Starting phenix.real_space_refine on Sat Mar 7 09:24:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d58_30577/03_2026/7d58_30577.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d58_30577/03_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_30577/03_2026/7d58_30577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d58_30577/03_2026/7d58_30577.map" model { file = "/net/cci-nas-00/data/ceres_data/7d58_30577/03_2026/7d58_30577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d58_30577/03_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: {'RNA': 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: 8.17, 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: 3.26 Conformation dependent library (CDL) restraints added in 1.6 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: 1.29 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: 10.93 Time building geometry restraints manager: 4.46 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=" 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=" N GLU B 752 " pdb=" CA GLU B 752 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.15e+00 bond pdb=" N LYS O 69 " pdb=" CA LYS O 69 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.17e-02 7.31e+03 2.85e+00 bond pdb=" N LEU D 78 " pdb=" CA LEU D 78 " ideal model delta sigma weight residual 1.457 1.478 -0.021 1.29e-02 6.01e+03 2.56e+00 bond pdb=" S1 SF4 P 400 " pdb="FE3 SF4 P 400 " ideal model delta sigma weight residual 2.280 2.325 -0.045 3.00e-02 1.11e+03 2.25e+00 ... (remaining 41412 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 54963 1.95 - 3.90: 1007 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: 22834 17.35 - 34.71: 1910 34.71 - 52.06: 475 52.06 - 69.42: 98 69.42 - 86.77: 40 Dihedral angle restraints: 25357 sinusoidal: 10855 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 25354 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: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 46.190 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.080 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:8.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2502 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= 0.339 Angle : 0.777 40.391 56126 Z= 0.408 Chirality : 0.536 21.381 6305 Planarity : 0.003 0.055 7071 Dihedral : 14.069 86.770 15981 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 covalent geometry : bond 0.00249 (41417) covalent geometry : angle 0.65968 (56108) hydrogen bonds : bond 0.20508 ( 1484) hydrogen bonds : angle 7.06966 ( 4293) metal coordination : bond 0.41105 ( 21) metal coordination : angle 22.89953 ( 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 : 1.284 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: 0.7522 time to fit residues: 884.5335 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 : 1.279 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 GLN A 114 HIS A 157 HIS A 182 ASN A 225 ASN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN A 400 ASN A 511 GLN A 623 GLN A 693 ASN A 738 GLN ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1180 ASN A1202 GLN ** A1231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1239 HIS ** A1286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1385 HIS ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN B 280 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 GLN B 648 HIS B 678 ASN ** B 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 959 HIS ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1021 HIS ** B1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN C 55 HIS C 172 HIS ** C 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 HIS D 76 HIS ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN G 115 GLN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 GLN I 99 ASN ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 45 HIS K 97 GLN L 23 HIS ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 ASN ** 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 68 HIS O 155 HIS ** O 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 483 GLN ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 62 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.150148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.122871 restraints weight = 98900.931| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 3.52 r_work: 0.3867 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3862 r_free = 0.3862 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3861 r_free = 0.3861 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4462 moved from start: 0.6404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.284 41438 Z= 0.353 Angle : 1.485 63.202 56126 Z= 0.785 Chirality : 0.166 6.761 6305 Planarity : 0.009 0.092 7071 Dihedral : 10.466 73.682 5950 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 22.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.27 % Favored : 92.60 % Rotamer: Outliers : 5.55 % Allowed : 16.10 % Favored : 78.35 % 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: -3.29 (0.10), residues: 4922 helix: -1.80 (0.10), residues: 1760 sheet: -1.11 (0.18), residues: 707 loop : -2.85 (0.10), residues: 2455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.002 ARG F 51 TYR 0.042 0.004 TYR A 434 PHE 0.046 0.005 PHE C 225 TRP 0.049 0.004 TRP B 476 HIS 0.018 0.003 HIS B 959 Details of bonding type rmsd covalent geometry : bond 0.00818 (41417) covalent geometry : angle 1.38510 (56108) hydrogen bonds : bond 0.06148 ( 1484) hydrogen bonds : angle 6.29361 ( 4293) metal coordination : bond 0.04205 ( 21) metal coordination : angle 29.91466 ( 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 1045 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 244 poor density : 801 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 LEU cc_start: 0.7369 (mt) cc_final: 0.6900 (mt) REVERT: A 211 LEU cc_start: 0.3056 (OUTLIER) cc_final: 0.2618 (mt) REVERT: A 234 ASP cc_start: 0.2829 (m-30) cc_final: 0.2491 (p0) REVERT: A 235 VAL cc_start: 0.8088 (t) cc_final: 0.7809 (t) REVERT: A 260 LEU cc_start: 0.4228 (OUTLIER) cc_final: 0.3695 (tt) REVERT: A 415 HIS cc_start: 0.5423 (OUTLIER) cc_final: 0.4203 (t-90) REVERT: A 428 MET cc_start: 0.6387 (OUTLIER) cc_final: 0.6184 (pp-130) REVERT: A 431 PHE cc_start: 0.6503 (m-80) cc_final: 0.6240 (m-80) REVERT: A 438 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.6282 (tp30) REVERT: A 440 MET cc_start: 0.7724 (tmm) cc_final: 0.7322 (ttp) REVERT: A 543 GLN cc_start: 0.3597 (OUTLIER) cc_final: 0.2679 (pp30) REVERT: A 578 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7832 (pmtt) REVERT: A 650 MET cc_start: 0.3192 (ptt) cc_final: 0.2463 (tpt) REVERT: A 651 ASP cc_start: 0.5511 (OUTLIER) cc_final: 0.5112 (p0) REVERT: A 767 CYS cc_start: 0.7060 (OUTLIER) cc_final: 0.6411 (p) REVERT: A 770 GLU cc_start: -0.0245 (OUTLIER) cc_final: -0.0705 (tt0) REVERT: A 808 ARG cc_start: 0.4818 (ppt170) cc_final: 0.4030 (ttm170) REVERT: A 885 GLN cc_start: 0.4071 (mm110) cc_final: 0.3781 (mm110) REVERT: A 921 PHE cc_start: 0.5304 (OUTLIER) cc_final: 0.4889 (m-80) REVERT: A 940 LEU cc_start: 0.5344 (OUTLIER) cc_final: 0.4734 (pp) REVERT: A 1085 ILE cc_start: 0.4012 (mt) cc_final: 0.3716 (mt) REVERT: A 1131 LYS cc_start: 0.5444 (tptt) cc_final: 0.5044 (tptt) REVERT: A 1294 MET cc_start: 0.2464 (mtm) cc_final: 0.1435 (pp-130) REVERT: B 160 GLU cc_start: 0.6214 (OUTLIER) cc_final: 0.5657 (pt0) REVERT: B 254 MET cc_start: 0.3052 (mtt) cc_final: 0.0808 (tpt) REVERT: B 281 MET cc_start: 0.3814 (pp-130) cc_final: 0.3601 (mmm) REVERT: B 349 ASN cc_start: 0.6469 (p0) cc_final: 0.6060 (m-40) REVERT: B 384 MET cc_start: 0.5609 (ppp) cc_final: 0.5147 (mmt) REVERT: B 415 MET cc_start: 0.4094 (OUTLIER) cc_final: 0.2885 (ttp) REVERT: B 694 MET cc_start: 0.3922 (ttp) cc_final: 0.3377 (pmm) REVERT: B 711 LEU cc_start: 0.6508 (mt) cc_final: 0.4629 (mt) REVERT: B 808 ILE cc_start: 0.6704 (mm) cc_final: 0.6447 (mt) REVERT: B 996 GLU cc_start: 0.4891 (mm-30) cc_final: 0.4019 (mp0) REVERT: B 1088 TYR cc_start: 0.6120 (p90) cc_final: 0.4016 (t80) REVERT: B 1089 SER cc_start: 0.5225 (m) cc_final: 0.4721 (p) REVERT: C 95 TYR cc_start: 0.5858 (m-10) cc_final: 0.5064 (m-10) REVERT: C 209 ASP cc_start: 0.4960 (p0) cc_final: 0.4586 (p0) REVERT: C 233 TYR cc_start: 0.5684 (OUTLIER) cc_final: 0.4181 (p90) REVERT: C 251 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7343 (tm-30) REVERT: D 4 LYS cc_start: 0.5067 (mptt) cc_final: 0.4675 (ptpt) REVERT: D 49 THR cc_start: 0.7251 (t) cc_final: 0.7034 (m) REVERT: E 85 LYS cc_start: 0.8605 (tptt) cc_final: 0.8113 (mmtm) REVERT: F 57 MET cc_start: 0.4486 (OUTLIER) cc_final: 0.4034 (mmm) REVERT: F 107 ARG cc_start: 0.2130 (OUTLIER) cc_final: 0.1278 (tpp-160) REVERT: G 39 VAL cc_start: -0.0574 (OUTLIER) cc_final: -0.0952 (t) REVERT: H 47 ILE cc_start: 0.6288 (OUTLIER) cc_final: 0.5487 (mp) REVERT: I 35 THR cc_start: 0.4997 (m) cc_final: 0.4746 (m) REVERT: I 60 GLU cc_start: 0.5865 (mm-30) cc_final: 0.5660 (mm-30) REVERT: K 29 MET cc_start: 0.6591 (tmm) cc_final: 0.6175 (tmm) REVERT: K 80 ILE cc_start: 0.5024 (mt) cc_final: 0.4653 (mt) REVERT: K 128 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.6247 (tpp-160) REVERT: M 73 LYS cc_start: 0.7079 (tttt) cc_final: 0.6455 (ptpt) REVERT: M 97 MET cc_start: 0.4080 (mpp) cc_final: 0.3469 (tmt) REVERT: M 214 ARG cc_start: 0.6604 (OUTLIER) cc_final: 0.6290 (pmm-80) REVERT: M 221 GLU cc_start: 0.6851 (mm-30) cc_final: 0.6219 (pt0) REVERT: M 248 MET cc_start: 0.4137 (ttm) cc_final: 0.3298 (ppp) REVERT: M 250 MET cc_start: 0.4303 (mmt) cc_final: 0.3993 (mmm) REVERT: N 330 LEU cc_start: 0.5640 (mp) cc_final: 0.5431 (mp) REVERT: N 376 LEU cc_start: 0.4981 (mm) cc_final: 0.4753 (mm) REVERT: O 1 MET cc_start: 0.7714 (mtm) cc_final: 0.7245 (mtm) REVERT: O 73 VAL cc_start: 0.6789 (OUTLIER) cc_final: 0.6577 (m) REVERT: O 107 VAL cc_start: -0.0076 (OUTLIER) cc_final: -0.0823 (m) REVERT: O 360 SER cc_start: 0.6647 (p) cc_final: 0.6121 (t) REVERT: P 232 MET cc_start: 0.6754 (tpp) cc_final: 0.6359 (tpp) REVERT: P 301 GLU cc_start: 0.6248 (pt0) cc_final: 0.5102 (mt-10) REVERT: P 309 TYR cc_start: 0.4400 (m-80) cc_final: 0.4021 (m-80) REVERT: Q 110 MET cc_start: 0.2209 (tmm) cc_final: 0.1450 (ttp) outliers start: 244 outliers final: 58 residues processed: 959 average time/residue: 0.6956 time to fit residues: 818.9334 Evaluate side-chains 654 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 573 time to evaluate : 1.463 ------------------------------------------------------------------------------- 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 260 LEU Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 543 GLN Chi-restraints excluded: chain A residue 578 LYS Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 921 PHE Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1049 THR Chi-restraints excluded: chain A residue 1106 GLU Chi-restraints excluded: chain A residue 1130 VAL 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 119 TYR Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 495 ASN Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 769 CYS Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 86 THR 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 233 TYR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 107 ARG Chi-restraints excluded: chain G residue 39 VAL 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 58 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 128 ARG Chi-restraints excluded: chain L residue 52 LEU 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 N residue 329 LEU Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 110 LEU Chi-restraints excluded: chain O residue 137 LYS Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 242 PHE Chi-restraints excluded: chain P residue 188 LEU Chi-restraints excluded: chain P residue 295 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 288 optimal weight: 3.9990 chunk 272 optimal weight: 0.4980 chunk 101 optimal weight: 3.9990 chunk 258 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 229 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 31 GLN A 192 ASN A 215 GLN A 241 ASN A 343 GLN A 400 ASN A 422 GLN A 599 GLN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 ASN A 824 HIS ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1286 HIS B 42 GLN B 159 ASN B 381 ASN B 475 GLN B 501 HIS B 683 ASN ** B 901 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN C 194 HIS C 213 HIS ** C 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 HIS F 72 GLN G 98 HIS G 116 GLN H 46 GLN H 76 ASN H 87 GLN I 104 HIS K 38 HIS K 97 GLN M 121 GLN M 125 HIS N 358 GLN ** O 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 374 HIS ** O 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 200 GLN P 201 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.150629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.123308 restraints weight = 99238.811| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 3.52 r_work: 0.3860 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3862 r_free = 0.3862 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3862 r_free = 0.3862 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4777 moved from start: 0.7777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.255 41438 Z= 0.222 Angle : 1.192 50.735 56126 Z= 0.645 Chirality : 0.165 6.339 6305 Planarity : 0.005 0.064 7071 Dihedral : 9.852 77.217 5944 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.23 % Allowed : 22.06 % Favored : 73.72 % Cbeta Deviations : 0.00 % 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: -2.45 (0.11), residues: 4922 helix: -0.86 (0.11), residues: 1779 sheet: -0.62 (0.18), residues: 716 loop : -2.59 (0.11), residues: 2427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 35 TYR 0.024 0.002 TYR H 97 PHE 0.028 0.002 PHE B 326 TRP 0.022 0.002 TRP Q 99 HIS 0.011 0.001 HIS D 118 Details of bonding type rmsd covalent geometry : bond 0.00558 (41417) covalent geometry : angle 1.09768 (56108) hydrogen bonds : bond 0.04392 ( 1484) hydrogen bonds : angle 5.25142 ( 4293) metal coordination : bond 0.01552 ( 21) metal coordination : angle 25.94676 ( 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 849 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 663 time to evaluate : 1.501 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: A 58 HIS cc_start: 0.2949 (OUTLIER) cc_final: 0.2145 (t70) REVERT: A 137 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6365 (pt) REVERT: A 211 LEU cc_start: 0.2686 (OUTLIER) cc_final: 0.2411 (mt) REVERT: A 234 ASP cc_start: 0.2717 (m-30) cc_final: 0.2192 (p0) REVERT: A 235 VAL cc_start: 0.8012 (t) cc_final: 0.7761 (t) REVERT: A 543 GLN cc_start: 0.4446 (OUTLIER) cc_final: 0.3573 (pp30) REVERT: A 572 LEU cc_start: 0.4589 (OUTLIER) cc_final: 0.3961 (mp) REVERT: A 680 MET cc_start: 0.6155 (OUTLIER) cc_final: 0.5930 (mpt) REVERT: A 900 PHE cc_start: 0.6536 (OUTLIER) cc_final: 0.5561 (t80) REVERT: A 912 MET cc_start: 0.3909 (mtt) cc_final: 0.3428 (mmt) REVERT: A 1085 ILE cc_start: 0.4067 (mt) cc_final: 0.3768 (mt) REVERT: A 1131 LYS cc_start: 0.5485 (tptt) cc_final: 0.4953 (tptt) REVERT: A 1148 THR cc_start: 0.5232 (OUTLIER) cc_final: 0.4918 (p) REVERT: A 1294 MET cc_start: 0.3127 (mtm) cc_final: 0.2341 (pmm) REVERT: A 1353 MET cc_start: 0.6142 (OUTLIER) cc_final: 0.5860 (mpt) REVERT: B 159 ASN cc_start: 0.7461 (OUTLIER) cc_final: 0.7186 (t0) REVERT: B 254 MET cc_start: 0.2664 (mtt) cc_final: 0.0793 (tpt) REVERT: B 271 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: B 340 ARG cc_start: 0.5273 (tpt170) cc_final: 0.4601 (mmm160) REVERT: B 349 ASN cc_start: 0.6523 (p0) cc_final: 0.6210 (m-40) REVERT: B 415 MET cc_start: 0.3617 (ptp) cc_final: 0.3243 (ttm) REVERT: B 711 LEU cc_start: 0.6127 (mt) cc_final: 0.5261 (mt) REVERT: B 808 ILE cc_start: 0.6939 (mm) cc_final: 0.6650 (mt) REVERT: B 870 MET cc_start: 0.4987 (pmm) cc_final: 0.4770 (ptm) REVERT: B 895 ASP cc_start: 0.5484 (m-30) cc_final: 0.5198 (m-30) REVERT: B 996 GLU cc_start: 0.6142 (mm-30) cc_final: 0.5859 (mp0) REVERT: B 1012 LEU cc_start: 0.6139 (mp) cc_final: 0.5741 (mt) REVERT: C 25 HIS cc_start: 0.5355 (OUTLIER) cc_final: 0.5102 (m170) REVERT: C 95 TYR cc_start: 0.6247 (m-10) cc_final: 0.5524 (m-10) REVERT: C 141 ARG cc_start: 0.7576 (mmm-85) cc_final: 0.6998 (ttm-80) REVERT: C 251 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7178 (tp30) REVERT: C 345 MET cc_start: 0.6691 (mpp) cc_final: 0.5939 (ppp) REVERT: E 85 LYS cc_start: 0.8457 (tptt) cc_final: 0.7824 (mmtm) REVERT: E 110 MET cc_start: 0.1423 (tpt) cc_final: 0.0872 (tpp) REVERT: E 165 LEU cc_start: 0.0507 (OUTLIER) cc_final: 0.0014 (pt) REVERT: F 107 ARG cc_start: 0.1947 (OUTLIER) cc_final: 0.1450 (tpp80) REVERT: G 7 MET cc_start: 0.5904 (mpt) cc_final: 0.4950 (ppp) REVERT: G 98 HIS cc_start: 0.7276 (m-70) cc_final: 0.6907 (m90) REVERT: G 142 MET cc_start: 0.0137 (mmt) cc_final: -0.0453 (mtp) REVERT: H 47 ILE cc_start: 0.6539 (OUTLIER) cc_final: 0.5828 (mp) REVERT: H 92 MET cc_start: 0.2779 (OUTLIER) cc_final: 0.2388 (ptp) REVERT: I 60 GLU cc_start: 0.6151 (mm-30) cc_final: 0.5903 (mm-30) REVERT: K 29 MET cc_start: 0.6416 (tmm) cc_final: 0.6076 (tmm) REVERT: K 37 ARG cc_start: 0.5171 (pmt170) cc_final: 0.4843 (ptm-80) REVERT: K 67 PHE cc_start: 0.7303 (OUTLIER) cc_final: 0.6836 (m-80) REVERT: K 80 ILE cc_start: 0.4886 (mt) cc_final: 0.4585 (mt) REVERT: M 65 LEU cc_start: 0.3840 (OUTLIER) cc_final: 0.3466 (tm) REVERT: M 73 LYS cc_start: 0.7146 (tttt) cc_final: 0.6616 (ptpt) REVERT: M 97 MET cc_start: 0.4276 (mpp) cc_final: 0.3434 (tmt) REVERT: M 221 GLU cc_start: 0.6514 (mm-30) cc_final: 0.6113 (pt0) REVERT: M 248 MET cc_start: 0.4172 (ttm) cc_final: 0.3501 (ppp) REVERT: M 250 MET cc_start: 0.4105 (mmt) cc_final: 0.3861 (mmm) REVERT: N 350 MET cc_start: 0.4868 (pmm) cc_final: 0.4568 (pmm) REVERT: O 1 MET cc_start: 0.7213 (mtm) cc_final: 0.6987 (mtm) REVERT: O 85 MET cc_start: 0.6458 (OUTLIER) cc_final: 0.6080 (mpp) REVERT: O 118 MET cc_start: 0.2649 (ttt) cc_final: 0.0265 (pp-130) REVERT: P 200 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7696 (pm20) REVERT: P 233 GLU cc_start: 0.7984 (mp0) cc_final: 0.7705 (tt0) REVERT: P 301 GLU cc_start: 0.5996 (pt0) cc_final: 0.4870 (mt-10) REVERT: Q 110 MET cc_start: 0.2342 (tmm) cc_final: 0.1711 (ttt) outliers start: 186 outliers final: 49 residues processed: 786 average time/residue: 0.6366 time to fit residues: 625.9331 Evaluate side-chains 605 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 536 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 58 HIS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 396 VAL 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 654 THR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 839 TYR Chi-restraints excluded: chain A residue 900 PHE Chi-restraints excluded: chain A residue 1148 THR 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 102 CYS 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 159 ASN Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 1021 HIS Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 61 LEU 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 258 SER Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 165 LEU 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 2 PHE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 99 VAL 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 H residue 92 MET Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain N residue 259 SER 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 91 TYR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 141 TYR Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain P residue 200 GLN Chi-restraints excluded: chain Q residue 108 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 230 optimal weight: 0.0050 chunk 42 optimal weight: 0.1980 chunk 187 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 437 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 481 optimal weight: 0.0170 chunk 406 optimal weight: 0.0040 chunk 482 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 198 optimal weight: 5.9990 overall best weight: 0.2444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN A 422 GLN A 534 ASN A 616 ASN A 673 GLN ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 GLN B 42 GLN B 159 ASN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 ASN B 692 GLN ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 HIS ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 402 ASN O 437 HIS ** O 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 200 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.151425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.123782 restraints weight = 99063.354| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 3.55 r_work: 0.3868 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3869 r_free = 0.3869 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3869 r_free = 0.3869 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4807 moved from start: 0.8219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.243 41438 Z= 0.190 Angle : 1.174 50.535 56126 Z= 0.632 Chirality : 0.164 6.315 6305 Planarity : 0.005 0.060 7071 Dihedral : 9.694 76.228 5944 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.69 % Favored : 94.29 % Rotamer: Outliers : 3.89 % Allowed : 24.33 % Favored : 71.78 % 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: -2.12 (0.11), residues: 4922 helix: -0.50 (0.12), residues: 1773 sheet: -0.44 (0.18), residues: 706 loop : -2.45 (0.11), residues: 2443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 54 TYR 0.066 0.002 TYR O 91 PHE 0.032 0.002 PHE O 242 TRP 0.028 0.001 TRP B 424 HIS 0.010 0.001 HIS D 118 Details of bonding type rmsd covalent geometry : bond 0.00505 (41417) covalent geometry : angle 1.07869 (56108) hydrogen bonds : bond 0.03690 ( 1484) hydrogen bonds : angle 5.00680 ( 4293) metal coordination : bond 0.00878 ( 21) metal coordination : angle 25.87796 ( 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 775 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 604 time to evaluate : 1.167 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 211 LEU cc_start: 0.2563 (OUTLIER) cc_final: 0.2070 (mt) REVERT: A 234 ASP cc_start: 0.3707 (m-30) cc_final: 0.3232 (p0) REVERT: A 235 VAL cc_start: 0.8207 (t) cc_final: 0.7903 (t) REVERT: A 543 GLN cc_start: 0.4484 (OUTLIER) cc_final: 0.3733 (pp30) REVERT: A 577 GLU cc_start: 0.7427 (pm20) cc_final: 0.7170 (pm20) REVERT: A 680 MET cc_start: 0.6133 (OUTLIER) cc_final: 0.5830 (mpt) REVERT: A 900 PHE cc_start: 0.6531 (OUTLIER) cc_final: 0.5990 (t80) REVERT: A 908 ASP cc_start: 0.3392 (p0) cc_final: 0.2555 (p0) REVERT: A 940 LEU cc_start: 0.5745 (OUTLIER) cc_final: 0.5401 (pp) REVERT: A 1085 ILE cc_start: 0.3964 (mt) cc_final: 0.3640 (mt) REVERT: A 1294 MET cc_start: 0.2917 (mtm) cc_final: 0.2627 (pmm) REVERT: A 1353 MET cc_start: 0.6151 (OUTLIER) cc_final: 0.5790 (mpt) REVERT: B 135 ARG cc_start: 0.5390 (ptp-110) cc_final: 0.5061 (ptp-110) REVERT: B 157 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8359 (pptt) REVERT: B 199 VAL cc_start: 0.4869 (OUTLIER) cc_final: 0.4493 (m) REVERT: B 254 MET cc_start: 0.2628 (mtt) cc_final: 0.0726 (tpt) REVERT: B 271 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6902 (mp0) REVERT: B 340 ARG cc_start: 0.5338 (tpt170) cc_final: 0.4628 (mmm160) REVERT: B 349 ASN cc_start: 0.6717 (p0) cc_final: 0.6434 (m-40) REVERT: B 415 MET cc_start: 0.3754 (ptp) cc_final: 0.3478 (mmm) REVERT: B 719 MET cc_start: 0.2473 (ttm) cc_final: 0.2159 (ttm) REVERT: B 725 ILE cc_start: 0.4229 (mp) cc_final: 0.3762 (mt) REVERT: B 808 ILE cc_start: 0.6806 (mm) cc_final: 0.6593 (mp) REVERT: B 1050 MET cc_start: 0.7165 (mmm) cc_final: 0.6762 (tpp) REVERT: C 25 HIS cc_start: 0.5357 (OUTLIER) cc_final: 0.5135 (m170) REVERT: C 95 TYR cc_start: 0.5883 (OUTLIER) cc_final: 0.5329 (m-10) REVERT: C 211 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7823 (tm) REVERT: C 251 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7309 (tp30) REVERT: C 345 MET cc_start: 0.6888 (OUTLIER) cc_final: 0.6327 (tpt) REVERT: D 1 MET cc_start: 0.2183 (mmt) cc_final: -0.0087 (mtt) REVERT: D 20 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.6358 (mp) REVERT: D 49 THR cc_start: 0.6923 (t) cc_final: 0.6653 (m) REVERT: E 85 LYS cc_start: 0.8500 (tptt) cc_final: 0.7920 (mmtm) REVERT: E 151 MET cc_start: -0.0269 (tpt) cc_final: -0.2725 (pp-130) REVERT: E 165 LEU cc_start: 0.0676 (OUTLIER) cc_final: 0.0325 (pt) REVERT: F 94 MET cc_start: 0.7535 (tmm) cc_final: 0.7289 (ttm) REVERT: G 7 MET cc_start: 0.5684 (mpt) cc_final: 0.4947 (ppp) REVERT: G 98 HIS cc_start: 0.7159 (m-70) cc_final: 0.6730 (m90) REVERT: G 142 MET cc_start: 0.0427 (mmt) cc_final: -0.0051 (mtp) REVERT: H 92 MET cc_start: 0.2443 (OUTLIER) cc_final: 0.2168 (ptp) REVERT: H 138 ASP cc_start: 0.7023 (p0) cc_final: 0.6396 (t0) REVERT: I 1 MET cc_start: 0.4372 (pmm) cc_final: 0.2934 (pp-130) REVERT: K 37 ARG cc_start: 0.5237 (pmt170) cc_final: 0.4957 (ptm-80) REVERT: K 67 PHE cc_start: 0.7016 (OUTLIER) cc_final: 0.6577 (m-80) REVERT: K 80 ILE cc_start: 0.4654 (mt) cc_final: 0.4363 (mt) REVERT: M 73 LYS cc_start: 0.7113 (tttt) cc_final: 0.6441 (pttt) REVERT: M 113 ARG cc_start: 0.5678 (pmm150) cc_final: 0.3715 (ptm160) REVERT: M 221 GLU cc_start: 0.6446 (mm-30) cc_final: 0.6170 (pt0) REVERT: M 248 MET cc_start: 0.4126 (ttm) cc_final: 0.3449 (ppp) REVERT: M 250 MET cc_start: 0.3951 (mmt) cc_final: 0.3701 (mmm) REVERT: O 85 MET cc_start: 0.6594 (OUTLIER) cc_final: 0.6207 (mpp) REVERT: O 118 MET cc_start: 0.2718 (ttt) cc_final: 0.0460 (pp-130) REVERT: O 140 ASP cc_start: 0.4389 (t70) cc_final: 0.4070 (t70) REVERT: O 290 SER cc_start: 0.6517 (p) cc_final: 0.6296 (t) REVERT: P 301 GLU cc_start: 0.5944 (pt0) cc_final: 0.5102 (mt-10) REVERT: Q 110 MET cc_start: 0.2428 (tmm) cc_final: 0.1826 (ttp) outliers start: 171 outliers final: 55 residues processed: 710 average time/residue: 0.5985 time to fit residues: 536.3304 Evaluate side-chains 614 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 541 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 543 GLN Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 839 TYR Chi-restraints excluded: chain A residue 900 PHE Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain B residue 49 TYR Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 744 MET Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 947 LEU Chi-restraints excluded: chain B residue 960 TYR Chi-restraints excluded: chain B residue 1021 HIS Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 165 LEU 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 125 ILE Chi-restraints excluded: chain G residue 2 PHE Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 74 HIS Chi-restraints excluded: chain M residue 75 GLU Chi-restraints excluded: chain M residue 205 TRP Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 38 VAL Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 91 TYR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain P residue 268 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 234 optimal weight: 0.5980 chunk 238 optimal weight: 8.9990 chunk 306 optimal weight: 0.7980 chunk 386 optimal weight: 0.6980 chunk 443 optimal weight: 20.0000 chunk 29 optimal weight: 0.7980 chunk 204 optimal weight: 2.9990 chunk 243 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 410 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN A 566 GLN ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN B 806 HIS ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN F 72 GLN ** G 115 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 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 437 HIS O 457 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.151770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.124131 restraints weight = 98570.477| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 3.56 r_work: 0.3872 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3873 r_free = 0.3873 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3873 r_free = 0.3873 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5050 moved from start: 0.8932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.242 41438 Z= 0.195 Angle : 1.168 50.540 56126 Z= 0.630 Chirality : 0.164 6.309 6305 Planarity : 0.005 0.065 7071 Dihedral : 9.631 76.295 5944 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.85 % Favored : 94.13 % Rotamer: Outliers : 3.93 % Allowed : 25.13 % Favored : 70.94 % 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: -1.90 (0.11), residues: 4922 helix: -0.29 (0.12), residues: 1764 sheet: -0.40 (0.18), residues: 738 loop : -2.34 (0.11), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 24 TYR 0.049 0.002 TYR Q 43 PHE 0.022 0.002 PHE A 849 TRP 0.015 0.001 TRP M 700 HIS 0.015 0.001 HIS B 405 Details of bonding type rmsd covalent geometry : bond 0.00512 (41417) covalent geometry : angle 1.07228 (56108) hydrogen bonds : bond 0.03580 ( 1484) hydrogen bonds : angle 4.87736 ( 4293) metal coordination : bond 0.00629 ( 21) metal coordination : angle 25.85822 ( 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 770 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 597 time to evaluate : 1.412 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 198 GLU cc_start: 0.7899 (mm-30) cc_final: 0.6990 (pp20) REVERT: A 211 LEU cc_start: 0.2695 (OUTLIER) cc_final: 0.2078 (mt) REVERT: A 234 ASP cc_start: 0.3850 (m-30) cc_final: 0.3113 (p0) REVERT: A 235 VAL cc_start: 0.8347 (t) cc_final: 0.8040 (t) REVERT: A 577 GLU cc_start: 0.7606 (pm20) cc_final: 0.7192 (pm20) REVERT: A 650 MET cc_start: 0.6016 (mmm) cc_final: 0.2298 (ttt) REVERT: A 680 MET cc_start: 0.5895 (OUTLIER) cc_final: 0.5646 (mpt) REVERT: A 840 SER cc_start: 0.1241 (OUTLIER) cc_final: 0.0732 (m) REVERT: A 900 PHE cc_start: 0.7012 (OUTLIER) cc_final: 0.6275 (t80) REVERT: A 940 LEU cc_start: 0.5893 (OUTLIER) cc_final: 0.5535 (pp) REVERT: A 1085 ILE cc_start: 0.3670 (mt) cc_final: 0.3287 (mt) REVERT: A 1374 LYS cc_start: 0.2075 (mptm) cc_final: 0.1763 (mptt) REVERT: B 155 PHE cc_start: 0.5052 (OUTLIER) cc_final: 0.3967 (t80) REVERT: B 157 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8526 (pptt) REVERT: B 158 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7818 (tt) REVERT: B 159 ASN cc_start: 