Starting phenix.real_space_refine on Sat Feb 7 16:48:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ce3_45492/02_2026/9ce3_45492.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ce3_45492/02_2026/9ce3_45492.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 { model { file = "/net/cci-nas-00/data/ceres_data/9ce3_45492/02_2026/9ce3_45492.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ce3_45492/02_2026/9ce3_45492.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ce3_45492/02_2026/9ce3_45492.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ce3_45492/02_2026/9ce3_45492.map" } 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= 0.010 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: 4 Type Number sf(0) Gaussians S 210 5.16 5 C 22371 2.51 5 N 6101 2.21 5 O 6404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35086 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1295, 10341 Classifications: {'peptide': 1295} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1239} Chain breaks: 5 Chain: "B" Number of atoms: 10200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1282, 10200 Classifications: {'peptide': 1282} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 56, 'TRANS': 1224} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 5042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 5042 Classifications: {'peptide': 616} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 592} Chain breaks: 2 Chain: "D" Number of atoms: 4773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4773 Classifications: {'peptide': 581} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 563} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2238 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 16, 'TRANS': 259} Chain: "F" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2372 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 291} Chain: "G" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 7.18, per 1000 atoms: 0.20 Number of scatterers: 35086 At special positions: 0 Unit cell: (153.27, 157.95, 416.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 210 16.00 O 6404 8.00 N 6101 7.00 C 22371 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: 2.81 Conformation dependent library (CDL) restraints added in 1.3 seconds 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8418 Finding SS restraints... Secondary structure from input PDB file: 214 helices and 13 sheets defined 70.5% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 41 through 49 Processing helix chain 'A' and resid 53 through 71 removed outlier: 3.998A pdb=" N GLU A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL A 67 " --> pdb=" O GLN A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 87 removed outlier: 3.562A pdb=" N VAL A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASP A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 113 Processing helix chain 'A' and resid 114 through 117 removed outlier: 3.644A pdb=" N GLY A 117 " --> pdb=" O GLU A 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 114 through 117' Processing helix chain 'A' and resid 118 through 129 removed outlier: 3.595A pdb=" N LEU A 122 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 159 through 171 Processing helix chain 'A' and resid 173 through 187 removed outlier: 3.717A pdb=" N ASN A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 193 removed outlier: 5.775A pdb=" N GLU A 193 " --> pdb=" O TYR A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 209 Processing helix chain 'A' and resid 211 through 229 removed outlier: 3.840A pdb=" N ILE A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 235 through 247 Processing helix chain 'A' and resid 248 through 251 removed outlier: 6.278A pdb=" N GLU A 251 " --> pdb=" O ASN A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 248 through 251' Processing helix chain 'A' and resid 252 through 265 Processing helix chain 'A' and resid 268 through 282 Processing helix chain 'A' and resid 283 through 286 Processing helix chain 'A' and resid 288 through 305 Processing helix chain 'A' and resid 315 through 318 Processing helix chain 'A' and resid 319 through 327 Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'A' and resid 354 through 372 Processing helix chain 'A' and resid 377 through 397 Processing helix chain 'A' and resid 403 through 414 Processing helix chain 'A' and resid 415 through 418 Processing helix chain 'A' and resid 419 through 433 Processing helix chain 'A' and resid 440 through 454 Processing helix chain 'A' and resid 458 through 477 Processing helix chain 'A' and resid 480 through 488 Processing helix chain 'A' and resid 488 through 494 removed outlier: 3.763A pdb=" N SER A 494 " --> pdb=" O ILE A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 499 Processing helix chain 'A' and resid 501 through 519 removed outlier: 3.945A pdb=" N GLY A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 536 removed outlier: 3.532A pdb=" N ILE A 530 " --> pdb=" O SER A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 555 removed outlier: 3.902A pdb=" N ALA A 555 " --> pdb=" O ALA A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 575 Processing helix chain 'A' and resid 580 through 601 removed outlier: 4.104A pdb=" N TYR A 598 " --> pdb=" O ILE A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 619 Processing helix chain 'A' and resid 686 through 700 Processing helix chain 'A' and resid 702 through 718 removed outlier: 3.516A pdb=" N LEU A 708 " --> pdb=" O LYS A 704 " (cutoff:3.500A) Proline residue: A 714 - end of helix Processing helix chain 'A' and resid 719 through 726 removed outlier: 3.785A pdb=" N ILE A 723 " --> pdb=" O TYR A 719 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 743 Processing helix chain 'A' and resid 744 through 750 Processing helix chain 'A' and resid 758 through 774 Proline residue: A 768 - end of helix Processing helix chain 'A' and resid 775 through 780 removed outlier: 5.050A pdb=" N ASN A 778 " --> pdb=" O SER A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 795 Processing helix chain 'A' and resid 796 through 798 No H-bonds generated for 'chain 'A' and resid 796 through 798' Processing helix chain 'A' and resid 800 through 815 Processing helix chain 'A' and resid 815 through 832 removed outlier: 5.330A pdb=" N LYS A 821 " --> pdb=" O ASP A 817 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) Proline residue: A 824 - end of helix removed outlier: 4.031A pdb=" N VAL A 828 " --> pdb=" O PRO A 824 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A 831 " --> pdb=" O VAL A 827 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS A 832 " --> pdb=" O VAL A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 852 removed outlier: 4.360A pdb=" N VAL A 841 " --> pdb=" O ALA A 837 " (cutoff:3.500A) Proline residue: A 842 - end of helix Processing helix chain 'A' and resid 861 through 873 Processing helix chain 'A' and resid 874 through 877 removed outlier: 3.731A pdb=" N ASN A 877 " --> pdb=" O PRO A 874 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 874 through 877' Processing helix chain 'A' and resid 882 through 900 Processing helix chain 'A' and