1 MET cc_start: 0.4667 (pmm) cc_final: 0.3837 (pp-130) REVERT: I 101 GLN cc_start: 0.4959 (pp30) cc_final: 0.4243 (mm-40) REVERT: J 33 ASP cc_start: 0.7950 (m-30) cc_final: 0.7744 (m-30) REVERT: J 41 LYS cc_start: 0.8858 (tmmt) cc_final: 0.8518 (tppp) REVERT: K 29 MET cc_start: 0.7002 (tmm) cc_final: 0.6680 (tmm) REVERT: K 77 GLU cc_start: 0.3852 (OUTLIER) cc_final: 0.1555 (mp0) REVERT: K 80 ILE cc_start: 0.5384 (mt) cc_final: 0.4940 (mt) REVERT: K 111 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7444 (pp) REVERT: L 51 ARG cc_start: 0.8317 (ppp80) cc_final: 0.8056 (ptp-170) REVERT: M 73 LYS cc_start: 0.7384 (tttt) cc_final: 0.6985 (ptmt) REVERT: M 221 GLU cc_start: 0.6585 (mm-30) cc_final: 0.5793 (pt0) REVERT: M 248 MET cc_start: 0.3982 (ttm) cc_final: 0.3452 (ppp) REVERT: N 350 MET cc_start: 0.5896 (pmm) cc_final: 0.5410 (pmm) REVERT: O 7 LYS cc_start: 0.6664 (tptp) cc_final: 0.6240 (pttp) REVERT: O 85 MET cc_start: 0.6989 (mpt) cc_final: 0.6605 (mmp) REVERT: O 91 TYR cc_start: 0.5906 (t80) cc_final: 0.5575 (t80) REVERT: O 118 MET cc_start: 0.2934 (ttt) cc_final: 0.1019 (pp-130) REVERT: P 301 GLU cc_start: 0.6428 (pt0) cc_final: 0.5343 (mt-10) REVERT: Q 44 LYS cc_start: 0.8206 (tppt) cc_final: 0.7975 (tppt) REVERT: Q 86 ARG cc_start: 0.4503 (mmt180) cc_final: 0.4074 (mmt-90) outliers start: 211 outliers final: 69 residues processed: 766 average time/residue: 0.5963 time to fit residues: 579.0606 Evaluate side-chains 632 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 544 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 577 GLU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 839 TYR Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain B residue 49 TYR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 648 HIS Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 1015 MET Chi-restraints excluded: chain B residue 1021 HIS Chi-restraints excluded: chain B residue 1069 MET Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 125 ARG Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 107 ARG Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 56 PHE Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 340 LEU Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 117 THR Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain O residue 377 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 464 optimal weight: 8.9990 chunk 114 optimal weight: 0.0670 chunk 317 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 486 optimal weight: 0.7980 chunk 155 optimal weight: 7.9990 chunk 483 optimal weight: 2.9990 chunk 291 optimal weight: 20.0000 chunk 352 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 overall best weight: 2.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN A 497 ASN B 159 ASN B 327 ASN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 ASN B 959 HIS B1021 HIS ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 HIS D 60 HIS ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN ** E 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN ** G 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 GLN H 76 ASN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 HIS ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 62 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.151401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.121907 restraints weight = 102814.187| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 3.72 r_work: 0.3826 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3824 r_free = 0.3824 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3824 r_free = 0.3824 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 moved from start: 1.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.248 41438 Z= 0.294 Angle : 1.327 58.679 56126 Z= 0.708 Chirality : 0.167 6.383 6305 Planarity : 0.007 0.065 7071 Dihedral : 9.973 74.759 5920 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.78 % Favored : 92.20 % Rotamer: Outliers : 5.41 % Allowed : 27.56 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.11), residues: 4922 helix: -0.85 (0.11), residues: 1761 sheet: -0.92 (0.18), residues: 720 loop : -2.57 (0.11), residues: 2441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG O 533 TYR 0.060 0.003 TYR Q 43 PHE 0.049 0.003 PHE A 6 TRP 0.036 0.002 TRP F 118 HIS 0.020 0.002 HIS B 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00706 / 0.29 (41417) covalent geometry : angle 1.23107 / 0.71 (56108) hydrogen bonds : bond 0.04841 / 3.21 ( 1484) hydrogen bonds : angle 5.62299 / 3.88 ( 4293) metal coordination : bond 0.01512 / 1.00 ( 21) metal coordination : angle 27.69700 / 14.01 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 652 time to evaluate : 1.597 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: A 116 MET cc_start: 0.5763 (ttm) cc_final: 0.4701 (mpp) REVERT: A 198 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7191 (pp20) REVERT: A 211 LEU cc_start: 0.3221 (OUTLIER) cc_final: 0.2592 (mt) REVERT: A 307 MET cc_start: 0.2951 (tpp) cc_final: 0.2642 (tpt) REVERT: A 422 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.6873 (pp30) REVERT: A 670 ASP cc_start: 0.7008 (OUTLIER) cc_final: 0.6536 (m-30) REVERT: A 770 GLU cc_start: 0.2986 (OUTLIER) cc_final: 0.2727 (tt0) REVERT: A 908 ASP cc_start: 0.5510 (p0) cc_final: 0.4567 (p0) REVERT: A 937 GLU cc_start: 0.4332 (tt0) cc_final: 0.2641 (tm-30) REVERT: A 1048 MET cc_start: 0.1399 (OUTLIER) cc_final: -0.0569 (mpt) REVERT: A 1106 GLU cc_start: 0.5858 (pm20) cc_final: 0.5481 (mm-30) REVERT: A 1275 MET cc_start: 0.7857 (mmt) cc_final: 0.7436 (mmt) REVERT: A 1305 ARG cc_start: 0.5787 (ptp-170) cc_final: 0.3230 (tpt170) REVERT: B 106 ASP cc_start: 0.8419 (t0) cc_final: 0.7637 (t0) REVERT: B 136 MET cc_start: 0.7901 (tpp) cc_final: 0.7680 (tpp) REVERT: B 199 VAL cc_start: 0.5747 (OUTLIER) cc_final: 0.5286 (m) REVERT: B 254 MET cc_start: 0.3311 (mtt) cc_final: 0.2243 (ptm) REVERT: B 387 ILE cc_start: 0.7148 (OUTLIER) cc_final: 0.6901 (mm) REVERT: B 426 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7284 (pp) REVERT: B 478 MET cc_start: 0.5161 (ppp) cc_final: 0.4548 (pmm) REVERT: B 499 MET cc_start: 0.6270 (OUTLIER) cc_final: 0.5771 (ptt) REVERT: B 637 GLU cc_start: 0.6683 (tt0) cc_final: 0.5830 (tp30) REVERT: B 660 GLU cc_start: 0.6006 (mm-30) cc_final: 0.5495 (tp30) REVERT: B 803 ILE cc_start: 0.5078 (mp) cc_final: 0.4810 (mp) REVERT: B 1013 LYS cc_start: 0.7748 (tptp) cc_final: 0.7392 (ttpp) REVERT: B 1014 HIS cc_start: 0.6233 (m-70) cc_final: 0.5869 (m-70) REVERT: B 1050 MET cc_start: 0.8086 (tpp) cc_final: 0.7318 (mtm) REVERT: B 1051 GLU cc_start: 0.7045 (mp0) cc_final: 0.6767 (mp0) REVERT: B 1089 SER cc_start: 0.6914 (m) cc_final: 0.6542 (p) REVERT: C 251 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7835 (mm-30) REVERT: C 345 MET cc_start: 0.6737 (mmt) cc_final: 0.6134 (ppp) REVERT: D 43 ASN cc_start: 0.7921 (m-40) cc_final: 0.7595 (m-40) REVERT: E 1 MET cc_start: 0.4197 (OUTLIER) cc_final: 0.3990 (mmm) REVERT: E 108 GLN cc_start: 0.7013 (mp-120) cc_final: 0.6387 (mp10) REVERT: E 110 MET cc_start: 0.2516 (OUTLIER) cc_final: 0.1022 (tpp) REVERT: F 115 TYR cc_start: 0.5012 (p90) cc_final: 0.4571 (p90) REVERT: G 9 ASP cc_start: 0.4028 (m-30) cc_final: 0.3777 (m-30) REVERT: G 48 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8200 (tm) REVERT: G 116 GLN cc_start: 0.5636 (tm130) cc_final: 0.5274 (tm-30) REVERT: G 142 MET cc_start: 0.0795 (OUTLIER) cc_final: 0.0589 (mmm) REVERT: H 65 TYR cc_start: 0.7616 (m-10) cc_final: 0.7388 (m-80) REVERT: I 1 MET cc_start: 0.4731 (pmm) cc_final: 0.3826 (pp-130) REVERT: I 101 GLN cc_start: 0.4882 (pp30) cc_final: 0.4467 (mm-40) REVERT: J 41 LYS cc_start: 0.8905 (tmmt) cc_final: 0.8601 (tppp) REVERT: K 29 MET cc_start: 0.7228 (tmm) cc_final: 0.6856 (tmm) REVERT: K 46 GLU cc_start: 0.8164 (pt0) cc_final: 0.7588 (pp20) REVERT: K 67 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7871 (m-80) REVERT: K 80 ILE cc_start: 0.5887 (mt) cc_final: 0.5311 (mt) REVERT: M 59 GLU cc_start: 0.6239 (pt0) cc_final: 0.5482 (pm20) REVERT: M 73 LYS cc_start: 0.7410 (tttt) cc_final: 0.6826 (ttpt) REVERT: M 104 SER cc_start: 0.6649 (m) cc_final: 0.6263 (p) REVERT: M 113 ARG cc_start: 0.5895 (ttm110) cc_final: 0.5412 (ptm160) REVERT: M 211 TYR cc_start: 0.6256 (m-10) cc_final: 0.6040 (m-10) REVERT: M 221 GLU cc_start: 0.6450 (mm-30) cc_final: 0.5764 (pt0) REVERT: M 248 MET cc_start: 0.4658 (ttm) cc_final: 0.3970 (ppp) REVERT: N 262 LYS cc_start: 0.5125 (OUTLIER) cc_final: 0.4840 (pptt) REVERT: N 350 MET cc_start: 0.6504 (pmm) cc_final: 0.5947 (pmm) REVERT: O 7 LYS cc_start: 0.6967 (tptp) cc_final: 0.6516 (pttm) REVERT: O 85 MET cc_start: 0.7239 (mpt) cc_final: 0.6744 (mmp) REVERT: O 90 ARG cc_start: 0.6045 (ttt180) cc_final: 0.5426 (mtm180) REVERT: O 118 MET cc_start: 0.3227 (ttt) cc_final: 0.1190 (pp-130) REVERT: O 187 MET cc_start: 0.4561 (mpp) cc_final: 0.4321 (mpp) REVERT: O 526 TYR cc_start: 0.5932 (t80) cc_final: 0.5523 (t80) REVERT: P 220 ILE cc_start: 0.8039 (mm) cc_final: 0.7754 (pp) REVERT: P 301 GLU cc_start: 0.6465 (pt0) cc_final: 0.5899 (tt0) REVERT: Q 62 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7476 (mp10) REVERT: Q 110 MET cc_start: 0.5632 (ppp) cc_final: 0.4338 (ttp) REVERT: Q 111 MET cc_start: 0.1069 (tpp) cc_final: 0.0700 (tpp) outliers start: 238 outliers final: 79 residues processed: 816 average time/residue: 0.6259 time to fit residues: 643.6974 Evaluate side-chains 639 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 543 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 839 TYR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1049 THR Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 621 PHE Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 881 ILE Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 919 CYS Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 1015 MET Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1018 ASP Chi-restraints excluded: chain B residue 1021 HIS Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain H residue 56 PHE Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain M residue 54 GLN Chi-restraints excluded: chain M residue 75 GLU Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 255 LEU Chi-restraints excluded: chain N residue 262 LYS Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain O residue 5 GLU Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 91 TYR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 117 THR Chi-restraints excluded: chain O residue 137 LYS Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain O residue 437 HIS Chi-restraints excluded: chain O residue 529 CYS Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 311 THR Chi-restraints excluded: chain Q residue 62 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 335 optimal weight: 20.0000 chunk 203 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 320 optimal weight: 0.3980 chunk 102 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 