0.7912 (OUTLIER) cc_final: 0.7701 (t0) REVERT: B 199 VAL cc_start: 0.4841 (OUTLIER) cc_final: 0.4462 (m) REVERT: B 254 MET cc_start: 0.2697 (mtt) cc_final: 0.1688 (ptm) REVERT: B 271 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6974 (mp0) REVERT: B 340 ARG cc_start: 0.5472 (tpt170) cc_final: 0.4407 (mmm160) REVERT: B 349 ASN cc_start: 0.6766 (p0) cc_final: 0.6499 (m-40) REVERT: B 426 LEU cc_start: 0.6171 (OUTLIER) cc_final: 0.5921 (pp) REVERT: B 499 MET cc_start: 0.4473 (OUTLIER) cc_final: 0.3351 (ptp) REVERT: B 526 LEU cc_start: 0.5536 (OUTLIER) cc_final: 0.5300 (pt) REVERT: B 562 MET cc_start: 0.3077 (tpt) cc_final: 0.2263 (tmm) REVERT: B 660 GLU cc_start: 0.4817 (OUTLIER) cc_final: 0.3247 (tp30) REVERT: B 719 MET cc_start: 0.3621 (ttm) cc_final: 0.3390 (OUTLIER) REVERT: B 729 GLU cc_start: 0.6615 (tp30) cc_final: 0.6362 (tp30) REVERT: B 784 ASN cc_start: 0.5113 (OUTLIER) cc_final: 0.4898 (p0) REVERT: B 1096 LYS cc_start: 0.8548 (mmtm) cc_final: 0.8234 (mmtm) REVERT: C 25 HIS cc_start: 0.5660 (OUTLIER) cc_final: 0.5105 (m90) REVERT: C 221 ASP cc_start: 0.5785 (t70) cc_final: 0.5551 (t0) REVERT: C 251 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7427 (tp30) REVERT: C 307 ILE cc_start: 0.6626 (OUTLIER) cc_final: 0.6021 (mm) REVERT: C 345 MET cc_start: 0.6753 (OUTLIER) cc_final: 0.6278 (tpt) REVERT: D 1 MET cc_start: 0.3141 (mmt) cc_final: 0.1269 (mtt) REVERT: D 20 LEU cc_start: 0.6734 (OUTLIER) cc_final: 0.6481 (mp) REVERT: E 85 LYS cc_start: 0.8474 (tptt) cc_final: 0.7903 (mmtm) REVERT: E 110 MET cc_start: 0.1776 (tpt) cc_final: 0.0865 (tpp) REVERT: E 151 MET cc_start: 0.0438 (OUTLIER) cc_final: -0.2376 (pp-130) REVERT: F 94 MET cc_start: 0.7704 (tmm) cc_final: 0.7472 (ttm) REVERT: F 107 ARG cc_start: 0.1920 (OUTLIER) cc_final: 0.1296 (tpp80) REVERT: G 7 MET cc_start: 0.5698 (mpt) cc_final: 0.5035 (ppp) REVERT: G 98 HIS cc_start: 0.6958 (m-70) cc_final: 0.6479 (m90) REVERT: H 138 ASP cc_start: 0.7191 (p0) cc_final: 0.6528 (t0) REVERT: I 1 MET cc_start: 0.4640 (pmm) cc_final: 0.3409 (pp-130) REVERT: I 60 GLU cc_start: 0.5628 (mm-30) cc_final: 0.5156 (mm-30) REVERT: I 91 MET cc_start: 0.6684 (mmp) cc_final: 0.5331 (tmm) REVERT: I 101 GLN cc_start: 0.4759 (pp30) cc_final: 0.3942 (mm-40) REVERT: K 67 PHE cc_start: 0.7203 (OUTLIER) cc_final: 0.6735 (m-80) REVERT: K 80 ILE cc_start: 0.4748 (mt) cc_final: 0.4415 (mt) REVERT: M 73 LYS cc_start: 0.7136 (tttt) cc_final: 0.6472 (pttt) REVERT: M 113 ARG cc_start: 0.5764 (pmm150) cc_final: 0.3804 (ptm160) REVERT: M 217 ARG cc_start: 0.0547 (ppt170) cc_final: 0.0197 (ppt170) REVERT: M 248 MET cc_start: 0.4233 (ttm) cc_final: 0.3364 (ppp) REVERT: M 250 MET cc_start: 0.3935 (mmt) cc_final: 0.3705 (mmm) REVERT: N 350 MET cc_start: 0.5254 (pmm) cc_final: 0.4949 (pmm) REVERT: O 85 MET cc_start: 0.6693 (OUTLIER) cc_final: 0.6264 (mmp) REVERT: O 118 MET cc_start: 0.2959 (ttt) cc_final: 0.0798 (pp-130) REVERT: O 138 THR cc_start: 0.6673 (m) cc_final: 0.6448 (p) REVERT: O 333 MET cc_start: 0.3233 (mmt) cc_final: 0.2957 (mmp) REVERT: P 175 GLU cc_start: 0.7390 (tm-30) cc_final: 0.7176 (pp20) REVERT: P 203 MET cc_start: 0.6773 (OUTLIER) cc_final: 0.6456 (mpp) REVERT: P 301 GLU cc_start: 0.5745 (pt0) cc_final: 0.5101 (tt0) REVERT: Q 62 GLN cc_start: 0.6947 (mt0) cc_final: 0.6527 (mp10) REVERT: Q 74 PHE cc_start: 0.6834 (t80) cc_final: 0.6129 (t80) REVERT: Q 110 MET cc_start: 0.2634 (tmm) cc_final: 0.1683 (ttp) REVERT: Q 111 MET cc_start: -0.0622 (tpp) cc_final: -0.0847 (tmm) outliers start: 173 outliers final: 56 residues processed: 703 average time/residue: 0.5989 time to fit residues: 530.7608 Evaluate side-chains 607 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 527 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 839 TYR Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 900 PHE Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1353 MET 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 119 TYR Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 155 PHE Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 660 GLU Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 960 TYR Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1021 HIS Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 151 MET 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 3 VAL Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 74 HIS Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain M residue 75 GLU Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 38 VAL Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 91 TYR Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain P residue 203 MET Chi-restraints excluded: chain P residue 268 LYS Chi-restraints excluded: chain Q residue 58 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 464 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 317 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 486 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 483 optimal weight: 7.9990 chunk 291 optimal weight: 6.9990 chunk 352 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN A 400 ASN ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN ** A 611 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 927 ASN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 GLN A1039 GLN A1047 GLN A1371 ASN ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN ** B 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 678 ASN B 692 GLN B 758 ASN ** B 901 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 HIS B1082 GLN B1093 HIS ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 HIS E 108 GLN ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 GLN I 32 HIS ** K 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 GLN ** O 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 445 ASN O 457 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.154358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.125113 restraints weight = 105042.260| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 3.79 r_work: 0.3869 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3869 r_free = 0.3869 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3869 r_free = 0.3869 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 1.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.239 41438 Z= 0.407 Angle : 1.575 57.540 56126 Z= 0.836 Chirality : 0.171 6.322 6305 Planarity : 0.010 0.210 7071 Dihedral : 10.922 80.431 5944 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 24.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.61 % Favored : 91.18 % Rotamer: Outliers : 6.00 % Allowed : 25.15 % Favored : 68.85 % Cbeta Deviations : 0.04 % 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: -2.94 (0.10), residues: 4922 helix: -1.45 (0.11), residues: 1752 sheet: -0.88 (0.19), residues: 671 loop : -2.69 (0.11), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.002 ARG A 430 TYR 0.043 0.004 TYR B 357 PHE 0.058 0.005 PHE B 50 TRP 0.055 0.004 TRP M 205 HIS 0.020 0.004 HIS A 820 Details of bonding type rmsd covalent geometry : bond 0.00947 (41417) covalent geometry : angle 1.49412 (56108) hydrogen bonds : bond 0.06755 ( 1484) hydrogen bonds : angle 6.53370 ( 4293) metal coordination : bond 0.02189 ( 21) metal coordination : angle 27.78223 ( 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 1106 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 264 poor density : 842 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: A 19 CYS cc_start: 0.7928 (t) cc_final: 0.7664 (m) REVERT: A 198 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7403 (pp20) REVERT: A 211 LEU cc_start: 0.3625 (OUTLIER) cc_final: 0.3067 (mt) REVERT: A 287 ILE cc_start: 0.4478 (mt) cc_final: 0.3720 (mt) REVERT: A 319 LEU cc_start: 0.8452 (tp) cc_final: 0.8161 (tm) REVERT: A 363 PHE cc_start: 0.7328 (m-80) cc_final: 0.6929 (m-80) REVERT: A 428 MET cc_start: 0.7487 (ppp) cc_final: 0.7282 (pmm) REVERT: A 544 ASP cc_start: 0.8963 (t0) cc_final: 0.8644 (t0) REVERT: A 652 LYS cc_start: 0.9182 (tmmt) cc_final: 0.8947 (tppt) REVERT: A 660 LYS cc_start: 0.5605 (OUTLIER) cc_final: 0.5368 (tttt) REVERT: A 916 ASP cc_start: 0.6342 (OUTLIER) cc_final: 0.5836 (m-30) REVERT: A 1236 MET cc_start: 0.3033 (pp-130) cc_final: 0.2374 (mtt) REVERT: A 1305 ARG cc_start: 0.6287 (ptp-170) cc_final: 0.4026 (tpt170) REVERT: A 1355 ILE cc_start: 0.8068 (tt) cc_final: 0.7341 (tt) REVERT: A 1385 HIS cc_start: 0.5418 (OUTLIER) cc_final: 0.5022 (t70) REVERT: B 224 TYR cc_start: 0.6613 (m-80) cc_final: 0.5987 (m-80) REVERT: B 243 MET cc_start: 0.3908 (tmm) cc_final: 0.1990 (mpp) REVERT: B 254 MET cc_start: 0.3763 (mtt) cc_final: 0.2728 (ptm) REVERT: B 328 PHE cc_start: 0.4315 (OUTLIER) cc_final: 0.3942 (t80) REVERT: B 632 TYR cc_start: 0.8084 (m-80) cc_final: 0.7760 (m-80) REVERT: B 637 GLU cc_start: 0.7624 (tt0) cc_final: 0.6979 (tm-30) REVERT: B 641 CYS cc_start: 0.7454 (m) cc_final: 0.6826 (m) REVERT: B 647 GLU cc_start: 0.7393 (mt-10) cc_final: 0.6712 (mt-10) REVERT: B 660 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.6008 (tp30) REVERT: B 1021 HIS cc_start: 0.7675 (OUTLIER) cc_final: 0.7438 (t-90) REVERT: B 1050 MET cc_start: 0.8359 (mmm) cc_final: 0.7814 (tpp) REVERT: B 1051 GLU cc_start: 0.7695 (mp0) cc_final: 0.7385 (mp0) REVERT: C 5 GLN cc_start: 0.8001 (mp10) cc_final: 0.7678 (mp10) REVERT: C 251 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8194 (mm-30) REVERT: C 340 LEU cc_start: 0.5924 (OUTLIER) cc_final: 0.5609 (tp) REVERT: D 1 MET cc_start: 0.4428 (mmt) cc_final: 0.2598 (mtt) REVERT: D 100 MET cc_start: 0.2589 (ttp) cc_final: 0.2346 (tmm) REVERT: E 76 PHE cc_start: 0.3551 (m-80) cc_final: 0.3319 (m-80) REVERT: E 110 MET cc_start: 0.3035 (tpt) cc_final: 0.2757 (tpt) REVERT: E 151 MET cc_start: 0.4237 (OUTLIER) cc_final: 0.2011 (ttp) REVERT: F 107 ARG cc_start: 0.4937 (OUTLIER) cc_final: 0.4336 (mmt90) REVERT: G 98 HIS cc_start: 0.7349 (m-70) cc_final: 0.6975 (m90) REVERT: H 65 TYR cc_start: 0.7670 (m-10) cc_final: 0.7280 (m-80) REVERT: I 1 MET cc_start: 0.3872 (pmm) cc_final: 0.2579 (pp-130) REVERT: J 19 GLU cc_start: 0.8155 (pm20) cc_final: 0.7931 (pp20) REVERT: K 28 