resid 901 through 906 removed outlier: 4.057A pdb=" N LYS A 906 " --> pdb=" O LEU A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 922 removed outlier: 4.499A pdb=" N PHE A 911 " --> pdb=" O ASP A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 937 removed outlier: 3.656A pdb=" N ARG A 936 " --> pdb=" O PHE A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1034 Processing helix chain 'A' and resid 1045 through 1053 Processing helix chain 'A' and resid 1076 through 1082 removed outlier: 3.965A pdb=" N LEU A1080 " --> pdb=" O GLY A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1192 Processing helix chain 'A' and resid 1228 through 1233 Processing helix chain 'A' and resid 1234 through 1239 removed outlier: 4.082A pdb=" N ALA A1238 " --> pdb=" O LEU A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1496 through 1506 removed outlier: 4.239A pdb=" N VAL A1500 " --> pdb=" O ASN A1496 " (cutoff:3.500A) Processing helix chain 'A' and resid 1524 through 1537 removed outlier: 3.965A pdb=" N GLU A1528 " --> pdb=" O SER A1524 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A1530 " --> pdb=" O SER A1526 " (cutoff:3.500A) Processing helix chain 'A' and resid 1557 through 1564 Processing helix chain 'A' and resid 1568 through 1577 Processing helix chain 'A' and resid 1585 through 1587 No H-bonds generated for 'chain 'A' and resid 1585 through 1587' Processing helix chain 'A' and resid 1623 through 1625 No H-bonds generated for 'chain 'A' and resid 1623 through 1625' Processing helix chain 'A' and resid 1634 through 1642 removed outlier: 4.634A pdb=" N HIS A1640 " --> pdb=" O ASP A1636 " (cutoff:3.500A) Processing helix chain 'A' and resid 1690 through 1694 removed outlier: 3.932A pdb=" N GLY A1693 " --> pdb=" O ASP A1690 " (cutoff:3.500A) Processing helix chain 'A' and resid 1707 through 1731 removed outlier: 4.102A pdb=" N ARG A1713 " --> pdb=" O PRO A1709 " (cutoff:3.500A) Processing helix chain 'A' and resid 1738 through 1761 Processing helix chain 'A' and resid 1762 through 1762 No H-bonds generated for 'chain 'A' and resid 1762 through 1762' Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'B' and resid 44 through 49 Processing helix chain 'B' and resid 53 through 69 removed outlier: 3.560A pdb=" N VAL B 67 " --> pdb=" O GLN B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 86 removed outlier: 3.506A pdb=" N ALA B 80 " --> pdb=" O HIS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 94 through 112 Processing helix chain 'B' and resid 113 through 116 Processing helix chain 'B' and resid 117 through 129 removed outlier: 4.011A pdb=" N ALA B 121 " --> pdb=" O GLY B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 148 Processing helix chain 'B' and resid 156 through 171 removed outlier: 4.039A pdb=" N ALA B 161 " --> pdb=" O GLU B 157 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASP B 162 " --> pdb=" O GLU B 158 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 188 removed outlier: 3.717A pdb=" N SER B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 193 removed outlier: 4.428A pdb=" N ASP B 192 " --> pdb=" O CYS B 189 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLU B 193 " --> pdb=" O TYR B 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 189 through 193' Processing helix chain 'B' and resid 194 through 207 removed outlier: 3.706A pdb=" N LEU B 204 " --> pdb=" O GLN B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 228 removed outlier: 3.805A pdb=" N ILE B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 247 Processing helix chain 'B' and resid 248 through 251 removed outlier: 6.935A pdb=" N GLU B 251 " --> pdb=" O ASN B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 248 through 251' Processing helix chain 'B' and resid 252 through 265 Processing helix chain 'B' and resid 267 through 282 removed outlier: 4.536A pdb=" N SER B 271 " --> pdb=" O HIS B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 286 Processing helix chain 'B' and resid 288 through 305 Processing helix chain 'B' and resid 315 through 326 Proline residue: B 321 - end of helix removed outlier: 3.732A pdb=" N GLN B 325 " --> pdb=" O PRO B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 349 Processing helix chain 'B' and resid 354 through 376 removed outlier: 3.643A pdb=" N ASN B 363 " --> pdb=" O ASP B 359 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR B 374 " --> pdb=" O GLN B 370 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 397 Processing helix chain 'B' and resid 403 through 414 Processing helix chain 'B' and resid 420 through 432 removed outlier: 3.516A pdb=" N LEU B 424 " --> pdb=" O GLU B 420 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 453 Processing helix chain 'B' and resid 458 through 477 Processing helix chain 'B' and resid 480 through 492 removed outlier: 4.343A pdb=" N ILE B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 496 Processing helix chain 'B' and resid 501 through 519 removed outlier: 4.255A pdb=" N LYS B 506 " --> pdb=" O HIS B 502 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B 507 " --> pdb=" O GLN B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 537 removed outlier: 4.034A pdb=" N LEU B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA B 536 " --> pdb=" O GLU B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 575 removed outlier: 4.101A pdb=" N ALA B 552 " --> pdb=" O ARG B 548 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA B 555 " --> pdb=" O ALA B 551 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B 558 " --> pdb=" O SER B 554 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASP B 559 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N VAL B 560 " --> pdb=" O SER B 556 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS B 561 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA B 563 " --> pdb=" O ASP B 559 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 601 removed outlier: 3.793A pdb=" N TYR B 598 " --> pdb=" O ILE B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 619 Processing helix chain 'B' and resid 685 through 700 removed outlier: 4.542A pdb=" N LEU B 689 " --> pdb=" O PRO B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 717 Proline residue: B 714 - end of helix Processing helix chain 'B' and resid 719 through 725 removed outlier: 4.030A pdb=" N ILE B 723 " --> pdb=" O TYR B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 743 Processing helix chain 'B' and resid 745 through 750 Processing helix chain 'B' and resid 758 through 774 Proline residue: B 768 - end of helix Processing helix chain 'B' and resid 775 through 777 No H-bonds generated for 'chain 'B' and resid 775 through 777' Processing helix chain 'B' and resid 781 through 795 Processing helix chain 'B' and resid 796 through 799 removed outlier: 6.212A pdb=" N ARG B 799 " --> pdb=" O LEU B 796 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 796 through 799' Processing helix chain 'B' and resid 800 through 815 removed outlier: 3.585A pdb=" N ILE B 810 " --> pdb=" O VAL B 806 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 832 removed outlier: 4.571A pdb=" N LYS B 821 " --> pdb=" O ASP B 817 " (cutoff:3.500A) Proline