ASN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN A 508 HIS A 820 HIS ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1371 ASN A1385 HIS B 423 ASN ** B 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 701 GLN D 60 HIS ** E 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN E 108 GLN F 72 GLN ** G 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 HIS ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 395 HIS ** O 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 189 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.151133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.121080 restraints weight = 101641.979| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 3.93 r_work: 0.3799 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3803 r_free = 0.3803 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3803 r_free = 0.3803 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 1.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.243 41438 Z= 0.223 Angle : 1.252 50.559 56126 Z= 0.667 Chirality : 0.166 6.316 6305 Planarity : 0.005 0.063 7071 Dihedral : 9.862 75.204 5920 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.91 % Favored : 94.07 % Rotamer: Outliers : 3.89 % Allowed : 30.85 % Favored : 65.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.11), residues: 4922 helix: -0.69 (0.12), residues: 1776 sheet: -0.78 (0.19), residues: 712 loop : -2.55 (0.11), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 108 TYR 0.028 0.002 TYR P 219 PHE 0.040 0.002 PHE H 56 TRP 0.040 0.002 TRP F 118 HIS 0.023 0.001 HIS B1021 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.22 (41417) covalent geometry : angle 1.15908 / 0.67 (56108) hydrogen bonds : bond 0.04138 / 2.74 ( 1484) hydrogen bonds : angle 5.35632 / 3.72 ( 4293) metal coordination : bond 0.00739 / 0.48 ( 21) metal coordination : angle 26.39266 / 13.64 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 597 time to evaluate : 1.584 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: A 116 MET cc_start: 0.5862 (ttm) cc_final: 0.4920 (mpp) REVERT: A 198 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7241 (pp20) REVERT: A 211 LEU cc_start: 0.3181 (OUTLIER) cc_final: 0.2524 (mt) REVERT: A 227 PHE cc_start: 0.4239 (OUTLIER) cc_final: 0.3674 (m-80) REVERT: A 307 MET cc_start: 0.2835 (tpp) cc_final: 0.2584 (tpt) REVERT: A 526 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8884 (ttpp) REVERT: A 577 GLU cc_start: 0.7694 (pm20) cc_final: 0.7490 (pm20) REVERT: A 670 ASP cc_start: 0.6786 (OUTLIER) cc_final: 0.6538 (m-30) REVERT: A 937 GLU cc_start: 0.4733 (tt0) cc_final: 0.2783 (tm-30) REVERT: A 1236 MET cc_start: 0.4911 (tmm) cc_final: 0.3462 (mtt) REVERT: A 1275 MET cc_start: 0.8097 (mmt) cc_final: 0.7620 (mmt) REVERT: A 1305 ARG cc_start: 0.6134 (ptp-170) cc_final: 0.3461 (tpt170) REVERT: A 1355 ILE cc_start: 0.7569 (tt) cc_final: 0.7043 (tt) REVERT: A 1375 ARG cc_start: 0.6923 (ttt180) cc_final: 0.6535 (tpp80) REVERT: B 49 TYR cc_start: 0.4840 (OUTLIER) cc_final: 0.4581 (t80) REVERT: B 106 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.7714 (t0) REVERT: B 136 MET cc_start: 0.7985 (tpp) cc_final: 0.7776 (tpp) REVERT: B 199 VAL cc_start: 0.5685 (OUTLIER) cc_final: 0.5174 (m) REVERT: B 254 MET cc_start: 0.3359 (mtt) cc_final: 0.2326 (ptm) REVERT: B 426 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7142 (pp) REVERT: B 478 MET cc_start: 0.5812 (ppp) cc_final: 0.5123 (pmm) REVERT: B 499 MET cc_start: 0.6824 (OUTLIER) cc_final: 0.6447 (ptt) REVERT: B 626 HIS cc_start: 0.6245 (m90) cc_final: 0.5973 (m-70) REVERT: B 637 GLU cc_start: 0.7466 (tt0) cc_final: 0.6425 (tm-30) REVERT: B 660 GLU cc_start: 0.5861 (mm-30) cc_final: 0.5406 (tp30) REVERT: B 729 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7449 (tm-30) REVERT: B 781 ARG cc_start: 0.7532 (mtt-85) cc_final: 0.7261 (mtt-85) REVERT: B 796 ASP cc_start: 0.4259 (OUTLIER) cc_final: 0.3953 (t70) REVERT: B 926 ASP cc_start: 0.8571 (m-30) cc_final: 0.8133 (m-30) REVERT: B 1013 LYS cc_start: 0.7937 (tptp) cc_final: 0.7507 (mtpp) REVERT: B 1050 MET cc_start: 0.8150 (tpp) cc_final: 0.7380 (mtm) REVERT: B 1051 GLU cc_start: 0.7193 (mp0) cc_final: 0.6902 (mp0) REVERT: B 1066 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7135 (pp20) REVERT: B 1069 MET cc_start: 0.5504 (pmm) cc_final: 0.4847 (pp-130) REVERT: B 1121 ASN cc_start: 0.7711 (t0) cc_final: 0.7496 (t160) REVERT: C 251 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7651 (tp30) REVERT: C 345 MET cc_start: 0.6729 (mmt) cc_final: 0.6243 (ppp) REVERT: D 107 ARG cc_start: 0.4495 (ptt180) cc_final: 0.4165 (ptt180) REVERT: E 108 GLN cc_start: 0.6743 (mp10) cc_final: 0.5961 (pp30) REVERT: E 110 MET cc_start: 0.2618 (OUTLIER) cc_final: 0.1263 (tpp) REVERT: E 151 MET cc_start: 0.3170 (OUTLIER) cc_final: 0.1374 (ttp) REVERT: H 65 TYR cc_start: 0.7636 (m-10) cc_final: 0.7399 (m-80) REVERT: I 1 MET cc_start: 0.4611 (pmm) cc_final: 0.3550 (pp-130) REVERT: I 91 MET cc_start: 0.6520 (mmp) cc_final: 0.5346 (mtt) REVERT: I 101 GLN cc_start: 0.5030 (pp30) cc_final: 0.4659 (mm-40) REVERT: J 41 LYS cc_start: 0.8947 (tmmt) cc_final: 0.8709 (tppp) REVERT: K 46 GLU cc_start: 0.8285 (pt0) cc_final: 0.7659 (pp20) REVERT: K 67 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7861 (m-80) REVERT: K 115 GLU cc_start: 0.7918 (pp20) cc_final: 0.7687 (pp20) REVERT: M 59 GLU cc_start: 0.6295 (pt0) cc_final: 0.5525 (pm20) REVERT: M 73 LYS cc_start: 0.7441 (tttt) cc_final: 0.7088 (ptmt) REVERT: M 104 SER cc_start: 0.6696 (m) cc_final: 0.6493 (p) REVERT: M 221 GLU cc_start: 0.6453 (mm-30) cc_final: 0.5741 (pt0) REVERT: M 248 MET cc_start: 0.4715 (ttm) cc_final: 0.3986 (ppp) REVERT: N 262 LYS cc_start: 0.5161 (OUTLIER) cc_final: 0.4953 (pptt) REVERT: N 350 MET cc_start: 0.6538 (pmm) cc_final: 0.5905 (pmm) REVERT: O 7 LYS cc_start: 0.7063 (tptp) cc_final: 0.6562 (pttm) REVERT: O 85 MET cc_start: 0.7251 (mpt) cc_final: 0.6778 (mmp) REVERT: O 90 ARG cc_start: 0.6381 (ttt180) cc_final: 0.5771 (mtm180) REVERT: O 118 MET cc_start: 0.3461 (ttt) cc_final: 0.1615 (pp-130) REVERT: P 301 GLU cc_start: 0.6317 (pt0) cc_final: 0.5646 (tt0) outliers start: 171 outliers final: 71 residues processed: 717 average time/residue: 0.6390 time to fit residues: 574.8500 Evaluate side-chains 629 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 541 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 886 TYR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1049 THR Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain B residue 49 TYR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 495 ASN Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 648 HIS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 729 GLU Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 972 VAL Chi-restraints excluded: chain B residue 1066 GLU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain G residue 98 HIS Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 56 PHE Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain M residue 39 TYR Chi-restraints excluded: chain M residue 75 GLU Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 255 LEU Chi-restraints excluded: chain N residue 262 LYS Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 117 THR Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain O residue 437 HIS Chi-restraints excluded: chain Q residue 58 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 296 optimal weight: 6.9990 chunk 417 optimal weight: 6.9990 chunk 481 optimal weight: 0.5980 chunk 183 optimal weight: 4.9990 chunk 242 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 263 optimal weight: 2.9990 chunk 317 optimal weight: 0.0570 chunk 107 optimal weight: 7.9990 chunk 325 optimal weight: 0.9990 chunk 282 optimal weight: 2.9990 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1277 ASN A1371 ASN A1385 HIS B 159 ASN ** B 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 HIS D 98 GLN F 72 GLN ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 437 HIS ** O 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.151432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.120950 restraints weight = 100822.162| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 4.06 r_work: 0.3793 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3797 r_free = 0.3797 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3797 r_free = 0.3797 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 1.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.244 41438 Z= 0.202 Angle : 1.241 50.664 56126 Z= 0.660 Chirality : 0.165 6.321 6305 Planarity : 0.005 0.069 7071 Dihedral : 9.718 74.173 5920 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.52 % Favored : 93.46 % Rotamer: Outliers : 3.16 % Allowed : 32.76 % Favored : 64.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.11), residues: 4922 helix: -0.44 (0.12), residues: 1772 sheet: -0.73 (0.18), residues: 718 loop : -2.45 (0.11), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 24 TYR 0.034 0.002 TYR H 90 PHE 0.022 0.002 PHE B 730 TRP 0.030 0.002 TRP F 118 HIS 0.048 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.20 (41417) covalent geometry : angle 1.14787 / 0.66 (56108) hydrogen bonds : bond 0.03876 / 2.55 ( 1484) hydrogen bonds : angle 5.21707 / 3.62 ( 4293) metal coordination : bond 0.00716 / 0.49 ( 21) metal coordination : angle 26.40777 / 13.62 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 580 time to evaluate : 1.557 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: A 116 MET cc_start: 0.5952 (ttm) cc_final: 0.4947 (mpp) REVERT: A 198 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7259 (pp20) REVERT: A 211 LEU cc_start: 0.3152 (OUTLIER) cc_final: 0.2632 (mp) REVERT: A 307 MET cc_start: 0.2934 (tpp) cc_final: 0.2567 (tpt) REVERT: A 526 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8862 (ttpp) REVERT: A 577 GLU cc_start: 0.7763 (pm20) cc_final: 0.7558 (pm20) REVERT: A 670 ASP cc_start: 0.6924 (OUTLIER) cc_final: 0.6679 (m-30) REVERT: A 743 THR cc_start: 0.7481 (OUTLIER) cc_final: 0.7174 (t) REVERT: A 770 GLU cc_start: 0.3187 (OUTLIER) cc_final: 0.1779 (tt0) REVERT: A 937 GLU cc_start: 0.4659 (tt0) cc_final: 0.3591 (tm-30) REVERT: A 1236 MET cc_start: 0.4948 (tmm) cc_final: 0.3473 (mtt) REVERT: A 1275 MET cc_start: 0.8113 (mmt) cc_final: 0.7822 (mmt) REVERT: A 1305 ARG cc_start: 0.6139 (ptp-170) cc_final: 0.3483 (tpt170) REVERT: A 1355 ILE cc_start: 0.7518 (tt) cc_final: 0.7238 (tt) REVERT: B 106 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7795 (t0) REVERT: B 188 ARG cc_start: 0.7798 (tmt90) cc_final: 0.7558 (tmm-80) REVERT: B 199 VAL cc_start: 0.5580 (OUTLIER) cc_final: 0.5089 (m) REVERT: B 254 MET cc_start: 0.3334 (mtt) cc_final: 0.2331 (ptm) REVERT: B 384 MET cc_start: 0.7649 (ppp) cc_final: 0.5811 (mmt) REVERT: B 426 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7371 (pp) REVERT: B 478 MET cc_start: 0.5869 (ppp) cc_final: 0.5177 (pmm) REVERT: B 499 MET cc_start: 0.6762 (OUTLIER) cc_final: 0.6469 (ptt) REVERT: B 626 HIS cc_start: 0.6141 (m90) cc_final: 0.5935 (m-70) REVERT: B 637 GLU cc_start: 0.7429 (tt0) cc_final: 0.6306 (tm-30) REVERT: B 660 GLU cc_start: 0.5961 (mm-30) cc_final: 0.5476 (tp30) REVERT: B 1050 MET cc_start: 0.8087 (tpp) cc_final: 0.7266 (mtm) REVERT: B 1051 GLU cc_start: 0.7056 (mp0) cc_final: 0.6717 (mp0) REVERT: B 1069 MET cc_start: 0.5431 (pmm) cc_final: 0.4941 (ppp) REVERT: C 141 ARG cc_start: 0.8364 (mmm-85) cc_final: 0.8150 (ttt90) REVERT: C 251 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7670 (tp30) REVERT: C 345 MET cc_start: 0.6849 (mmt) cc_final: 0.6386 (ppp) REVERT: D 33 ASN cc_start: 0.3824 (OUTLIER) cc_final: 0.3595 (m-40) REVERT: D 43 ASN cc_start: 0.8078 (m-40) cc_final: 0.7759 (m-40) REVERT: E 108 GLN cc_start: 0.6897 (mp10) cc_final: 0.6673 (mp-120) REVERT: E 110 MET cc_start: 0.2684 (OUTLIER) cc_final: 0.2099 (tpt) REVERT: E 151 MET cc_start: 0.3446 (OUTLIER) cc_final: 0.1562 (ttp) REVERT: F 101 LYS cc_start: 0.8554 (mppt) cc_final: 0.7946 (mppt) REVERT: H 37 MET cc_start: 0.6953 (ppp) cc_final: 0.5702 (ppp) REVERT: H 65 TYR cc_start: 0.7716 (m-10) cc_final: 0.7444 (m-80) REVERT: I 1 MET cc_start: 0.4621 (pmm) cc_final: 0.3686 (pp-130) REVERT: I 91 MET cc_start: 0.6535 (mmp) cc_final: 0.5400 (mtt) REVERT: I 101 GLN cc_start: 0.5148 (pp30) cc_final: 0.4943 (mm-40) REVERT: J 41 LYS cc_start: 0.9038 (tmmt) cc_final: 0.8730 (tppp) REVERT: K 46 GLU cc_start: 0.8283 (pt0) cc_final: 0.7666 (pp20) REVERT: K 87 ARG cc_start: 0.7783 (ttp80) cc_final: 0.7558 (ttp80) REVERT: K 112 ASP cc_start: 0.8092 (t0) cc_final: 0.7732 (m-30) REVERT: L 15 MET cc_start: 0.6587 (OUTLIER) cc_final: 0.6036 (ttm) REVERT: M 54 GLN cc_start: 0.6805 (OUTLIER) cc_final: 0.6315 (pp30) REVERT: M 73 LYS cc_start: 0.7453 (tttt) cc_final: 0.7132 (ptmt) REVERT: M 221 GLU cc_start: 0.6355 (mm-30) cc_final: 0.5700 (pt0) REVERT: M 248 MET cc_start: 0.4676 (ttm) cc_final: 0.3969 (ppp) REVERT: N 262 LYS cc_start: 0.5175 (OUTLIER) cc_final: 0.4962 (pptt) REVERT: N 350 MET cc_start: 0.6563 (pmm) cc_final: 0.6164 (pmm) REVERT: O 7 LYS cc_start: 0.7079 (tptp) cc_final: 0.6576 (pttm) REVERT: O 85 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.6932 (mmp) REVERT: O 90 ARG cc_start: 0.6123 (ttt180) cc_final: 0.5533 (mtm180) REVERT: O 118 MET cc_start: 0.3330 (ttt) cc_final: 0.1772 (pp-130) REVERT: O 424 TYR cc_start: 0.5508 (m-80) cc_final: 0.5277 (m-80) REVERT: P 220 ILE cc_start: 0.7616 (mm) cc_final: 0.7227 (pp) REVERT: P 301 GLU cc_start: 0.6477 (pt0) cc_final: 0.6147 (tt0) REVERT: Q 62 GLN cc_start: 0.7975 (mt0) cc_final: 0.7367 (mp10) REVERT: Q 110 MET cc_start: 0.5929 (ppp) cc_final: 0.4428 (ttp) outliers start: 139 outliers final: 70 residues processed: 681 average time/residue: 0.6354 time to fit residues: 542.4688 Evaluate side-chains 620 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 533 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1049 THR Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain B residue 49 TYR Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 495 ASN Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 648 HIS Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 803 ILE Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1018 ASP Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain G residue 98 HIS Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain L residue 15 MET Chi-restraints excluded: chain M residue 39 TYR Chi-restraints excluded: chain M residue 54 GLN Chi-restraints excluded: chain M residue 75 GLU Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 255 LEU Chi-restraints excluded: chain N residue 262 LYS Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain N residue 340 LEU Chi-restraints excluded: chain N residue 372 GLU Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 27 HIS Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 117 THR Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 328 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 432 optimal weight: 3.9990 chunk 241 optimal weight: 4.9990 chunk 425 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 223 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 chunk 109 optimal weight: 0.4980 chunk 316 optimal weight: 0.0040 chunk 12 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 chunk 19 optimal weight: 0.0770 overall best weight: 0.4150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1371 ASN ** B 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 HIS F 72 GLN ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 437 HIS ** O 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 182 GLN Q 62 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.151696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.121267 restraints weight = 101167.270| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 3.93 r_work: 0.3803 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3805 r_free = 0.3805 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3805 r_free = 0.3805 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 1.