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7476 (tm-30) REVERT: K 44 LEU cc_start: 0.7044 (mm) cc_final: 0.6598 (mp) REVERT: K 67 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.8024 (m-80) REVERT: K 74 HIS cc_start: 0.8557 (OUTLIER) cc_final: 0.8186 (m90) REVERT: K 79 LYS cc_start: 0.8343 (tppt) cc_final: 0.7922 (tppt) REVERT: K 84 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8066 (mt) REVERT: K 87 ARG cc_start: 0.7965 (tmm160) cc_final: 0.7614 (tmm160) REVERT: L 15 MET cc_start: 0.6848 (OUTLIER) cc_final: 0.6115 (tpp) REVERT: L 16 ILE cc_start: 0.8813 (pp) cc_final: 0.8271 (pp) REVERT: L 55 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: M 57 GLU cc_start: 0.7425 (pt0) cc_final: 0.7189 (pm20) REVERT: M 59 GLU cc_start: 0.6855 (pt0) cc_final: 0.5889 (pm20) REVERT: M 73 LYS cc_start: 0.7635 (tttt) cc_final: 0.7114 (ttpt) REVERT: M 108 THR cc_start: 0.6915 (m) cc_final: 0.6540 (m) REVERT: M 113 ARG cc_start: 0.6737 (pmm150) cc_final: 0.6163 (ppp80) REVERT: M 136 ARG cc_start: 0.5820 (ptp90) cc_final: 0.5464 (mpt180) REVERT: M 244 GLU cc_start: 0.8277 (pt0) cc_final: 0.8034 (pm20) REVERT: M 248 MET cc_start: 0.4843 (ttm) cc_final: 0.4290 (ppp) REVERT: M 250 MET cc_start: 0.5173 (mmt) cc_final: 0.4772 (mpm) REVERT: N 349 THR cc_start: 0.7135 (m) cc_final: 0.6796 (m) REVERT: N 350 MET cc_start: 0.6835 (pmm) cc_final: 0.6474 (ptm) REVERT: N 385 CYS cc_start: 0.6524 (OUTLIER) cc_final: 0.6320 (p) REVERT: O 7 LYS cc_start: 0.7349 (tptp) cc_final: 0.6941 (pttm) REVERT: O 15 GLU cc_start: 0.5553 (OUTLIER) cc_final: 0.4296 (mm-30) REVERT: O 85 MET cc_start: 0.7535 (mpt) cc_final: 0.7093 (mmp) REVERT: O 90 ARG cc_start: 0.6663 (ttt180) cc_final: 0.5801 (ptt180) REVERT: O 118 MET cc_start: 0.4712 (ttt) cc_final: 0.2078 (pp-130) REVERT: O 138 THR cc_start: 0.7506 (m) cc_final: 0.7206 (p) REVERT: O 367 ARG cc_start: 0.5186 (mtt180) cc_final: 0.4830 (ttp80) REVERT: O 392 LYS cc_start: 0.4924 (mmtt) cc_final: 0.4007 (tmtm) REVERT: O 424 TYR cc_start: 0.5560 (m-80) cc_final: 0.5152 (m-80) REVERT: O 468 GLU cc_start: 0.8249 (pp20) cc_final: 0.7913 (pp20) REVERT: O 500 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7350 (mp0) REVERT: P 220 ILE cc_start: 0.8151 (mm) cc_final: 0.7849 (pp) outliers start: 264 outliers final: 63 residues processed: 1014 average time/residue: 0.6462 time to fit residues: 810.2256 Evaluate side-chains 670 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 590 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 660 LYS Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1385 HIS Chi-restraints excluded: chain B residue 49 TYR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 660 GLU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 1021 HIS Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 101 LYS Chi-restraints excluded: chain F residue 107 ARG Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 74 HIS Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain L residue 15 MET Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 55 PHE Chi-restraints excluded: chain M residue 39 TYR Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 259 SER Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain N residue 385 CYS Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 38 VAL Chi-restraints excluded: chain O residue 141 TYR Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain O residue 403 PHE Chi-restraints excluded: chain O residue 443 ILE Chi-restraints excluded: chain O residue 489 GLU Chi-restraints excluded: chain P residue 174 SER Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain Q residue 58 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 335 optimal weight: 10.0000 chunk 203 optimal weight: 0.8980 chunk 234 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 320 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 ASN ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 HIS A 528 ASN ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 GLN A1277 ASN A1286 HIS B 399 GLN B 683 ASN B 701 GLN B 738 ASN B 850 GLN B1021 HIS B1115 GLN B1118 GLN D 35 HIS D 60 HIS D 98 GLN E 108 GLN E 142 HIS F 72 GLN G 67 HIS ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 GLN K 45 HIS ** K 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN M 66 ASN ** O 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** 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: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.152471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.121575 restraints weight = 102873.316| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 3.78 r_work: 0.3804 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3805 r_free = 0.3805 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3805 r_free = 0.3805 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 1.4895 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= 0.214 Angle : 1.267 50.551 56126 Z= 0.676 Chirality : 0.166 6.309 6305 Planarity : 0.006 0.058 7071 Dihedral : 10.086 77.587 5944 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.73 % Favored : 94.21 % Rotamer: Outliers : 3.87 % Allowed : 31.65 % Favored : 64.48 % Cbeta Deviations : 0.00 % 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: -2.30 (0.11), residues: 4922 helix: -0.71 (0.12), residues: 1747 sheet: -0.61 (0.19), residues: 699 loop : -2.46 (0.11), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 24 TYR 0.028 0.002 TYR F 115 PHE 0.051 0.002 PHE A1379 TRP 0.032 0.002 TRP M 205 HIS 0.011 0.001 HIS D 118 Details of bonding type rmsd covalent geometry : bond 0.00559 (41417) covalent geometry : angle 1.17929 (56108) hydrogen bonds : bond 0.04336 ( 1484) hydrogen bonds : angle 5.37650 ( 4293) metal coordination : bond 0.00741 ( 21) metal coordination : angle 25.96214 ( 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 830 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 660 time to evaluate : 1.518 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: A 198 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7433 (pp20) REVERT: A 211 LEU cc_start: 0.3576 (OUTLIER) cc_final: 0.2859 (mt) REVERT: A 355 ASN cc_start: 0.7179 (t0) cc_final: 0.6250 (m110) REVERT: A 458 ASP cc_start: 0.8043 (t0) cc_final: 0.7824 (t0) REVERT: A 528 ASN cc_start: 0.8406 (m-40) cc_final: 0.7940 (m110) REVERT: A 668 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8307 (tm) REVERT: A 770 GLU cc_start: 0.3085 (OUTLIER) cc_final: 0.2884 (tt0) REVERT: A 1305 ARG cc_start: 0.6459 (ptp-170) cc_final: 0.4167 (tpt170) REVERT: A 1375 ARG cc_start: 0.6641 (ttt180) cc_final: 0.6326 (tpp80) REVERT: B 180 ILE cc_start: 0.7375 (OUTLIER) cc_final: 0.6988 (tp) REVERT: B 224 TYR cc_start: 0.5741 (m-80) cc_final: 0.4981 (m-80) REVERT: B 226 ARG cc_start: 0.5874 (mpt-90) cc_final: 0.5390 (mpt-90) REVERT: B 243 MET cc_start: 0.3393 (tmm) cc_final: 0.2395 (mpp) REVERT: B 254 MET cc_start: 0.3630 (mtt) cc_final: 0.2701 (ptm) REVERT: B 343 ILE cc_start: 0.6068 (OUTLIER) cc_final: 0.5844 (tp) REVERT: B 406 MET cc_start: 0.4303 (tpp) cc_final: 0.3696 (tpp) REVERT: B 478 MET cc_start: 0.6251 (pmm) cc_final: 0.6014 (pmm) REVERT: B 562 MET cc_start: 0.3777 (tpt) cc_final: 0.2839 (mmm) REVERT: B 637 GLU cc_start: 0.8260 (tt0) cc_final: 0.7310 (tm-30) REVERT: B 647 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6528 (mt-10) REVERT: B 660 GLU cc_start: 0.6310 (OUTLIER) cc_final: 0.6078 (tp30) REVERT: B 668 CYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8851 (t) REVERT: B 674 TYR cc_start: 0.8260 (m-10) cc_final: 0.8038 (m-80) REVERT: B 691 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8541 (mptt) REVERT: B 862 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7933 (t) REVERT: B 1050 MET cc_start: 0.7742 (mmm) cc_final: 0.7400 (tpp) REVERT: B 1051 GLU cc_start: 0.7566 (mp0) cc_final: 0.7322 (mp0) REVERT: B 1121 ASN cc_start: 0.8170 (t0) cc_final: 0.7825 (t160) REVERT: C 171 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8370 (ptt90) REVERT: C 251 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8161 (mm-30) REVERT: C 283 PHE cc_start: 0.6986 (OUTLIER) cc_final: 0.6014 (t80) REVERT: C 345 MET cc_start: 0.6662 (mtt) cc_final: 0.5718 (ppp) REVERT: D 1 MET cc_start: 0.4213 (mmt) cc_final: 0.2642 (mtt) REVERT: E 110 MET cc_start: 0.2622 (tpt) cc_final: 0.1839 (tpp) REVERT: E 151 MET cc_start: 0.4488 (OUTLIER) cc_final: 0.2673 (ttp) REVERT: F 83 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7968 (pp) REVERT: G 7 MET cc_start: 0.6429 (OUTLIER) cc_final: 0.5585 (ppp) REVERT: G 98 HIS cc_start: 0.7076 (m-70) cc_final: 0.6824 (m90) REVERT: G 132 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7326 (mp0) REVERT: H 65 TYR cc_start: 0.7741 (m-10) cc_final: 0.7418 (m-80) REVERT: H 100 GLU cc_start: 0.3977 (pt0) cc_final: 0.3627 (pt0) REVERT: I 1 MET cc_start: 0.4193 (pmm) cc_final: 0.2732 (pp-130) REVERT: I 91 MET cc_start: 0.6249 (mmp) cc_final: 0.5167 (mtt) REVERT: K 29 MET cc_start: 0.7122 (tmm) cc_final: 0.6898 (tmm) REVERT: K 67 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.7977 (m-80) REVERT: K 125 LYS cc_start: 0.7845 (mmpt) cc_final: 0.7114 (tppp) REVERT: L 13 GLN cc_start: 0.6281 (pp30) cc_final: 0.5192 (pm20) REVERT: L 15 MET cc_start: 0.6881 (OUTLIER) cc_final: 0.6640 (tpp) REVERT: L 16 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8504 (mp) REVERT: M 57 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7175 (pm20) REVERT: M 59 GLU cc_start: 0.6613 (pt0) cc_final: 0.6009 (mp0) REVERT: M 60 MET cc_start: 0.7745 (tmm) cc_final: 0.7503 (tmm) REVERT: M 73 LYS cc_start: 0.7783 (tttt) cc_final: 0.7338 (ttpt) REVERT: M 108 THR cc_start: 0.6876 (m) cc_final: 0.6472 (m) REVERT: M 113 ARG cc_start: 0.6622 (pmm150) cc_final: 0.5990 (ppp80) REVERT: M 136 ARG cc_start: 0.5828 (ptp90) cc_final: 0.5546 (mpt180) REVERT: M 248 MET cc_start: 0.4836 (ttm) cc_final: 0.4197 (ppp) REVERT: M 250 MET cc_start: 0.5036 (mmt) cc_final: 0.4641 (mpm) REVERT: N 349 THR cc_start: 0.6903 (m) cc_final: 0.6606 (m) REVERT: N 350 MET cc_start: 0.7177 (pmm) cc_final: 0.6793 (ptm) REVERT: N 385 CYS cc_start: 0.6445 (OUTLIER) cc_final: 0.5940 (p) REVERT: O 7 LYS cc_start: 0.7282 (tptp) cc_final: 0.6858 (pttm) REVERT: O 15 GLU cc_start: 0.5388 (OUTLIER) cc_final: 0.4667 (mm-30) REVERT: O 85 MET cc_start: 0.7474 (mpt) cc_final: 0.7023 (mmp) REVERT: O 90 ARG cc_start: 0.6101 (ttt180) cc_final: 0.5818 (mtm180) REVERT: O 118 MET cc_start: 0.4256 (ttt) cc_final: 0.2691 (pp-130) REVERT: O 133 MET cc_start: 0.3832 (OUTLIER) cc_final: 0.3606 (pp-130) REVERT: O 140 ASP cc_start: 0.7240 (t0) cc_final: 0.6817 (t0) REVERT: O 375 ILE cc_start: 0.5964 (tt) cc_final: 0.5518 (pt) REVERT: O 392 LYS cc_start: 0.5128 (mmtt) cc_final: 0.4381 (tmtm) REVERT: O 424 TYR cc_start: 0.5186 (m-80) cc_final: 0.4753 (m-80) REVERT: O 434 MET cc_start: 0.3676 (ptt) cc_final: 0.3076 (pp-130) REVERT: P 220 ILE cc_start: 0.8167 (mm) cc_final: 0.7888 (pp) REVERT: Q 62 GLN cc_start: 0.7933 (mt0) cc_final: 0.7384 (mp10) REVERT: Q 111 MET cc_start: 0.1472 (tpp) cc_final: 0.1234 (tpp) outliers start: 170 outliers final: 51 residues processed: 765 average time/residue: 0.6509 time to fit residues: 617.4175 Evaluate side-chains 643 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 571 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1290 LEU Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 648 HIS Chi-restraints excluded: chain B residue 660 GLU Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 691 LYS Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 1021 HIS Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain E residue 26 TYR Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 69 THR 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 83 LEU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 84 ILE 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 K residue 35 THR Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain L residue 15 MET Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain M residue 39 TYR Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain M residue 75 GLU Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 385 CYS Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 38 VAL Chi-restraints excluded: chain O residue 133 MET Chi-restraints excluded: chain O residue 141 TYR Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain O residue 489 GLU Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain Q residue 52 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 296 optimal weight: 10.0000 chunk 417 optimal weight: 9.9990 chunk 481 optimal weight: 7.9990 chunk 183 optimal weight: 0.2980 chunk 242 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 263 optimal weight: 0.1980 chunk 317 optimal weight: 0.1980 chunk 107 optimal weight: 0.8980 chunk 325 optimal weight: 10.0000 chunk 282 optimal weight: 4.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 GLN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1385 HIS B 159 ASN B 282 GLN B 850 GLN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 HIS ** C 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 HIS E 108 GLN F 72 GLN ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 GLN O 244 GLN ** O 377 GLN ** 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 182 GLN Q 62 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.151906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.120367 restraints weight = 101733.883| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 4.15 r_work: 0.3765 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3768 r_free = 0.3768 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3768 r_free = 0.3768 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 1.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.242 41438 Z= 0.201 Angle : 1.240 50.500 56126 Z= 0.661 Chirality : 0.165 6.296 6305 Planarity : 0.005 0.070 7071 Dihedral : 9.838 76.274 5944 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.20 % Favored : 93.78 % Rotamer: Outliers : 3.07 % Allowed : 33.38 % Favored : 63.55 % Cbeta Deviations : 0.00 % 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: -0.37 (0.12), residues: 1749 sheet: -0.51 (0.19), residues: 715 loop : -2.32 (0.11), residues: 2458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 781 TYR 0.028 0.002 TYR J 29 PHE 0.036 0.002 PHE A1379 TRP 0.014 0.001 TRP A 595 HIS 0.019 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00530 (41417) covalent geometry : angle 1.15191 (56108) hydrogen bonds : bond 0.03876 ( 1484) hydrogen bonds : angle 5.09233 ( 4293) metal coordination : bond 0.00541 ( 21) metal coordination : angle 25.66265 ( 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 755 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 620 time to evaluate : 1.547 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: A 198 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7526 (pp20) REVERT: A 355 ASN cc_start: 0.7138 (t0) cc_final: 0.6247 (m110) REVERT: A 458 ASP cc_start: 0.7970 (t0) cc_final: 0.7695 (t0) REVERT: A 528 ASN cc_start: 0.8539 (m-40) cc_final: 0.8121 (m110) REVERT: A 668 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8208 (tm) REVERT: A 770 GLU cc_start: 0.2866 (OUTLIER) cc_final: 0.2596 (tt0) REVERT: A 940 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7533 (pp) REVERT: A 1227 VAL cc_start: 0.5292 (t) cc_final: 0.4727 (t) REVERT: A 1236 MET cc_start: 0.5465 (tmm) cc_final: 0.3614 (ptp) REVERT: A 1305 ARG cc_start: 0.6516 (ptp-170) cc_final: 0.4152 (tpt170) REVERT: A 1375 ARG cc_start: 0.6754 (ttt180) cc_final: 0.6518 (tpp80) REVERT: B 188 ARG cc_start: 0.8049 (tmt90) cc_final: 0.7731 (tmm-80) REVERT: B 199 VAL cc_start: 0.5783 (OUTLIER) cc_final: 0.5311 (m) REVERT: B 224 TYR cc_start: 0.5704 (m-80) cc_final: 0.4959 (m-80) REVERT: B 226 ARG cc_start: 0.5892 (mpt-90) cc_final: 0.5414 (mpt-90) REVERT: B 254 MET cc_start: 0.3611 (mtt) cc_final: 0.2695 (ptm) REVERT: B 281 MET cc_start: 0.4347 (ppp) cc_final: 0.2562 (mmp) REVERT: B 406 MET cc_start: 0.4360 (tpp) cc_final: 0.3734 (tpp) REVERT: B 413 ASN cc_start: 0.8724 (t0) cc_final: 0.8301 (p0) REVERT: B 476 TRP cc_start: 0.8031 (OUTLIER) cc_final: 0.7491 (m100) REVERT: B 562 MET cc_start: 0.3911 (tpt) cc_final: 0.3297 (tmm) REVERT: B 592 LEU cc_start: 0.6474 (OUTLIER) cc_final: 0.6137 (pp) REVERT: B 637 GLU cc_start: 0.8258 (tt0) cc_final: 0.7316 (tm-30) REVERT: B 647 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6449 (mt-10) REVERT: B 660 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.6155 (tp30) REVERT: B 668 CYS cc_start: 0.9130 (m) cc_final: 0.8882 (t) REVERT: B 691 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8475 (mptt) REVERT: B 1050 MET cc_start: 0.7803 (mmm) cc_final: 0.7237 (mtm) REVERT: B 1051 GLU cc_start: 0.7503 (mp0) cc_final: 0.7147 (mp0) REVERT: C 251 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8209 (mm-30) REVERT: C 283 PHE cc_start: 0.7075 (OUTLIER) cc_final: 0.5959 (t80) REVERT: C 330 MET cc_start: 0.6329 (mmm) cc_final: 0.5796 (mtm) REVERT: D 1 MET cc_start: 0.4347 (mmt) cc_final: 0.3148 (mtt) REVERT: D 43 ASN cc_start: 0.8123 (m-40) cc_final: 0.7568 (m-40) REVERT: D 78 LEU cc_start: 0.7251 (mp) cc_final: 0.6021 (tm) REVERT: E 84 ILE cc_start: 0.7686 (mp) cc_final: 0.7412 (pt) REVERT: E 151 MET cc_start: 0.4565 (OUTLIER) cc_final: 0.2919 (ttp) REVERT: F 80 MET cc_start: 0.7309 (tmm) cc_final: 0.7093 (ppp) REVERT: F 83 LEU cc_start: 0.8273 (pp) cc_final: 0.8010 (pp) REVERT: G 7 MET cc_start: 0.5793 (pmm) cc_final: 0.5268 (ptm) REVERT: G 20 ARG cc_start: 0.6583 (ptm-80) cc_final: 0.6379 (ptm-80) REVERT: G 98 HIS cc_start: 0.7018 (m-70) cc_final: 0.6805 (m90) REVERT: G 132 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7452 (mp0) REVERT: H 37 MET cc_start: 0.6827 (ppp) cc_final: 0.5403 (mtt) REVERT: H 65 TYR cc_start: 0.7707 (m-10) cc_final: 0.7399 (m-80) REVERT: I 91 MET cc_start: 0.6368 (mmp) cc_final: 0.5363 (mtt) REVERT: K 29 MET cc_start: 0.7194 (tmm) cc_final: 0.6964 (tmm) REVERT: K 67 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.7971 (m-80) REVERT: K 79 LYS cc_start: 0.8062 (tppt) cc_final: 0.7738 (tppt) REVERT: K 125 LYS cc_start: 0.7737 (mmpt) cc_final: 0.7109 (tppp) REVERT: L 13 GLN cc_start: 0.6154 (pp30) cc_final: 0.5085 (pm20) REVERT: L 16 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.7810 (mm) REVERT: L 27 GLU cc_start: 0.7972 (mp0) cc_final: 0.7329 (mp0) REVERT: M 25 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6634 (mp) REVERT: M 57 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7108 (pm20) REVERT: M 60 MET cc_start: 0.7443 (tmm) cc_final: 0.7223 (tmm) REVERT: M 73 LYS cc_start: 0.7885 (tttt) cc_final: 0.7509 (ptmt) REVERT: M 108 THR cc_start: 0.6923 (m) cc_final: 0.6502 (m) REVERT: M 113 ARG cc_start: 0.6537 (pmm150) cc_final: 0.5831 (ppp80) REVERT: M 136 ARG cc_start: 0.5781 (ptp90) cc_final: 0.5423 (mpt180) REVERT: M 248 MET cc_start: 0.4752 (ttm) cc_final: 0.4219 (ppp) REVERT: M 250 MET cc_start: 0.4984 (mmt) cc_final: 0.4628 (mpm) REVERT: N 249 VAL cc_start: 0.5644 (m) cc_final: 0.5397 (m) REVERT: N 349 THR cc_start: 0.6950 (m) cc_final: 0.6628 (m) REVERT: N 350 MET cc_start: 0.7250 (pmm) cc_final: 0.6958 (ptm) REVERT: N 385 CYS cc_start: 0.6898 (OUTLIER) cc_final: 0.6417 (p) REVERT: O 7 LYS cc_start: 0.7149 (tptp) cc_final: 0.6753 (pttp) REVERT: O 15 GLU cc_start: 0.5488 (OUTLIER) cc_final: 0.4802 (mm-30) REVERT: O 57 LEU cc_start: 0.8431 (mt) cc_final: 0.8228 (mm) REVERT: O 85 MET cc_start: 0.7583 (mpt) cc_final: 0.7253 (mmp) REVERT: O 90 ARG cc_start: 0.6243 (ttt180) cc_final: 0.5970 (mtm180) REVERT: O 118 MET cc_start: 0.3926 (ttt) cc_final: 0.2662 (ppp) REVERT: O 133 MET cc_start: 0.4346 (ptp) cc_final: 0.3939 (pp-130) REVERT: O 140 ASP cc_start: 0.7348 (t0) cc_final: 0.6935 (t0) REVERT: O 365 ILE cc_start: 0.5800 (OUTLIER) cc_final: 0.5547 (mp) REVERT: O 375 ILE cc_start: 0.5912 (tt) cc_final: 0.5504 (pt) REVERT: O 424 TYR cc_start: 0.5073 (m-80) cc_final: 0.4563 (m-80) REVERT: O 425 THR cc_start: 0.5963 (t) cc_final: 0.5687 (p) REVERT: O 434 MET cc_start: 0.3778 (ptt) cc_final: 0.3184 (pp-130) REVERT: P 220 ILE cc_start: 0.8189 (mm) cc_final: 0.7919 (pp) REVERT: Q 62 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7738 (mt0) REVERT: Q 