residue: B 824 - end of helix removed outlier: 3.706A pdb=" N VAL B 828 " --> pdb=" O PRO B 824 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N HIS B 832 " --> pdb=" O VAL B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 852 removed outlier: 4.098A pdb=" N VAL B 841 " --> pdb=" O ALA B 837 " (cutoff:3.500A) Proline residue: B 842 - end of helix removed outlier: 3.605A pdb=" N ARG B 852 " --> pdb=" O SER B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 873 Processing helix chain 'B' and resid 874 through 877 removed outlier: 3.637A pdb=" N ASN B 877 " --> pdb=" O PRO B 874 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 874 through 877' Processing helix chain 'B' and resid 882 through 900 Processing helix chain 'B' and resid 901 through 921 removed outlier: 4.287A pdb=" N LYS B 906 " --> pdb=" O LEU B 902 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ASP B 907 " --> pdb=" O PRO B 903 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE B 908 " --> pdb=" O PHE B 904 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Proline residue: B 910 - end of helix Processing helix chain 'B' and resid 932 through 937 Processing helix chain 'B' and resid 1005 through 1034 Processing helix chain 'B' and resid 1045 through 1053 Processing helix chain 'B' and resid 1074 through 1082 Processing helix chain 'B' and resid 1182 through 1186 Processing helix chain 'B' and resid 1227 through 1238 Processing helix chain 'B' and resid 1496 through 1506 removed outlier: 4.306A pdb=" N VAL B1500 " --> pdb=" O ASN B1496 " (cutoff:3.500A) Processing helix chain 'B' and resid 1512 through 1516 Processing helix chain 'B' and resid 1524 through 1537 removed outlier: 3.680A pdb=" N GLU B1528 " --> pdb=" O SER B1524 " (cutoff:3.500A) Processing helix chain 'B' and resid 1557 through 1563 Processing helix chain 'B' and resid 1568 through 1577 removed outlier: 3.620A pdb=" N GLY B1577 " --> pdb=" O GLU B1573 " (cutoff:3.500A) Processing helix chain 'B' and resid 1585 through 1587 No H-bonds generated for 'chain 'B' and resid 1585 through 1587' Processing helix chain 'B' and resid 1634 through 1642 removed outlier: 4.080A pdb=" N HIS B1640 " --> pdb=" O ASP B1636 " (cutoff:3.500A) Processing helix chain 'B' and resid 1707 through 1731 removed outlier: 3.502A pdb=" N SER B1730 " --> pdb=" O HIS B1726 " (cutoff:3.500A) Processing helix chain 'B' and resid 1738 through 1762 Processing helix chain 'C' and resid 7 through 13 Processing helix chain 'C' and resid 18 through 36 Processing helix chain 'C' and resid 39 through 53 Processing helix chain 'C' and resid 54 through 63 Processing helix chain 'C' and resid 67 through 82 removed outlier: 3.708A pdb=" N HIS C 71 " --> pdb=" O PRO C 67 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS C 82 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 99 Processing helix chain 'C' and resid 101 through 109 removed outlier: 4.531A pdb=" N HIS C 105 " --> pdb=" O SER C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 122 Processing helix chain 'C' and resid 125 through 140 Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 168 removed outlier: 6.935A pdb=" N LEU C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ASP C 153 " --> pdb=" O GLN C 149 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU C 166 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS C 168 " --> pdb=" O TRP C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 195 removed outlier: 3.756A pdb=" N LEU C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 208 Processing helix chain 'C' and resid 212 through 225 removed outlier: 4.717A pdb=" N LYS C 221 " --> pdb=" O GLU C 217 " (cutoff:3.500A) Proline residue: C 222 - end of helix Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 237 through 243 removed outlier: 4.195A pdb=" N LEU C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 248 removed outlier: 3.727A pdb=" N TRP C 247 " --> pdb=" O ASP C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 261 Processing helix chain 'C' and resid 604 through 612 removed outlier: 4.024A pdb=" N PHE C 608 " --> pdb=" O TYR C 604 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU C 609 " --> pdb=" O ASP C 605 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL C 610 " --> pdb=" O HIS C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 620 removed outlier: 3.572A pdb=" N HIS C 617 " --> pdb=" O PRO C 613 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N HIS C 618 " --> pdb=" O LYS C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 663 Processing helix chain 'C' and resid 668 through 674 Processing helix chain 'C' and resid 675 through 679 removed outlier: 3.934A pdb=" N HIS C 678 " --> pdb=" O ASP C 675 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE C 679 " --> pdb=" O TRP C 676 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 675 through 679' Processing helix chain 'C' and resid 684 through 794 removed outlier: 3.518A pdb=" N LEU C 720 " --> pdb=" O ASN C 716 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG C 721 " --> pdb=" O ARG C 717 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS C 725 " --> pdb=" O ARG C 721 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA C 734 " --> pdb=" O GLU C 730 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU C 764 " --> pdb=" O ARG C 760 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN C 765 " --> pdb=" O TYR C 761 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU C 766 " --> pdb=" O ASN C 762 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG C 780 " --> pdb=" O HIS C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 867 Processing helix chain 'C' and resid 868 through 872 removed outlier: 3.538A pdb=" N SER C 871 " --> pdb=" O ASN C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 873 through 970 removed outlier: 3.691A pdb=" N MET C 879 " --> pdb=" O LYS C 875 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU C 896 " --> pdb=" O ARG C 892 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN C 897 " --> pdb=" O SER C 893 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA C 943 " --> pdb=" O GLY C 939 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 15 removed outlier: 4.048A pdb=" N ASP D 15 " --> pdb=" O LEU D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 36 removed outlier: 3.795A pdb=" N ALA D 27 " --> pdb=" O ASP D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 53 Processing helix chain 'D' and resid 54 through 63 removed outlier: 3.575A pdb=" N THR D 63 " --> pdb=" O HIS D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 85 through 99 removed outlier: 3.855A pdb=" N LEU D 99 " --> pdb=" O HIS D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 109 removed outlier: 3.702A pdb=" N LEU D 107 " --> pdb=" O LYS D 104 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER D 108 " --> pdb=" O HIS D 105 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN D 109 " --> pdb=" O LYS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 123 Processing helix chain 'D' and resid 125 through 140 Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 146 through 168 removed outlier: 7.109A pdb=" N LEU