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.244 41438 Z= 0.200 Angle : 1.249 50.542 56126 Z= 0.661 Chirality : 0.165 6.317 6305 Planarity : 0.005 0.066 7071 Dihedral : 9.656 73.613 5920 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.80 % Allowed : 33.63 % Favored : 63.57 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.11), residues: 4922 helix: -0.32 (0.12), residues: 1762 sheet: -0.66 (0.18), residues: 723 loop : -2.39 (0.11), residues: 2437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 24 TYR 0.035 0.002 TYR H 90 PHE 0.031 0.002 PHE C 336 TRP 0.029 0.002 TRP A 310 HIS 0.011 0.001 HIS M 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.20 (41417) covalent geometry : angle 1.15662 / 0.66 (56108) hydrogen bonds : bond 0.03793 / 2.51 ( 1484) hydrogen bonds : angle 5.10601 / 3.55 ( 4293) metal coordination : bond 0.00730 / 0.49 ( 21) metal coordination : angle 26.30586 / 13.59 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 555 time to evaluate : 1.610 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: A 116 MET cc_start: 0.5997 (ttm) cc_final: 0.5025 (mpp) REVERT: A 198 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7278 (pp20) REVERT: A 307 MET cc_start: 0.2776 (tpp) cc_final: 0.2480 (tpt) REVERT: A 526 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.8901 (ttpp) REVERT: A 577 GLU cc_start: 0.7819 (pm20) cc_final: 0.7619 (pm20) REVERT: A 594 LEU cc_start: 0.5294 (OUTLIER) cc_final: 0.5087 (pp) REVERT: A 670 ASP cc_start: 0.6896 (OUTLIER) cc_final: 0.6673 (m-30) REVERT: A 743 THR cc_start: 0.7458 (OUTLIER) cc_final: 0.7148 (t) REVERT: A 801 GLN cc_start: 0.5475 (pm20) cc_final: 0.4373 (tt0) REVERT: A 937 GLU cc_start: 0.4823 (tt0) cc_final: 0.3268 (tm-30) REVERT: A 1022 TYR cc_start: 0.3030 (t80) cc_final: 0.2376 (t80) REVERT: A 1023 MET cc_start: 0.7467 (mmp) cc_final: 0.7237 (mmt) REVERT: A 1236 MET cc_start: 0.5006 (tmm) cc_final: 0.3496 (mtt) REVERT: A 1275 MET cc_start: 0.8192 (mmt) cc_final: 0.7755 (mmt) REVERT: A 1305 ARG cc_start: 0.5985 (ptp-170) cc_final: 0.3328 (tpt170) REVERT: A 1375 ARG cc_start: 0.8593 (tpp80) cc_final: 0.8077 (ttt180) REVERT: B 106 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7660 (t0) REVERT: B 188 ARG cc_start: 0.7873 (tmt90) cc_final: 0.7556 (tmm-80) REVERT: B 199 VAL cc_start: 0.5643 (OUTLIER) cc_final: 0.5177 (m) REVERT: B 254 MET cc_start: 0.3310 (mtt) cc_final: 0.2343 (ptm) REVERT: B 384 MET cc_start: 0.7510 (ppp) cc_final: 0.5805 (mmt) REVERT: B 426 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7259 (pp) REVERT: B 478 MET cc_start: 0.5792 (ppp) cc_final: 0.5102 (pmm) REVERT: B 637 GLU cc_start: 0.7431 (tt0) cc_final: 0.6369 (tm-30) REVERT: B 660 GLU cc_start: 0.5752 (mm-30) cc_final: 0.5269 (tp30) REVERT: B 862 THR cc_start: 0.7663 (OUTLIER) cc_final: 0.7267 (p) REVERT: B 1050 MET cc_start: 0.8033 (tpp) cc_final: 0.7345 (mtm) REVERT: B 1051 GLU cc_start: 0.7214 (mp0) cc_final: 0.6675 (mp0) REVERT: B 1069 MET cc_start: 0.5568 (pmm) cc_final: 0.5005 (ppp) REVERT: B 1105 ARG cc_start: 0.7455 (pmm-80) cc_final: 0.7224 (mtm180) REVERT: C 141 ARG cc_start: 0.8315 (mmm-85) cc_final: 0.8113 (ttt90) REVERT: C 251 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7900 (mm-30) REVERT: C 345 MET cc_start: 0.6898 (mmt) cc_final: 0.6411 (ppp) REVERT: D 33 ASN cc_start: 0.3752 (OUTLIER) cc_final: 0.3519 (m-40) REVERT: D 43 ASN cc_start: 0.8029 (m-40) cc_final: 0.7756 (m-40) REVERT: E 108 GLN cc_start: 0.6813 (mp10) cc_final: 0.6513 (mp-120) REVERT: E 110 MET cc_start: 0.1917 (OUTLIER) cc_final: 0.1206 (tpt) REVERT: E 151 MET cc_start: 0.3578 (OUTLIER) cc_final: 0.1707 (ttp) REVERT: F 58 THR cc_start: 0.7140 (m) cc_final: 0.6834 (p) REVERT: F 101 LYS cc_start: 0.8555 (mppt) cc_final: 0.7992 (mppt) REVERT: H 37 MET cc_start: 0.6710 (ppp) cc_final: 0.5661 (ppp) REVERT: H 65 TYR cc_start: 0.7668 (m-10) cc_final: 0.7414 (m-80) REVERT: I 1 MET cc_start: 0.4624 (pmm) cc_final: 0.3403 (pp-130) REVERT: I 3 LEU cc_start: 0.4755 (mt) cc_final: 0.4432 (tp) REVERT: I 91 MET cc_start: 0.6319 (mmp) cc_final: 0.5266 (mtt) REVERT: J 41 LYS cc_start: 0.9015 (tmmt) cc_final: 0.8730 (tppp) REVERT: K 46 GLU cc_start: 0.8273 (pt0) cc_final: 0.7699 (pp20) REVERT: M 73 LYS cc_start: 0.7538 (tttt) cc_final: 0.7064 (ttpt) REVERT: M 221 GLU cc_start: 0.6251 (mm-30) cc_final: 0.5754 (pt0) REVERT: M 248 MET cc_start: 0.4770 (ttm) cc_final: 0.3981 (ppp) REVERT: N 262 LYS cc_start: 0.5238 (OUTLIER) cc_final: 0.5006 (pptt) REVERT: N 350 MET cc_start: 0.6724 (pmm) cc_final: 0.6291 (pmm) REVERT: O 7 LYS cc_start: 0.6983 (tptp) cc_final: 0.6474 (pttm) REVERT: O 85 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.6970 (mmp) REVERT: O 90 ARG cc_start: 0.6109 (ttt180) cc_final: 0.5686 (mtm180) REVERT: O 118 MET cc_start: 0.3396 (ttt) cc_final: 0.2017 (pp-130) REVERT: O 138 THR cc_start: 0.7319 (m) cc_final: 0.7050 (p) REVERT: O 148 PHE cc_start: 0.5125 (t80) cc_final: 0.4660 (t80) REVERT: O 424 TYR cc_start: 0.5311 (m-80) cc_final: 0.5068 (m-80) REVERT: O 500 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: P 220 ILE cc_start: 0.7633 (mm) cc_final: 0.7190 (pp) REVERT: P 232 MET cc_start: 0.6689 (tpp) cc_final: 0.6364 (tpp) REVERT: P 250 MET cc_start: 0.4648 (tpt) cc_final: 0.3790 (ppp) REVERT: P 252 ILE cc_start: 0.6549 (OUTLIER) cc_final: 0.6139 (pp) REVERT: Q 62 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7570 (mp10) outliers start: 123 outliers final: 71 residues processed: 641 average time/residue: 0.6516 time to fit residues: 523.2383 Evaluate side-chains 612 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 524 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain A residue 425 HIS Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1049 THR Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 495 ASN Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 