110 MET cc_start: 0.6087 (ppp) cc_final: 0.5618 (tpt) REVERT: Q 111 MET cc_start: 0.1822 (tpp) cc_final: 0.1116 (tpp) outliers start: 135 outliers final: 56 residues processed: 708 average time/residue: 0.6419 time to fit residues: 562.9217 Evaluate side-chains 629 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 555 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 648 HIS Chi-restraints excluded: chain B residue 660 GLU Chi-restraints excluded: chain B residue 691 LYS Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 803 ILE Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 39 TYR Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain M residue 75 GLU Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 385 CYS Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 38 VAL Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain O residue 365 ILE Chi-restraints excluded: chain O residue 489 GLU Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 62 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 432 optimal weight: 9.9990 chunk 241 optimal weight: 7.9990 chunk 425 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 316 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 ASN A 476 HIS A 497 ASN B 282 GLN B 381 ASN B 408 GLN B 517 ASN B 642 ASN B 683 ASN B 850 GLN B 887 GLN ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1093 HIS B1100 HIS B1115 GLN ** B1118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN C 305 HIS ** E 64 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 126 GLN ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN O 14 GLN O 113 ASN O 377 GLN ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 437 HIS ** O 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 182 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.141100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.104962 restraints weight = 97237.209| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 4.07 r_work: 0.3516 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 1.7819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.237 41438 Z= 0.329 Angle : 1.434 50.558 56126 Z= 0.768 Chirality : 0.169 6.307 6305 Planarity : 0.008 0.109 7071 Dihedral : 10.485 79.154 5944 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.96 % Favored : 91.95 % Rotamer: Outliers : 3.18 % Allowed : 33.77 % Favored : 63.05 % Cbeta Deviations : 0.02 % 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: -2.59 (0.11), residues: 4922 helix: -1.07 (0.11), residues: 1770 sheet: -0.85 (0.19), residues: 721 loop : -2.52 (0.11), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG A 99 TYR 0.051 0.004 TYR F 109 PHE 0.040 0.004 PHE B 559 TRP 0.077 0.004 TRP A 595 HIS 0.036 0.003 HIS G 71 Details of bonding type rmsd covalent geometry : bond 0.00809 (41417) covalent geometry : angle 1.35931 (56108) hydrogen bonds : bond 0.06149 ( 1484) hydrogen bonds : angle 5.81859 ( 4293) metal coordination : bond 0.00923 ( 21) metal coordination : angle 25.62173 ( 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 865 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 725 time to evaluate : 1.138 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 198 GLU cc_start: 0.8462 (mm-30) cc_final: 0.7935 (pp20) REVERT: A 228 LYS cc_start: 0.6807 (mtmm) cc_final: 0.6548 (mmtt) REVERT: A 316 GLN cc_start: 0.8581 (mm110) cc_final: 0.8268 (mm-40) REVERT: A 355 ASN cc_start: 0.8286 (t0) cc_final: 0.7491 (m-40) REVERT: A 528 ASN cc_start: 0.8846 (m-40) cc_final: 0.8538 (m110) REVERT: A 554 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9133 (tm) REVERT: A 655 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8571 (pt) REVERT: A 1071 LYS cc_start: 0.8398 (tttt) cc_final: 0.8039 (ttmm) REVERT: A 1075 ASN cc_start: 0.8254 (m-40) cc_final: 0.7889 (m110) REVERT: A 1142 LEU cc_start: 0.6193 (mm) cc_final: 0.5947 (mm) REVERT: A 1227 VAL cc_start: 0.5900 (t) cc_final: 0.5425 (t) REVERT: A 1273 TYR cc_start: 0.9016 (t80) cc_final: 0.8797 (t80) REVERT: A 1305 ARG cc_start: 0.7110 (ptp-170) cc_final: 0.6628 (ptt-90) REVERT: A 1351 ILE cc_start: 0.9079 (tt) cc_final: 0.8778 (pt) REVERT: B 186 LYS cc_start: 0.7870 (mttt) cc_final: 0.7544 (mmmm) REVERT: B 188 ARG cc_start: 0.8393 (tmt90) cc_final: 0.8078 (tmm-80) REVERT: B 220 GLN cc_start: 0.8296 (tp-100) cc_final: 0.7418 (tm-30) REVERT: B 226 ARG cc_start: 0.6409 (mpt-90) cc_final: 0.5848 (mpt-90) REVERT: B 240 PHE cc_start: 0.6920 (m-10) cc_final: 0.6241 (m-80) REVERT: B 243 MET cc_start: 0.4840 (tmm) cc_final: 0.4522 (mpp) REVERT: B 254 MET cc_start: 0.4272 (mtt) cc_final: 0.3413 (mtp) REVERT: B 262 MET cc_start: 0.7382 (ppp) cc_final: 0.6621 (ptm) REVERT: B 405 HIS cc_start: 0.6860 (p90) cc_final: 0.6555 (p90) REVERT: B 413 ASN cc_start: 0.8867 (t0) cc_final: 0.8566 (p0) REVERT: B 427 LYS cc_start: 0.8793 (tppt) cc_final: 0.8209 (ptmt) REVERT: B 592 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8640 (pt) REVERT: B 632 TYR cc_start: 0.9079 (m-80) cc_final: 0.8749 (m-80) REVERT: B 641 CYS cc_start: 0.8655 (m) cc_final: 0.8357 (p) REVERT: B 660 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.5684 (tp30) REVERT: B 781 ARG cc_start: 0.8668 (mmm160) cc_final: 0.8414 (tpm170) REVERT: B 1112 LEU cc_start: 0.9188 (tp) cc_final: 0.8933 (OUTLIER) REVERT: C 5 GLN cc_start: 0.8522 (mp10) cc_final: 0.8243 (mp10) REVERT: C 43 ASP cc_start: 0.9179 (OUTLIER) cc_final: 0.8846 (p0) REVERT: C 345 MET cc_start: 0.6820 (mtm) cc_final: 0.5794 (ppp) REVERT: D 73 LEU cc_start: 0.8055 (mp) cc_final: 0.7835 (tp) REVERT: D 78 LEU cc_start: 0.7274 (mp) cc_final: 0.5938 (tm) REVERT: D 110 GLU cc_start: 0.6342 (mp0) cc_final: 0.5283 (mm-30) REVERT: E 108 GLN cc_start: 0.6837 (mp10) cc_final: 0.6351 (mp10) REVERT: E 110 MET cc_start: 0.3566 (tpt) cc_final: 0.3256 (tpp) REVERT: E 151 MET cc_start: 0.5876 (OUTLIER) cc_final: 0.4852 (mtp) REVERT: F 83 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8073 (pp) REVERT: F 117 ASP cc_start: 0.8769 (p0) cc_final: 0.8507 (m-30) REVERT: G 40 TYR cc_start: 0.7884 (OUTLIER) cc_final: 0.7448 (t80) REVERT: G 95 GLU cc_start: 0.9067 (tm-30) cc_final: 0.8672 (pm20) REVERT: G 98 HIS cc_start: 0.7294 (m-70) cc_final: 0.6852 (m90) REVERT: H 25 VAL cc_start: 0.8668 (t) cc_final: 0.8441 (p) REVERT: H 37 MET cc_start: 0.7202 (ppp) cc_final: 0.6858 (mtt) REVERT: H 147 LYS cc_start: 0.7442 (mttt) cc_final: 0.7183 (tppp) REVERT: I 91 MET cc_start: 0.6220 (mmp) cc_final: 0.5099 (mtt) REVERT: J 26 GLN cc_start: 0.9065 (tm-30) cc_final: 0.8697 (pp30) REVERT: J 57 GLU cc_start: 0.8738 (tp30) cc_final: 0.8440 (OUTLIER) REVERT: K 47 GLU cc_start: 0.7337 (mm-30) cc_final: 0.6988 (mm-30) REVERT: K 48 ASP cc_start: 0.7580 (p0) cc_final: 0.7196 (p0) REVERT: K 67 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8293 (m-80) REVERT: K 125 LYS cc_start: 0.8046 (mmpt) cc_final: 0.7633 (ttpt) REVERT: L 13 GLN cc_start: 0.6720 (pp30) cc_final: 0.5698 (pm20) REVERT: L 15 MET cc_start: 0.7402 (tpt) cc_final: 0.7172 (tpt) REVERT: L 16 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8352 (pp) REVERT: M 57 GLU cc_start: 0.7516 (pt0) cc_final: 0.7117 (pm20) REVERT: M 59 GLU cc_start: 0.6852 (pt0) cc_final: 0.5919 (pm20) REVERT: M 60 MET cc_start: 0.7542 (tmm) cc_final: 0.7317 (tmm) REVERT: M 108 THR cc_start: 0.7327 (m) cc_final: 0.6364 (p) REVERT: M 113 ARG cc_start: 0.7245 (pmm150) cc_final: 0.6679 (ppp80) REVERT: M 248 MET cc_start: 0.5222 (ttm) cc_final: 0.4889 (ppp) REVERT: M 250 MET cc_start: 0.5677 (mmt) cc_final: 0.5337 (mpm) REVERT: N 249 VAL cc_start: 0.6096 (m) cc_final: 0.5096 (m) REVERT: N 349 THR cc_start: 0.7407 (m) cc_final: 0.7126 (m) REVERT: O 11 LEU cc_start: 0.7954 (mt) cc_final: 0.7391 (mt) REVERT: O 15 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.5534 (mm-30) REVERT: O 93 TYR cc_start: 0.5198 (t80) cc_final: 0.4762 (t80) REVERT: O 96 LYS cc_start: 0.5473 (ptmt) cc_final: 0.5244 (tmmt) REVERT: O 118 MET cc_start: 0.4339 (ttt) cc_final: 0.3697 (pmm) REVERT: O 148 PHE cc_start: 0.6765 (t80) cc_final: 0.6167 (t80) REVERT: O 274 SER cc_start: 0.8793 (m) cc_final: 0.8510 (p) REVERT: O 434 MET cc_start: 0.5347 (ptt) cc_final: 0.4787 (pp-130) REVERT: O 526 TYR cc_start: 0.7084 (OUTLIER) cc_final: 0.6839 (t80) REVERT: P 220 ILE cc_start: 0.8258 (mm) cc_final: 0.7982 (pp) REVERT: P 310 MET cc_start: 0.8738 (ttm) cc_final: 0.8523 (ttm) REVERT: Q 62 GLN cc_start: 0.7869 (mt0) cc_final: 0.7582 (mt0) REVERT: Q 80 GLU cc_start: 0.3937 (pm20) cc_final: 0.3584 (pm20) REVERT: Q 110 MET cc_start: 0.6767 (ppp) cc_final: 0.6424 (ppp) outliers start: 140 outliers final: 51 residues processed: 827 average time/residue: 0.6746 time to fit residues: 684.0026 Evaluate side-chains 627 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 566 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 894 THR 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 174 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 648 HIS Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 660 GLU Chi-restraints excluded: chain B residue 812 ASP Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 881 ILE Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 305 HIS 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 69 THR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 40 TYR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain M residue 75 GLU Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 38 VAL Chi-restraints excluded: chain O residue 141 TYR Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain O residue 489 GLU Chi-restraints excluded: chain O residue 526 TYR Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 306 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 464 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 199 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 182 optimal weight: 0.5980 chunk 92 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 186 optimal weight: 0.2980 chunk 281 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 ASN A 469 HIS A 599 GLN A1039 GLN A1249 ASN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 806 HIS B 850 GLN ** B1118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1132 ASN C 23 ASN C 25 HIS C 305 HIS ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 HIS E 64 HIS F 72 GLN ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 GLN I 10 ASN I 32 HIS K 85 GLN ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 113 ASN O 286 GLN ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 437 HIS ** O 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 182 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.143143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.107906 restraints weight = 96291.761| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 4.15 r_work: 0.3559 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 1.8031 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= 0.214 Angle : 1.310 50.464 56126 Z= 0.693 Chirality : 0.166 6.314 6305 Planarity : 0.006 0.069 7071 Dihedral : 10.004 77.431 5944 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.51 % Favored : 94.45 % Rotamer: Outliers : 1.91 % Allowed : 37.18 % Favored : 60.91 % 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: -2.06 (0.11), residues: 4922 helix: -0.52 (0.12), residues: 1733 sheet: -0.71 (0.18), residues: 733 loop : -2.24 (0.11), residues: 2456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 187 TYR 0.034 0.002 TYR C 306 PHE 0.041 0.002 PHE A1379 TRP 0.046 0.002 TRP A 595 HIS 0.011 0.001 HIS M 220 Details of bonding type rmsd covalent geometry : bond 0.00555 (41417) covalent geometry : angle 1.22934 (56108) hydrogen bonds : bond 0.04250 ( 1484) hydrogen bonds : angle 5.22325 ( 4293) metal coordination : bond 0.00769 ( 21) metal coordination : angle 25.25472 ( 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 729 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 645 time to evaluate : 1.654 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: A 198 GLU cc_start: 0.8462 (mm-30) cc_final: 0.7962 (pp20) REVERT: A 228 LYS cc_start: 0.6912 (mtmm) cc_final: 0.6522 (mmtt) REVERT: A 240 MET cc_start: 0.7638 (mtp) cc_final: 0.7395 (mtp) REVERT: A 316 GLN cc_start: 0.8561 (mm110) cc_final: 0.8199 (mm-40) REVERT: A 355 ASN cc_start: 0.8343 (t0) cc_final: 0.7555 (m-40) REVERT: A 465 GLN cc_start: 0.7741 (tp40) cc_final: 0.6656 (tm-30) REVERT: A 504 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7708 (mt-10) REVERT: A 528 ASN cc_start: 0.8690 (m-40) cc_final: 0.8364 (m110) REVERT: A 554 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9063 (tm) REVERT: A 577 GLU cc_start: 0.8437 (pm20) cc_final: 0.8224 (pm20) REVERT: A 846 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8652 (mt-10) REVERT: A 1011 VAL cc_start: 0.4052 (p) cc_final: 0.2805 (t) REVERT: A 1071 LYS cc_start: 0.8352 (tttt) cc_final: 0.8061 (ttmm) REVERT: A 1075 ASN cc_start: 0.8211 (m-40) cc_final: 0.7861 (m110) REVERT: A 1185 MET cc_start: 0.4594 (tpp) cc_final: 0.3539 (tpp) REVERT: A 1305 ARG cc_start: 0.7094 (ptp-170) cc_final: 0.6802 (ptt-90) REVERT: A 1349 MET cc_start: 0.8615 (ptp) cc_final: 0.7848 (ppp) REVERT: B 183 GLN cc_start: 0.7148 (pp30) cc_final: 0.6858 (pp30) REVERT: B 220 GLN cc_start: 0.8412 (tp-100) cc_final: 0.7643 (tm-30) REVERT: B 226 ARG cc_start: 0.6363 (mpt-90) cc_final: 0.5841 (mpt-90) REVERT: B 240 PHE cc_start: 0.6658 (m-10) cc_final: 0.6183 (m-80) REVERT: B 243 MET cc_start: 0.4623 (tmm) cc_final: 0.4279 (mpt) REVERT: B 254 MET cc_start: 0.4445 (mtt) cc_final: 0.3568 (mtp) REVERT: B 262 MET cc_start: 0.7223 (ppp) cc_final: 0.6297 (ptp) REVERT: B 281 MET cc_start: 0.4342 (ppp) cc_final: 0.2390 (mmt) REVERT: B 328 PHE cc_start: 0.4801 (t80) cc_final: 0.3856 (t80) REVERT: B 387 ILE cc_start: 0.7688 (mm) cc_final: 0.7383 (tp) REVERT: B 406 MET cc_start: 0.5199 (mmm) cc_final: 0.3380 (mmm) REVERT: B 413 ASN cc_start: 0.8865 (t0) cc_final: 0.8585 (p0) REVERT: B 427 LYS cc_start: 0.8816 (tppt) cc_final: 0.8325 (ptmt) REVERT: B 592 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8299 (pt) REVERT: B 632 TYR cc_start: 0.9130 (m-80) cc_final: 0.8858 (m-80) REVERT: B 647 GLU cc_start: 0.8193 (pm20) cc_final: 0.7695 (pm20) REVERT: B 791 MET cc_start: 0.7178 (pmm) cc_final: 0.6027 (mmm) REVERT: B 975 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.7822 (t0) REVERT: C 5 GLN cc_start: 0.8332 (mp10) cc_final: 0.8111 (mp10) REVERT: C 43 ASP cc_start: 0.9139 (OUTLIER) cc_final: 0.8766 (p0) REVERT: D 78 LEU cc_start: 0.7355 (mp) cc_final: 0.6178 (tm) REVERT: D 110 GLU cc_start: 0.6493 (mp0) cc_final: 0.5346 (mm-30) REVERT: E 110 MET cc_start: 0.3508 (tpt) cc_final: 0.2408 (tpt) REVERT: E 151 MET cc_start: 0.5785 (OUTLIER) cc_final: 0.5234 (mtp) REVERT: F 83 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8128 (pp) REVERT: G 98 HIS cc_start: 0.7330 (m-70) cc_final: 0.7041 (m90) REVERT: H 36 LYS cc_start: 0.7093 (mmpt) cc_final: 0.6886 (mmpt) REVERT: H 37 MET cc_start: 0.7167 (ppp) cc_final: 0.6832 (mtt) REVERT: H 65 TYR cc_start: 0.7675 (m-10) cc_final: 0.7402 (m-10) REVERT: H 89 GLU cc_start: 0.8547 (mt-10) cc_final: 0.7946 (pt0) REVERT: H 100 GLU cc_start: 0.7666 (pm20) cc_final: 0.7427 (pm20) REVERT: I 91 MET cc_start: 0.6038 (mmp) cc_final: 0.5061 (mtt) REVERT: J 26 GLN cc_start: 0.9105 (tm-30) cc_final: 0.8732 (pp30) REVERT: J 57 GLU cc_start: 0.8563 (tp30) cc_final: 0.8301 (tp30) REVERT: K 47 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6944 (mm-30) REVERT: K 78 SER cc_start: 0.7227 (t) cc_final: 0.6918 (t) REVERT: K 87 ARG cc_start: 0.7445 (tmm160) cc_final: 0.7162 (tmm160) REVERT: K 125 LYS cc_start: 0.7938 (mmpt) cc_final: 0.7465 (tmmt) REVERT: L 13 GLN cc_start: 0.6723 (pp30) cc_final: 0.5781 (pm20) REVERT: L 27 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7909 (mm-30) REVERT: M 57 GLU cc_start: 0.7502 (pt0) cc_final: 0.7101 (pm20) REVERT: M 59 GLU cc_start: 0.6809 (pt0) cc_final: 0.5876 (pm20) REVERT: M 113 ARG cc_start: 0.7114 (pmm150) cc_final: 0.6887 (ppp80) REVERT: M 248 MET cc_start: 0.5155 (ttm) cc_final: 0.4902 (ppp) REVERT: M 699 MET cc_start: 0.5520 (ppp) cc_final: 0.5219 (ppp) REVERT: N 259 SER cc_start: 0.6306 (t) cc_final: 0.6088 (m) REVERT: O 7 LYS cc_start: 0.7908 (tppt) cc_final: 0.7576 (tppp) REVERT: O 11 LEU cc_start: 0.7934 (mt) cc_final: 0.7547 (mm) REVERT: O 15 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.5657 (mp0) REVERT: O 19 GLU cc_start: 0.7685 (pm20) cc_final: 0.7424 (pm20) REVERT: O 93 TYR cc_start: 0.4730 (t80) cc_final: 0.4258 (t80) REVERT: O 133 MET cc_start: 0.4065 (ptt) cc_final: 0.3534 (pp-130) REVERT: O 148 PHE cc_start: 0.6930 (t80) cc_final: 0.6570 (t80) REVERT: O 270 MET cc_start: 0.8540 (tpp) cc_final: 0.8125 (tpt) REVERT: O 274 SER cc_start: 0.8750 (m) cc_final: 0.8523 (p) REVERT: O 434 MET cc_start: 0.5531 (ptt) cc_final: 0.5271 (pp-130) REVERT: O 526 TYR cc_start: 0.6783 (t80) cc_final: 0.6533 (t80) REVERT: O 533 ARG cc_start: 0.5494 (tpm170) cc_final: 0.5007 (tpm170) REVERT: P 220 ILE cc_start: 0.8223 (mm) cc_final: 0.7938 (pp) REVERT: P 250 MET cc_start: 0.5618 (tpp) cc_final: 0.5296 (tpp) REVERT: Q 110 MET cc_start: 0.6683 (ppp) cc_final: 0.6425 (ppp) outliers start: 84 outliers final: 36 residues processed: 697 average time/residue: 0.6789 time to fit residues: 583.4963 Evaluate side-chains 578 residues out of total 4400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 535 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain A residue 1306 PHE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 881 ILE Chi-restraints excluded: chain B residue 975 ASP Chi-restraints excluded: chain B residue 1065 LEU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain E residue 26 TYR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 40 TYR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain M residue 75 GLU Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 38 VAL Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain O residue 489 GLU Chi-restraints excluded: chain O residue 520 ILE Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 306 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 130 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 410 optimal weight: 0.4980 chunk 388 optimal weight: 0.7980 chunk 322 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 236 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 HIS A 497 ASN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1385 HIS B 282 GLN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 HIS B 517 ASN B 850 GLN ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 437 HIS O 445 ASN ** O 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 182 GLN P 189 GLN Q 62 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.142531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.106601 restraints weight = 96899.730| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 4.07 r_work: 0.3550 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3556 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3556 r_free = 0.3556 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3556 r_free = 0.3556 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 1.8212 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= 0.212 Angle : 1.303 50.468 56126 Z= 0.689 Chirality : 0.165 6.324 6305 Planarity : 0.005 0.060 7071 Dihedral : 9.828 75.125 5944 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.40 % Favored : 93.58 % Rotamer: Outliers : 1.66 % Allowed : 38.45 % Favored : 59.89 % 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: -1.87 (0.11), residues: 4922 helix: -0.26 (0.12), residues: 1732 sheet: -0.69 (0.18), residues: 729 loop : -2.19 (0.12), residues: 2461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG M 150 TYR 0.097 0.002 TYR E 26 PHE 0.037 0.002 PHE A1379 TRP 0.035 0.002 TRP A 595 HIS 0.011 0.001 HIS M 220 Details of bonding type rmsd covalent geometry : bond 0.00558 (41417) covalent geometry : angle 1.22248 (56108) hydrogen bonds : bond 0.04068 ( 1484) hydrogen bonds : angle 5.12710 ( 4293) metal coordination : bond 0.00679 ( 21) metal coordination : angle 25.13498 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19398.10 seconds wall clock time: 329 minutes 55.95 seconds (19795.95 seconds total)