D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ASP D 153 " --> pdb=" O GLN D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 195 Processing helix chain 'D' and resid 195 through 208 Processing helix chain 'D' and resid 209 through 211 No H-bonds generated for 'chain 'D' and resid 209 through 211' Processing helix chain 'D' and resid 212 through 224 removed outlier: 4.451A pdb=" N LYS D 221 " --> pdb=" O GLU D 217 " (cutoff:3.500A) Proline residue: D 222 - end of helix Processing helix chain 'D' and resid 225 through 227 No H-bonds generated for 'chain 'D' and resid 225 through 227' Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 238 through 242 Processing helix chain 'D' and resid 243 through 249 Processing helix chain 'D' and resid 251 through 262 removed outlier: 3.742A pdb=" N ILE D 262 " --> pdb=" O GLU D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 632 Processing helix chain 'D' and resid 646 through 667 removed outlier: 3.692A pdb=" N GLN D 654 " --> pdb=" O ASP D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 728 removed outlier: 4.402A pdb=" N ALA D 728 " --> pdb=" O ILE D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 730 through 742 Processing helix chain 'D' and resid 743 through 779 Processing helix chain 'D' and resid 779 through 789 Processing helix chain 'D' and resid 789 through 808 Processing helix chain 'D' and resid 808 through 831 Processing helix chain 'D' and resid 840 through 867 removed outlier: 4.142A pdb=" N GLN D 844 " --> pdb=" O SER D 840 " (cutoff:3.500A) Processing helix chain 'D' and resid 874 through 968 Processing helix chain 'E' and resid 19 through 34 removed outlier: 3.921A pdb=" N ASP E 34 " --> pdb=" O ILE E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 49 Processing helix chain 'E' and resid 52 through 64 removed outlier: 4.499A pdb=" N ALA E 57 " --> pdb=" O SER E 53 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LEU E 58 " --> pdb=" O MET E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 72 No H-bonds generated for 'chain 'E' and resid 70 through 72' Processing helix chain 'E' and resid 73 through 95 Processing helix chain 'E' and resid 103 through 116 Processing helix chain 'E' and resid 128 through 145 removed outlier: 3.718A pdb=" N GLU E 143 " --> pdb=" O LYS E 139 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 164 Processing helix chain 'E' and resid 168 through 195 removed outlier: 3.861A pdb=" N GLN E 172 " --> pdb=" O ASP E 168 " (cutoff:3.500A) Proline residue: E 174 - end of helix removed outlier: 3.650A pdb=" N ASN E 182 " --> pdb=" O GLU E 178 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ARG E 187 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N LEU E 188 " --> pdb=" O GLU E 184 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU E 189 " --> pdb=" O ASP E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 201 Processing helix chain 'E' and resid 202 through 208 Processing helix chain 'E' and resid 216 through 229 removed outlier: 5.018A pdb=" N ARG E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL E 223 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS E 226 " --> pdb=" O ARG E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 246 removed outlier: 3.851A pdb=" N VAL E 236 " --> pdb=" O CYS E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 251 Processing helix chain 'E' and resid 255 through 265 Processing helix chain 'E' and resid 270 through 286 Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing sheet with id=AA1, first strand: chain 'A' and resid 622 through 623 removed outlier: 4.554A pdb=" N LEU A 629 " --> pdb=" O SER A 641 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1518 through 1519 Processing sheet with id=AA3, first strand: chain 'A' and resid 1580 through 1583 removed outlier: 8.653A pdb=" N PHE A1606 " --> pdb=" O ILE A1621 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE A1621 " --> pdb=" O PHE A1606 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N TYR A1608 " --> pdb=" O PHE A1619 " (cutoff:3.500A) removed outlier: 10.143A pdb=" N VAL A1646 " --> pdb=" O THR A1542 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LYS A1544 " --> pdb=" O VAL A1646 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ILE A1648 " --> pdb=" O LYS A1544 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA A1546 " --> pdb=" O ILE A1648 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N TYR A1650 " --> pdb=" O ALA A1546 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU A1548 " --> pdb=" O TYR A1650 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N SER A1647 " --> pdb=" O VAL A1671 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL A1673 " --> pdb=" O SER A1647 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL A1649 " --> pdb=" O VAL A1673 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ASN A1651 " --> pdb=" O PRO A1675 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N CYS A1680 " --> pdb=" O LEU A1676 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 622 through 623 removed outlier: 4.438A pdb=" N LEU B 629 " --> pdb=" O SER B 641 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N GLY B 682 " --> pdb=" O SER B 641 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TYR B 643 " --> pdb=" O GLY B 682 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1580 through 1583 removed outlier: 8.567A pdb=" N PHE B1606 " --> pdb=" O ILE B1621 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE B1621 " --> pdb=" O PHE B1606 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TYR B1608 " --> pdb=" O PHE B1619 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N VAL B1646 " --> pdb=" O THR B1542 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LYS B1544 " --> pdb=" O VAL B1646 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ILE B1648 " --> pdb=" O LYS B1544 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA B1546 " --> pdb=" O ILE B1648 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N TYR B1650 " --> pdb=" O ALA B1546 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B1548 " --> pdb=" O TYR B1650 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N SER B1647 " --> pdb=" O VAL B1671 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL B1673 " --> pdb=" O SER B1647 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL B1649 " --> pdb=" O VAL B1673 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ASN B1651 " --> pdb=" O PRO B1675 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1580 through 1583 removed outlier: 8.567A pdb=" N PHE B1606 " --> pdb=" O ILE B1621 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE B1621 " --> pdb=" O PHE B1606 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TYR B1608 " --> pdb=" O PHE B1619 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N VAL B1646 " --> pdb=" O THR B1542 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LYS B1544 " --> pdb=" O VAL B1646 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ILE B1648 " --> pdb=" O LYS B1544 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA B1546 " --> pdb=" O ILE B1648 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N TYR B1650 " --> pdb=" O