648 HIS Chi-restraints excluded: chain B residue 719 MET Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 803 ILE Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 98 HIS Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 39 TYR Chi-restraints excluded: chain M residue 75 GLU Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 255 LEU Chi-restraints excluded: chain N residue 262 LYS Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 27 HIS Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 117 THR Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain O residue 500 GLU Chi-restraints excluded: chain P residue 191 LYS Chi-restraints excluded: chain P residue 239 LEU Chi-restraints excluded: chain P residue 252 ILE Chi-restraints excluded: chain Q residue 62 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 464 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 199 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 91 optimal weight: 0.0670 chunk 182 optimal weight: 0.0000 chunk 92 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 186 optimal weight: 0.0570 chunk 281 optimal weight: 1.9990 overall best weight: 0.3840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 GLN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1371 ASN B 144 ASN B 282 GLN ** B 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1121 ASN D 60 HIS F 72 GLN ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 HIS ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 437 HIS ** O 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.151491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.121384 restraints weight = 98161.586| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 3.62 r_work: 0.3822 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3816 r_free = 0.3816 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3816 r_free = 0.3816 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 1.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.244 41438 Z= 0.199 Angle : 1.255 50.534 56126 Z= 0.663 Chirality : 0.165 6.313 6305 Planarity : 0.005 0.077 7071 Dihedral : 9.618 73.225 5920 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.39 % Allowed : 34.24 % Favored : 63.37 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.11), residues: 4922 helix: -0.28 (0.12), residues: 1766 sheet: -0.68 (0.18), residues: 750 loop : -2.36 (0.12), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG K 87 TYR 0.029 0.002 TYR H 90 PHE 0.046 0.002 PHE A 363 TRP 0.041 0.002 TRP A 310 HIS 0.013 0.001 HIS B 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.20 (41417) covalent geometry : angle 1.16402 / 0.66 (56108) hydrogen bonds : bond 0.03674 / 2.42 ( 1484) hydrogen bonds : angle 5.05951 / 3.52 ( 4293) metal coordination : bond 0.00640 / 0.44 ( 21) metal coordination : angle 26.20665 / 13.57 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 562 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.4294 (ptp) cc_final: 0.4013 (mtt) REVERT: A 116 MET cc_start: 0.5995 (ttm) cc_final: 0.5072 (mpp) REVERT: A 198 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7278 (pp20) REVERT: A 307 MET cc_start: 0.3260 (tpp) cc_final: 0.2952 (tpt) REVERT: A 526 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8865 (ttpp) REVERT: A 577 GLU cc_start: 0.7902 (pm20) cc_final: 0.7674 (pm20) REVERT: A 594 LEU cc_start: 0.5552 (OUTLIER) cc_final: 0.5337 (pp) REVERT: A 670 ASP cc_start: 0.6967 (OUTLIER) cc_final: 0.6742 (m-30) REVERT: A 743 THR cc_start: 0.7393 (OUTLIER) cc_final: 0.7096 (t) REVERT: A 801 GLN cc_start: 0.5496 (pm20) cc_final: 0.4430 (tt0) REVERT: A 879 LEU cc_start: 0.3455 (OUTLIER) cc_final: 0.2921 (tp) REVERT: A 937 GLU cc_start: 0.4738 (tt0) cc_final: 0.2827 (tm-30) REVERT: A 1022 TYR cc_start: 0.3009 (t80) cc_final: 0.2463 (t80) REVERT: A 1028 GLU cc_start: 0.7860 (mm-30) cc_final: 0.6641 (mt-10) REVERT: A 1236 MET cc_start: 0.5015 (tmm) cc_final: 0.4397 (tmm) REVERT: A 1275 MET cc_start: 0.8271 (mmt) cc_final: 0.7791 (mmt) REVERT: A 1305 ARG cc_start: 0.5946 (ptp-170) cc_final: 0.3311 (tpt170) REVERT: A 1375 ARG cc_start: 0.8569 (tpp80) cc_final: 0.8070 (ttt180) REVERT: B 106 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7841 (t0) REVERT: B 188 ARG cc_start: 0.7826 (tmt90) cc_final: 0.7569 (tmm-80) REVERT: B 199 VAL cc_start: 0.5571 (OUTLIER) cc_final: 0.5108 (m) REVERT: B 254 MET cc_start: 0.3225 (mtt) cc_final: 0.2335 (ptm) REVERT: B 281 MET cc_start: 0.4444 (ppp) cc_final: 0.2868 (mmp) REVERT: B 384 MET cc_start: 0.7505 (ppp) cc_final: 0.5804 (mmt) REVERT: B 426 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7296 (pp) REVERT: B 478 MET cc_start: 0.5780 (ppp) cc_final: 0.5089 (pmm) REVERT: B 562 MET cc_start: 0.3321 (tpt) cc_final: 0.2160 (tmm) REVERT: B 637 GLU cc_start: 0.7437 (tt0) cc_final: 0.6408 (tm-30) REVERT: B 660 GLU cc_start: 0.5908 (mm-30) cc_final: 0.5437 (tp30) REVERT: B 862 THR cc_start: 0.7683 (OUTLIER) cc_final: 0.7308 (p) REVERT: B 1050 MET cc_start: 0.7997 (tpp) cc_final: 0.7275 (mtm) REVERT: B 1051 GLU cc_start: 0.7191 (mp0) cc_final: 0.6643 (mp0) REVERT: B 1069 MET cc_start: 0.5681 (pmm) cc_final: 0.5164 (ppp) REVERT: C 251 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7931 (mm-30) REVERT: C 345 MET cc_start: 0.6979 (mmt) cc_final: 0.6513 (ppp) REVERT: D 33 ASN cc_start: 0.3720 (OUTLIER) cc_final: 0.3482 (m-40) REVERT: E 90 TYR cc_start: 0.7336 (t80) cc_final: 0.7114 (t80) REVERT: E 108 GLN cc_start: 0.6866 (mp10) cc_final: 0.6534 (mp-120) REVERT: E 110 MET cc_start: 0.1882 (OUTLIER) cc_final: 0.1139 (tpt) REVERT: E 151 MET cc_start: 0.3784 (OUTLIER) cc_final: 0.1922 (ttp) REVERT: F 58 THR cc_start: 0.7205 (m) cc_final: 0.6869 (p) REVERT: F 90 LEU cc_start: 0.8006 (tp) cc_final: 0.7747 (tp) REVERT: H 37 MET cc_start: 0.6496 (ppp) cc_final: 0.5951 (ppp) REVERT: H 65 TYR cc_start: 0.7603 (m-10) cc_final: 0.7365 (m-80) REVERT: I 1 MET cc_start: 0.4623 (pmm) cc_final: 0.3733 (pp-130) REVERT: I 91 MET cc_start: 0.6348 (mmp) cc_final: 0.5385 (mtt) REVERT: K 46 GLU cc_start: 0.8226 (pt0) cc_final: 0.7675 (pp20) REVERT: K 87 ARG cc_start: 0.7639 (ttp80) cc_final: 0.7088 (tmm160) REVERT: M 26 TYR cc_start: 0.5227 (OUTLIER) cc_final: 0.5007 (t80) REVERT: M 54 GLN cc_start: 0.6863 (OUTLIER) cc_final: 0.6429 (pp30) REVERT: M 73 LYS cc_start: 0.7529 (tttt) cc_final: 0.7211 (ptmt) REVERT: M 221 GLU cc_start: 0.6209 (mm-30) cc_final: 0.5747 (pt0) REVERT: M 248 MET cc_start: 0.4765 (ttm) cc_final: 0.4021 (ppp) REVERT: M 699 MET cc_start: 0.3320 (ppp) cc_final: 0.1016 (pmt) REVERT: N 262 LYS cc_start: 0.5386 (OUTLIER) cc_final: 0.5148 (pptt) REVERT: N 271 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6260 (pp) REVERT: N 350 MET cc_start: 0.6743 (pmm) cc_final: 0.6464 (pmm) REVERT: O 7 LYS cc_start: 0.6944 (tptp) cc_final: 0.6455 (pttm) REVERT: O 85 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.6914 (mmp) REVERT: O 90 ARG cc_start: 0.6120 (ttt180) cc_final: 0.5732 (mtm180) REVERT: O 118 MET cc_start: 0.3424 (ttt) cc_final: 0.2049 (pp-130) REVERT: O 138 THR cc_start: 0.7318 (m) cc_final: 0.7085 (p) REVERT: O 394 MET cc_start: 0.6329 (tmm) cc_final: 0.4837 (pp-130) REVERT: O 424 TYR cc_start: 0.5397 (m-80) cc_final: 0.5145 (m-80) REVERT: P 220 ILE cc_start: 0.7661 (mm) cc_final: 0.7217 (pp) REVERT: P 232 MET cc_start: 0.6788 (tpp) cc_final: 0.6353 (tpp) REVERT: P 235 ILE cc_start: 0.5229 (pp) cc_final: 0.4988 (pp) REVERT: P 295 ASP cc_start: 0.7109 (t0) cc_final: 0.6793 (t0) REVERT: Q 62 GLN cc_start: 0.8082 (mt0) cc_final: 0.7674 (mt0) outliers start: 105 outliers final: 63 residues processed: 635 average time/residue: 0.6683 time to fit residues: 533.0247 Evaluate side-chains 609 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 528 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 58 HIS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain A residue 425 HIS Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1049 THR Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 495 ASN Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 719 MET Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 1018 ASP Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 98 HIS Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 26 TYR Chi-restraints excluded: chain M residue 39 TYR Chi-restraints excluded: chain M residue 54 GLN Chi-restraints excluded: chain M residue 75 GLU Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 255 LEU Chi-restraints excluded: chain N residue 262 LYS Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 27 HIS Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 117 THR Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain P residue 191 LYS Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain Q residue 74 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 130 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 410 optimal weight: 9.9990 chunk 388 optimal weight: 10.0000 chunk 322 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 12 optimal weight: 0.0670 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 GLN ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 HIS ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1371 ASN ** B 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 758 ASN B1132 ASN ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 HIS F 72 GLN ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.149710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.117777 restraints weight = 100712.117| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 3.74 r_work: 0.3766 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3759 r_free = 0.3759 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3759 r_free = 0.3759 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (22 function evaluations) r_final: 0.3759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 1.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.242 41438 Z= 0.233 Angle : 1.281 50.556 56126 Z= 0.682 Chirality : 0.166 6.324 6305 Planarity : 0.006 0.102 7071 Dihedral : 9.650 73.182 5920 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.85 % Favored : 93.13 % Rotamer: Outliers : 2.50 % Allowed : 34.61 % Favored : 62.89 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.11), residues: 4922 helix: -0.31 (0.12), residues: 1766 sheet: -0.65 (0.18), residues: 736 loop : -2.39 (0.11), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG K 87 TYR 0.032 0.002 TYR Q 73 PHE 0.148 0.002 PHE Q 74 TRP 0.036 0.002 TRP A 310 HIS 0.012 0.001 HIS B 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.23 (41417) covalent geometry : angle 1.19239 / 0.68 (56108) hydrogen bonds : bond 0.04049 / 2.65 ( 1484) hydrogen bonds : angle 5.12837 / 3.57 ( 4293) metal coordination : bond 0.00691 / 0.42 ( 21) metal coordination : angle 26.09605 / 13.70 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18739.39 seconds wall clock time: 319 minutes 8.31 seconds (19148.31 seconds total)