ALA B1546 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B1548 " --> pdb=" O TYR B1650 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N SER B1647 " --> pdb=" O VAL B1671 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL B1673 " --> pdb=" O SER B1647 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL B1649 " --> pdb=" O VAL B1673 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ASN B1651 " --> pdb=" O PRO B1675 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N CYS B1680 " --> pdb=" O LEU B1676 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 13 through 18 removed outlier: 6.281A pdb=" N GLY F 28 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA F 16 " --> pdb=" O ALA F 26 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA F 26 " --> pdb=" O ALA F 16 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N PHE F 18 " --> pdb=" O CYS F 24 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N CYS F 24 " --> pdb=" O PHE F 18 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE F 33 " --> pdb=" O LYS F 46 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS F 46 " --> pdb=" O PHE F 33 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL F 35 " --> pdb=" O LYS F 44 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 56 through 58 removed outlier: 4.058A pdb=" N HIS F 56 " --> pdb=" O VAL F 69 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ASP F 80 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N THR F 86 " --> pdb=" O ASP F 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 96 through 102 removed outlier: 3.962A pdb=" N MET F 113 " --> pdb=" O LEU F 110 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR F 118 " --> pdb=" O GLN F 125 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLN F 125 " --> pdb=" O THR F 118 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 140 through 141 Processing sheet with id=AB2, first strand: chain 'F' and resid 182 through 187 removed outlier: 4.485A pdb=" N SER F 198 " --> pdb=" O LEU F 203 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU F 203 " --> pdb=" O SER F 198 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASP F 208 " --> pdb=" O LEU F 214 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU F 214 " --> pdb=" O ASP F 208 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 229 through 232 removed outlier: 3.786A pdb=" N CYS F 229 " --> pdb=" O SER F 242 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 273 through 277 removed outlier: 3.696A pdb=" N SER F 292 " --> pdb=" O CYS F 288 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG F 306 " --> pdb=" O LEU F 297 " (cutoff:3.500A) 2272 hydrogen bonds defined for protein. 6642 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: 7.39 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10194 1.33 - 1.45: 5280 1.45 - 1.57: 19997 1.57 - 1.69: 0 1.69 - 1.81: 318 Bond restraints: 35789 Sorted by residual: bond pdb=" N MET B1210 " pdb=" CA MET B1210 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.25e-02 6.40e+03 7.33e+00 bond pdb=" N LEU B1216 " pdb=" CA LEU B1216 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.23e-02 6.61e+03 7.07e+00 bond pdb=" N LEU B1212 " pdb=" CA LEU B1212 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.28e-02 6.10e+03 6.12e+00 bond pdb=" N GLU B1213 " pdb=" CA GLU B1213 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.09e+00 bond pdb=" N SER B1217 " pdb=" CA SER B1217 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.41e-02 5.03e+03 5.95e+00 ... (remaining 35784 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 47051 1.73 - 3.46: 1165 3.46 - 5.18: 188 5.18 - 6.91: 25 6.91 - 8.64: 4 Bond angle restraints: 48433 Sorted by residual: angle pdb=" C HIS A 495 " pdb=" N ILE A 496 " pdb=" CA ILE A 496 " ideal model delta sigma weight residual 120.24 124.10 -3.86 6.30e-01 2.52e+00 3.76e+01 angle pdb=" N LEU B1209 " pdb=" CA LEU B1209 " pdb=" C LEU B1209 " ideal model delta sigma weight residual 109.76 101.97 7.79 1.59e+00 3.96e-01 2.40e+01 angle pdb=" C VAL B 766 " pdb=" N VAL B 767 " pdb=" CA VAL B 767 " ideal model delta sigma weight residual 120.24 122.89 -2.65 6.30e-01 2.52e+00 1.77e+01 angle pdb=" N SER C 673 " pdb=" CA SER C 673 " pdb=" C SER C 673 " ideal model delta sigma weight residual 109.83 115.79 -5.96 1.55e+00 4.16e-01 1.48e+01 angle pdb=" C THR B 154 " pdb=" N TYR B 155 " pdb=" CA TYR B 155 " ideal model delta sigma weight residual 121.54 128.65 -7.11 1.91e+00 2.74e-01 1.39e+01 ... (remaining 48428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 20211 17.66 - 35.31: 1323 35.31 - 52.97: 247 52.97 - 70.62: 62 70.62 - 88.28: 18 Dihedral angle restraints: 21861 sinusoidal: 8950 harmonic: 12911 Sorted by residual: dihedral pdb=" CA GLN B 354 " pdb=" C GLN B 354 " pdb=" N VAL B 355 " pdb=" CA VAL B 355 " ideal model delta harmonic sigma weight residual 180.00 -151.31 -28.69 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA PRO C 668 " pdb=" C PRO C 668 " pdb=" N LEU C 669 " pdb=" CA LEU C 669 " ideal model delta harmonic sigma weight residual -180.00 -151.55 -28.45 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA GLY A1511 " pdb=" C GLY A1511 " pdb=" N ASP A1512 " pdb=" CA ASP A1512 " ideal model delta harmonic sigma weight residual 180.00 -153.15 -26.85 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 21858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 4945 0.071 - 0.142: 587 0.142 - 0.212: 16 0.212 - 0.283: 1 0.283 - 0.354: 1 Chirality restraints: 5550 Sorted by residual: chirality pdb=" CA LEU B1209 " pdb=" N LEU B1209 " pdb=" C LEU B1209 " pdb=" CB LEU B1209 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA LEU B1212 " pdb=" N LEU B1212 " pdb=" C LEU B1212 " pdb=" CB LEU B1212 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA ILE F 230 " pdb=" N ILE F 230 " pdb=" C ILE F 230 " pdb=" CB ILE F 230 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.91e-01 ... (remaining 5547 not shown) Planarity restraints: 6169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 787 " 0.016 2.00e-02 2.50e+03 3.15e-02 9.95e+00 pdb=" C GLU D 787 " -0.055 2.00e-02 2.50e+03 pdb=" O GLU D 787 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU D 788 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 953 " -0.234 9.50e-02 1.11e+02 1.05e-01 6.76e+00 pdb=" NE ARG C 953 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG C 953 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 953 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 953 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 776 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.56e+00 pdb=" C HIS D 776 " -0.044 2.00e-02 2.50e+03 pdb=" O HIS D 776 " 0.017 2.00e-02 2.50e+03 pdb=" N SER D 777 " 0.015 2.00e-02 2.50e+03 ... (remaining 6166 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3529 2.74 - 3.28: 36656 3.28 - 3.82: 59627 3.82 - 4.36: 73770 4.36 - 4.90: 122076 Nonbonded interactions: 295658 Sorted by model distance: nonbonded pdb=" O GLN E 179 " pdb=" ND2 ASN E 182 " model vdw 2.201 3.120 nonbonded pdb=" O VAL B 721 " pdb=" OG1 THR B 725 " model vdw 2.216 3.040 nonbonded pdb=" OD2 ASP B1603 " pdb=" NE2 HIS B1640 " model vdw 2.245 3.120 nonbonded pdb=" OG SER A 608 " pdb=" OD2 ASP A 702 " model vdw 2.249 3.040 nonbonded pdb=" OE2 GLU C 272 " pdb=" NH1 ARG C 715 " model vdw 2.286 3.120 ... (remaining 295653 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 41 through 417 or (resid 418 and (name N or name CA or nam \ e C or name O or name CB )) or resid 419 through 536 or (resid 537 and (name N o \ r name CA or name C or name O or name CB )) or resid 542 through 652 or resid 67 \ 8 through 923 or resid 928 through 1240 or resid 1490 through 1762)) selection = (chain 'B' and (resid 41 through 537 or resid 542 through 652 or resid 678 throu \ gh 1762)) } ncs_group { reference = (chain 'C' and (resid 6 through 265 or resid 267 or resid 609 through 610 or res \ id 612 or resid 622 through 671 or resid 688 through 831 or resid 839 through 87 \ 0 or (resid 871 and (name N or name CA or name C or name O or name CB )) or resi \ d 872 through 969)) selection = (chain 'D' and (resid 6 through 615 or resid 647 through 649 or resid 651 throug \ h 969)) } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 16.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 30.350 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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 : 0.005 0.061 35789 Z= 0.250 Angle : 0.674 8.642 48433 Z= 0.373 Chirality : 0.045 0.354 5550 Planarity : 0.006 0.105 6169 Dihedral : 12.714 88.277 13443 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.69 % Allowed : 5.01 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.49 (0.13), residues: 4311 helix: 0.53 (0.10), residues: 2669 sheet: 0.20 (0.28), residues: 273 loop : 0.25 (0.18), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1201 TYR 0.028 0.002 TYR B 349 PHE 0.034 0.003 PHE A 239 TRP 0.020 0.003 TRP C 676 HIS 0.012 0.001 HIS D 712 Details of bonding type rmsd covalent geometry : bond 0.00512 (35789) covalent geometry : angle 0.67421 (48433) hydrogen bonds : bond 0.11838 ( 2259) hydrogen bonds : angle 6.13531 ( 6642) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1254 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 1227 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.7522 (mt) cc_final: 0.6819 (mt) REVERT: A 123 PHE cc_start: 0.7739 (m-80) cc_final: 0.7381 (m-80) REVERT: A 167 TRP cc_start: 0.6735 (m100) cc_final: 0.6147 (t60) REVERT: A 168 MET cc_start: 0.7918 (mtp) cc_final: 0.7413 (mtm) REVERT: A 182 ASN cc_start: 0.8273 (m-40) cc_final: 0.7998 (m-40) REVERT: A 186 PHE cc_start: 0.7613 (m-80) cc_final: 0.7242 (m-80) REVERT: A 190 TYR cc_start: 0.6921 (m-80) cc_final: 0.6651 (m-80) REVERT: A 204 LEU cc_start: 0.8183 (mt) cc_final: 0.7954 (mt) REVERT: A 234 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7376 (tp30) REVERT: A 251 GLU cc_start: 0.7946 (mp0) cc_final: 0.7686 (mp0) REVERT: A 280 MET cc_start: 0.8945 (mtm) cc_final: 0.8660 (mtp) REVERT: A 287 GLU cc_start: 0.7538 (mp0) cc_final: 0.7331 (mp0) REVERT: A 288 ASP cc_start: 0.7608 (t0) cc_final: 0.7036 (t0) REVERT: A 307 HIS cc_start: 0.8270 (m-70) cc_final: 0.7925 (m170) REVERT: A 325 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7680 (mm-40) REVERT: A 340 LEU cc_start: 0.8889 (mt) cc_final: 0.8601 (mt) REVERT: A 397 GLN cc_start: 0.8212 (mt0) cc_final: 0.7983 (mt0) REVERT: A 405 GLU cc_start: 0.7575 (tt0) cc_final: 0.7322 (tp30) REVERT: A 479 PHE cc_start: 0.7268 (m-80) cc_final: 0.6998 (m-80) REVERT: A 482 GLU cc_start: 0.7886 (tt0) cc_final: 0.7522 (tm-30) REVERT: A 499 ASP cc_start: 0.7632 (t0) cc_final: 0.7418 (m-30) REVERT: A 596 LEU cc_start: 0.8924 (tp) cc_final: 0.8674 (tp) REVERT: A 620 LEU cc_start: 0.9145 (mt) cc_final: 0.8910 (mt) REVERT: A 707 LYS cc_start: 0.8812 (tmtt) cc_final: 0.8434 (tppp) REVERT: A 712 ARG cc_start: 0.8227 (mtt-85) cc_final: 0.7926 (mmm-85) REVERT: A 766 VAL cc_start: 0.9079 (t) cc_final: 0.8796 (p) REVERT: A 778 ASN cc_start: 0.8631 (m-40) cc_final: 0.8334 (m-40) REVERT: A 782 LYS cc_start: 0.8206 (mttt) cc_final: 0.7776 (mppt) REVERT: A 788 MET cc_start: 0.8089 (ttp) cc_final: 0.7756 (ttm) REVERT: A 791 CYS cc_start: 0.8448 (m) cc_final: 0.8189 (m) REVERT: A 879 SER cc_start: 0.8664 (t) cc_final: 0.8445 (m) REVERT: A 880 LYS cc_start: 0.8525 (mttt) cc_final: 0.8269 (mtmm) REVERT: A 1019 HIS cc_start: 0.8051 (m-70) cc_final: 0.7727 (m170) REVERT: A 1024 GLU cc_start: 0.8036 (tt0) cc_final: 0.7627 (tm-30) REVERT: A 1047 VAL cc_start: 0.9069 (p) cc_final: 0.8844 (t) REVERT: A 1213 GLU cc_start: 0.7865 (mp0) cc_final: 0.7411 (mp0) REVERT: A 1239 GLU cc_start: 0.7286 (tp30) cc_final: 0.6979 (tp30) REVERT: A 1243 GLU cc_start: 0.7188 (tp30) cc_final: 0.6719 (tp30) REVERT: A 1495 ILE cc_start: 0.8746 (mm) cc_final: 0.8524 (mp) REVERT: A 1602 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7639 (tt0) REVERT: A 1668 PHE cc_start: 0.8167 (m-10) cc_final: 0.7930 (m-80) REVERT: A 1691 MET cc_start: 0.8889 (tpp) cc_final: 0.8622 (mmm) REVERT: A 1707 ASN cc_start: 0.8458 (m-40) cc_final: 0.8247 (m110) REVERT: B 87 ASP cc_start: 0.6793 (p0) cc_final: 0.6515 (p0) REVERT: B 88 LEU cc_start: 0.8415 (mt) cc_final: 0.8193 (mm) REVERT: B 104 LEU cc_start: 0.8848 (tp) cc_final: 0.8438 (tm) REVERT: B 108 ILE cc_start: 0.8718 (mt) cc_final: 0.8283 (mt) REVERT: B 115 ARG cc_start: 0.7828 (mtm110) cc_final: 0.7057 (mtm180) REVERT: B 136 LEU cc_start: 0.8077 (mp) cc_final: 0.7769 (mm) REVERT: B 144 LYS cc_start: 0.8756 (mtpt) cc_final: 0.8331 (ttmm) REVERT: B 186 PHE cc_start: 0.8428 (m-80) cc_final: 0.7875 (m-80) REVERT: B 218 SER cc_start: 0.8470 (m) cc_final: 0.8265 (t) REVERT: B 267 HIS cc_start: 0.8312 (OUTLIER) cc_final: 0.8098 (t-90) REVERT: B 277 CYS cc_start: 0.8421 (m) cc_final: 0.7932 (p) REVERT: B 324 TYR cc_start: 0.7120 (OUTLIER) cc_final: 0.6838 (m-10) REVERT: B 380 LEU cc_start: 0.8610 (tp) cc_final: 0.8228 (tp) REVERT: B 382 THR cc_start: 0.8856 (m) cc_final: 0.8494 (p) REVERT: B 426 LEU cc_start: 0.9130 (tp) cc_final: 0.8414 (tm) REVERT: B 467 ASP cc_start: 0.7909 (t70) cc_final: 0.7674 (t70) REVERT: B 470 SER cc_start: 0.8597 (t) cc_final: 0.8223 (p) REVERT: B 471 PHE cc_start: 0.8447 (t80) cc_final: 0.8227 (t80) REVERT: B 510 GLN cc_start: 0.8057 (mt0) cc_final: 0.7655 (tm-30) REVERT: B 511 LEU cc_start: 0.8615 (tt) cc_final: 0.8122 (tm) REVERT: B 514 ASP cc_start: 0.7728 (m-30) cc_final: 0.7041 (m-30) REVERT: B 553 TYR cc_start: 0.6836 (t80) cc_final: 0.6344 (t80) REVERT: B 557 LEU cc_start: 0.8341 (mt) cc_final: 0.7947 (mt) REVERT: B 601 SER cc_start: 0.8104 (m) cc_final: 0.7891 (p) REVERT: B 683 SER cc_start: 0.8794 (t) cc_final: 0.8492 (t) REVERT: B 685 PRO cc_start: 0.9117 (Cg_endo) cc_final: 0.8865 (Cg_exo) REVERT: B 703 TRP cc_start: 0.8354 (t-100) cc_final: 0.8143 (t-100) REVERT: B 704 LYS cc_start: 0.8495 (mttt) cc_final: 0.8023 (mppt) REVERT: B 707 LYS cc_start: 0.8799 (tttt) cc_final: 0.8380 (tttm) REVERT: B 757 PHE cc_start: 0.8032 (t80) cc_final: 0.7823 (t80) REVERT: B 761 ASP cc_start: 0.7974 (m-30) cc_final: 0.7649 (m-30) REVERT: B 763 HIS cc_start: 0.8418 (m-70) cc_final: 0.8175 (m-70) REVERT: B 764 LEU cc_start: 0.8637 (mt) cc_final: 0.8383 (mm) REVERT: B 782 LYS cc_start: 0.8829 (mttt) cc_final: 0.8527 (mttp) REVERT: B 797 ILE cc_start: 0.9207 (mt) cc_final: 0.8997 (tp) REVERT: B 800 CYS cc_start: 0.8008 (p) cc_final: 0.7740 (p) REVERT: B 828 VAL cc_start: 0.9082 (t) cc_final: 0.8720 (m) REVERT: B 1020 LEU cc_start: 0.8858 (mt) cc_final: 0.8615 (mt) REVERT: B 1028 ASP cc_start: 0.8320 (t70) cc_final: 0.7703 (t0) REVERT: B 1222 ASP cc_start: 0.7488 (m-30) cc_final: 0.7129 (m-30) REVERT: B 1229 GLN cc_start: 0.8503 (tt0) cc_final: 0.7870 (tm-30) REVERT: B 1230 GLU cc_start: 0.7944 (mp0) cc_final: 0.7585 (mp0) REVERT: B 1590 ASP cc_start: 0.7750 (m-30) cc_final: 0.7488 (m-30) REVERT: B 1602 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7424 (mm-30) REVERT: B 1614 ILE cc_start: 0.8158 (mp) cc_final: 0.7768 (tt) REVERT: B 1656 ASP cc_start: 0.7628 (p0) cc_final: 0.7165 (p0) REVERT: B 1756 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7851 (pp20) REVERT: C 18 MET cc_start: 0.6970 (mmt) cc_final: 0.6406 (mmt) REVERT: C 30 LYS cc_start: 0.8906 (mttt) cc_final: 0.8605 (mmmm) REVERT: C 88 SER cc_start: 0.9057 (m) cc_final: 0.8815 (p) REVERT: C 153 ASP cc_start: 0.7107 (OUTLIER) cc_final: 0.6296 (t0) REVERT: C 620 VAL cc_start: 0.8708 (p) cc_final: 0.8468 (m) REVERT: C 676 TRP cc_start: 0.6325 (m100) cc_final: 0.6111 (m100) REVERT: C 688 ILE cc_start: 0.9075 (mt) cc_final: 0.8812 (tt) REVERT: C 702 LEU cc_start: 0.8870 (tp) cc_final: 0.8660 (tm) REVERT: C 719 LEU cc_start: 0.8767 (mm) cc_final: 0.8521 (tp) REVERT: C 722 LYS cc_start: 0.8416 (tppt) cc_final: 0.8156 (tmtt) REVERT: C 736 MET cc_start: 0.8280 (mmm) cc_final: 0.7785 (mmm) REVERT: C 746 ASP cc_start: 0.7665 (m-30) cc_final: 0.7449 (m-30) REVERT: C 756 LYS cc_start: 0.8719 (tttt) cc_final: 0.8297 (ttpt) REVERT: C 771 MET cc_start: 0.8071 (tpp) cc_final: 0.7818 (tpp) REVERT: C 799 LYS cc_start: 0.8711 (tttt) cc_final: 0.8404 (tttp) REVERT: C 819 ASN cc_start: 0.8508 (t0) cc_final: 0.8271 (t0) REVERT: C 830 GLN cc_start: 0.8600 (tp40) cc_final: 0.8179 (mm-40) REVERT: C 845 MET cc_start: 0.8569 (ttp) cc_final: 0.8186 (ttt) REVERT: C 846 GLU cc_start: 0.8258 (tt0) cc_final: 0.7807 (tm-30) REVERT: C 863 LEU cc_start: 0.8936 (tp) cc_final: 0.8710 (tm) REVERT: C 864 GLU cc_start: 0.8045 (tt0) cc_final: 0.7727 (tp30) REVERT: C 874 THR cc_start: 0.7924 (p) cc_final: 0.7525 (t) REVERT: C 876 GLU cc_start: 0.8107 (pt0) cc_final: 0.7831 (pm20) REVERT: C 878 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7622 (mt-10) REVERT: C 880 MET cc_start: 0.8303 (mmm) cc_final: 0.7932 (mtp) REVERT: C 907 LYS cc_start: 0.8405 (tptt) cc_final: 0.8196 (mmmm) REVERT: C 925 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7677 (mm-30) REVERT: C 945 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7593 (mm-30) REVERT: D 36 ASP cc_start: 0.7545 (t0) cc_final: 0.7093 (t0) REVERT: D 45 LEU cc_start: 0.8848 (mt) cc_final: 0.8597 (tt) REVERT: D 59 HIS cc_start: 0.8005 (m90) cc_final: 0.7779 (m-70) REVERT: D 85 THR cc_start: 0.7871 (p) cc_final: 0.7613 (p) REVERT: D 136 LEU cc_start: 0.9101 (tp) cc_final: 0.8894 (tm) REVERT: D 201 SER cc_start: 0.8931 (t) cc_final: 0.8708 (p) REVERT: D 225 GLU cc_start: 0.7462 (tt0) cc_final: 0.7214 (tt0) REVERT: D 649 LEU cc_start: 0.9319 (tp) cc_final: 0.9060 (tm) REVERT: D 665 ASN cc_start: 0.8606 (m-40) cc_final: 0.8395 (m-40) REVERT: D 691 LEU cc_start: 0.9197 (tp) cc_final: 0.8833 (tt) REVERT: D 694 GLN cc_start: 0.8603 (mm110) cc_final: 0.8201 (mp10) REVERT: D 714 LEU cc_start: 0.8726 (mt) cc_final: 0.8448 (mt) REVERT: D 749 MET cc_start: 0.7930 (ttp) cc_final: 0.7514 (ttp) REVERT: D 794 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7878 (mm110) REVERT: D 805 ASN cc_start: 0.8128 (m-40) cc_final: 0.7867 (m-40) REVERT: D 846 GLU cc_start: 0.8038 (tt0) cc_final: 0.7529 (tp30) REVERT: D 854 VAL cc_start: 0.8970 (t) cc_final: 0.8765 (m) REVERT: D 860 GLU cc_start: 0.7852 (tp30) cc_final: 0.7422 (tp30) REVERT: D 863 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8586 (mt) REVERT: D 867 GLN cc_start: 0.8061 (pt0) cc_final: 0.7847 (pt0) REVERT: D 868 ASN cc_start: 0.7653 (m110) cc_final: 0.6707 (m-40) REVERT: D 880 MET cc_start: 0.8416 (mmp) cc_final: 0.8063 (mmp) REVERT: D 885 ARG cc_start: 0.7637 (ttm-80) cc_final: 0.7088 (mtp85) REVERT: D 886 LYS cc_start: 0.8686 (tptt) cc_final: 0.8403 (ttpp) REVERT: D 903 ASP cc_start: 0.8122 (m-30) cc_final: 0.7588 (t0) REVERT: D 907 LYS cc_start: 0.8375 (mmtt) cc_final: 0.8064 (mmmm) REVERT: D 918 LYS cc_start: 0.8552 (tptt) cc_final: 0.8290 (mttm) REVERT: D 920 ASP cc_start: 0.7977 (t70) cc_final: 0.7747 (t0) REVERT: D 925 GLU cc_start: 0.7987 (tp30) cc_final: 0.7772 (tm-30) REVERT: E 30 ILE cc_start: 0.8237 (mt) cc_final: 0.7951 (mt) REVERT: E 34 ASP cc_start: 0.8064 (m-30) cc_final: 0.7832 (m-30) REVERT: E 38 ASP cc_start: 0.7835 (t0) cc_final: 0.7344 (t0) REVERT: E 40 GLU cc_start: 0.7737 (tt0) cc_final: 0.7485 (tt0) REVERT: E 55 TYR cc_start: 0.8354 (m-80) cc_final: 0.8040 (m-80) REVERT: E 72 GLU cc_start: 0.7816 (tt0) cc_final: 0.7586 (tt0) REVERT: E 93 LYS cc_start: 0.8770 (mttt) cc_final: 0.8483 (mtpp) REVERT: E 106 GLU cc_start: 0.8234 (tt0) cc_final: 0.8030 (tt0) REVERT: E 143 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8696 (mm-30) REVERT: E 144 MET cc_start: 0.8529 (mtt) cc_final: 0.8105 (mtt) REVERT: E 249 LYS cc_start: 0.8171 (tptt) cc_final: 0.7764 (tptt) REVERT: F 35 VAL cc_start: 0.7105 (t) cc_final: 0.6787 (p) REVERT: F 41 LEU cc_start: 0.8498 (tp) cc_final: 0.8142 (mt) REVERT: F 44 LYS cc_start: 0.7768 (mmmt) cc_final: 0.7498 (mmmt) REVERT: F 60 LEU cc_start: 0.7722 (tp) cc_final: 0.7502 (tm) REVERT: F 144 ASN cc_start: 0.4464 (OUTLIER) cc_final: 0.4257 (t0) REVERT: F 296 PHE cc_start: 0.6218 (t80) cc_final: 0.5480 (t80) outliers start: 27 outliers final: 11 residues processed: 1247 average time/residue: 0.7246 time to fit residues: 1066.9259 Evaluate side-chains 990 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 974 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 1223 ILE Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 678 HIS Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain F residue 144 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.3980 chunk 401 optimal weight: 0.5980 chunk 424 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 ASN A 404 GLN A 444 ASN A 502 HIS A 695 GLN A 777 HIS A 832 HIS A1019 HIS A1532 GLN A1667 ASN B 354 GLN B 373 GLN B 794 GLN ** B 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 HIS B1503 GLN B1588 GLN ** B1616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1670 HIS C 617 HIS C 755 GLN C 762 ASN ** C 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 ASN D 65 GLN D 253 HIS D 655 GLN D 710 GLN D 776 HIS ** D 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 823 HIS D 867 GLN D 870 HIS D 926 GLN E 179 GLN ** F 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.144123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.118803 restraints weight = 73010.311| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.72 r_work: 0.3575 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 35789 Z= 0.234 Angle : 0.730 13.820 48433 Z= 0.370 Chirality : 0.044 0.184 5550 Planarity : 0.005 0.056 6169 Dihedral : 5.496 58.295 4770 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.19 % Allowed : 15.87 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.84 (0.13), residues: 4311 helix: 0.84 (0.10), residues: 2684 sheet: 0.09 (0.28), residues: 293 loop : 0.37 (0.19), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 689 TYR 0.020 0.002 TYR B 719 PHE 0.030 0.002 PHE F 251 TRP 0.030 0.003 TRP B 441 HIS 0.017 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00514 (35789) covalent geometry : angle 0.72978 (48433) hydrogen bonds : bond 0.05036 ( 2259) hydrogen bonds : angle 5.35870 ( 6642) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1162 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 998 time to evaluate : 1.416 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: A 119 LEU cc_start: 0.7654 (mt) cc_final: 0.6987 (mt) REVERT: A 123 PHE cc_start: 0.7872 (m-80) cc_final: 0.7402 (m-80) REVERT: A 167 TRP cc_start: 0.7008 (m100) cc_final: 0.6577 (t60) REVERT: A 168 MET cc_start: 0.7470 (mtp) cc_final: 0.7114 (mmm) REVERT: A 182 ASN cc_start: 0.8199 (m-40) cc_final: 0.7854 (m-40) REVERT: A 186 PHE cc_start: 0.7953 (m-80) cc_final: 0.7478 (m-80) REVERT: A 190 TYR cc_start: 0.7200 (m-80) cc_final: 0.6955 (m-80) REVERT: A 234 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7421 (tp30) REVERT: A 251 GLU cc_start: 0.8094 (mp0) cc_final: 0.7768 (mp0) REVERT: A 288 ASP cc_start: 0.7517 (t0) cc_final: 0.7051 (t0) REVERT: A 307 HIS cc_start: 0.8324 (m-70) cc_final: 0.7941 (m-70) REVERT: A 313 ARG cc_start: 0.8295 (mpp80) cc_final: 0.7928 (mtm180) REVERT: A 325 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7659 (mp10) REVERT: A 340 LEU cc_start: 0.8837 (mt) cc_final: 0.8574 (mt) REVERT: A 393 GLU cc_start: 0.7867 (pp20) cc_final: 0.7250 (pp20) REVERT: A 405 GLU cc_start: 0.7838 (tt0) cc_final: 0.7403 (tp30) REVERT: A 430 ARG cc_start: 0.8309 (mmt-90) cc_final: 0.8005 (mmm160) REVERT: A 479 PHE cc_start: 0.7499 (m-80) cc_final: 0.7164 (m-80) REVERT: A 482 GLU cc_start: 0.8159 (tt0) cc_final: 0.7836 (tm-30) REVERT: A 483 GLU cc_start: 0.7801 (mp0) cc_final: 0.7358 (mp0) REVERT: A 596 LEU cc_start: 0.8864 (tp) cc_final: 0.8650 (tp) REVERT: A 622 ARG cc_start: 0.8190 (mpp80) cc_final: 0.7971 (mmm-85) REVERT: A 693 LEU cc_start: 0.8724 (mt) cc_final: 0.8507 (mt) REVERT: A 695 GLN cc_start: 0.8408 (mt0) cc_final: 0.8175 (tp40) REVERT: A 702 ASP cc_start: 0.7603 (t0) cc_final: 0.7369 (t0) REVERT: A 707 LYS cc_start: 0.8960 (tmtt) cc_final: 0.8616 (tppp) REVERT: A 712 ARG cc_start: 0.8514 (mtt-85) cc_final: 0.8216 (mmm-85) REVERT: A 750 LEU cc_start: 0.8904 (mt) cc_final: 0.8630 (mm) REVERT: A 759 ARG cc_start: 0.8118 (tpt-90) cc_final: 0.7716 (mmt90) REVERT: A 766 VAL cc_start: 0.9016 (t) cc_final: 0.8728 (p) REVERT: A 778 ASN cc_start: 0.8676 (m-40) cc_final: 0.8404 (m110) REVERT: A 782 LYS cc_start: 0.8105 (mttt) cc_final: 0.7659 (mppt) REVERT: A 788 MET cc_start: 0.7977 (ttp) cc_final: 0.7724 (ttm) REVERT: A 791 CYS cc_start: 0.8259 (m) cc_final: 0.8048 (m) REVERT: A 798 HIS cc_start: 0.7788 (m-70) cc_final: 0.7568 (m-70) REVERT: A 860 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.8599 (m-10) REVERT: A 880 LYS cc_start: 0.8707 (mttt) cc_final: 0.8297 (mtmm) REVERT: A 919 ASN cc_start: 0.7843 (m-40) cc_final: 0.7558 (m-40) REVERT: A 1016 LYS cc_start: 0.8275 (mttt) cc_final: 0.7989 (tppt) REVERT: A 1021 GLU cc_start: 0.7364 (mm-30) cc_final: 0.7127 (mm-30) REVERT: A 1213 GLU cc_start: 0.7341 (mp0) cc_final: 0.6985 (mp0) REVERT: A 1239 GLU cc_start: 0.7147 (tp30) cc_final: 0.6942 (tp30) REVERT: A 1243 GLU cc_start: 0.7260 (tp30) cc_final: 0.6820 (tp30) REVERT: A 1495 ILE cc_start: 0.8640 (mm) cc_final: 0.8373 (mp) REVERT: A 1528 GLU cc_start: 0.7229 (pp20) cc_final: 0.6862 (pp20) REVERT: A 1529 ARG cc_start: 0.7684 (tpp-160) cc_final: 0.7195 (tpp-160) REVERT: A 1588 GLN cc_start: 0.7846 (tp-100) cc_final: 0.7043 (tp-100) REVERT: A 1602 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7785 (tt0) REVERT: A 1668 PHE cc_start: 0.8151 (m-10) cc_final: 0.7948 (m-80) REVERT: A 1691 MET cc_start: 0.8756 (tpp) cc_final: 0.8412 (mmm) REVERT: B 136 LEU cc_start: 0.7653 (mp) cc_final: 0.7394 (mm) REVERT: B 144 LYS cc_start: 0.8826 (mtpt) cc_final: 0.8470 (ttmm) REVERT: B 152 HIS cc_start: 0.7779 (t70) cc_final: 0.7413 (t70) REVERT: B 167 TRP cc_start: 0.7955 (t60) cc_final: 0.7742 (t60) REVERT: B 186 PHE cc_start: 0.8372 (m-80) cc_final: 0.7729 (m-80) REVERT: B 267 HIS cc_start: 0.8034 (OUTLIER) cc_final: 0.7513 (t-90) REVERT: B 277 CYS cc_start: 0.8029 (m) cc_final: 0.7769 (p) REVERT: B 288 ASP cc_start: 0.6989 (m-30) cc_final: 0.6766 (m-30) REVERT: B 325 GLN cc_start: 0.8248 (mp10) cc_final: 0.7996 (mp10) REVERT: B 366 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7597 (tm-30) REVERT: B 380 LEU cc_start: 0.8506 (tp) cc_final: 0.8147 (tp) REVERT: B 430 ARG cc_start: 0.8515 (ttm110) cc_final: 0.8304 (ttm110) REVERT: B 432 GLN cc_start: 0.8742 (mt0) cc_final: 0.8502 (mp10) REVERT: B 467 ASP cc_start: 0.8009 (t70) cc_final: 0.7772 (t0) REVERT: B 470 SER cc_start: 0.8577 (t) cc_final: 0.8149 (p) REVERT: B 471 PHE cc_start: 0.8602 (t80) cc_final: 0.8364 (t80) REVERT: B 510 GLN cc_start: 0.8263 (mt0) cc_final: 0.7778 (tm-30) REVERT: B 511 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8201 (tm) REVERT: B 514 ASP cc_start: 0.7739 (m-30) cc_final: 0.7075 (m-30) REVERT: B 553 TYR cc_start: 0.6783 (t80) cc_final: 0.6083 (t80) REVERT: B 557 LEU cc_start: 0.8321 (mt) cc_final: 0.7737 (mt) REVERT: B 601 SER cc_start: 0.8144 (m) cc_final: 0.7925 (p) REVERT: B 628 ARG cc_start: 0.8723 (ptm160) cc_final: 0.8066 (mtm110) REVERT: B 683 SER cc_start: 0.9019 (t) cc_final: 0.8006 (p) REVERT: B 691 ARG cc_start: 0.8189 (ttm-80) cc_final: 0.7898 (mtm-85) REVERT: B 704 LYS cc_start: 0.8605 (mttt) cc_final: 0.8107 (mppt) REVERT: B 707 LYS cc_start: 0.8798 (tttt) cc_final: 0.8391 (ttpp) REVERT: B 757 PHE cc_start: 0.7873 (t80) cc_final: 0.7641 (t80) REVERT: B 761 ASP cc_start: 0.7950 (m-30) cc_final: 0.7645 (m-30) REVERT: B 764 LEU cc_start: 0.8632 (mt) cc_final: 0.8390 (mm) REVERT: B 782 LYS cc_start: 0.8677 (mttt) cc_final: 0.8378 (mttp) REVERT: B 793 GLU cc_start: 0.7965 (tt0) cc_final: 0.7719 (tm-30) REVERT: B 797 ILE cc_start: 0.9149 (mt) cc_final: 0.8859 (tt) REVERT: B 800 CYS cc_start: 0.7679 (p) cc_final: 0.7361 (p) REVERT: B 818 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8467 (mt) REVERT: B 829 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7730 (tppp) REVERT: B 880 LYS cc_start: 0.8593 (mptt) cc_final: 0.8276 (mmpt) REVERT: B 906 LYS cc_start: 0.8743 (tttm) cc_final: 0.7706 (tttp) REVERT: B 914 LYS cc_start: 0.8959 (tppt) cc_final: 0.8531 (tppt) REVERT: B 1017 ASN cc_start: 0.8732 (t0) cc_final: 0.8383 (t0) REVERT: B 1028 ASP cc_start: 0.7980 (t70) cc_final: 0.7473 (t0) REVERT: B 1222 ASP cc_start: 0.7587 (m-30) cc_final: 0.7227 (m-30) REVERT: B 1230 GLU cc_start: 0.8098 (mp0) cc_final: 0.7862 (mp0) REVERT: B 1516 LYS cc_start: 0.8637 (mttt) cc_final: 0.8291 (mtmm) REVERT: B 1573 GLU cc_start: 0.8027 (mp0) cc_final: 0.7577 (mp0) REVERT: B 1602 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7730 (mm-30) REVERT: B 1656 ASP cc_start: 0.7779 (p0) cc_final: 0.7368 (p0) REVERT: B 1757 GLU cc_start: 0.7349 (mm-30) cc_final: 0.6952 (mm-30) REVERT: C 10 LEU cc_start: 0.8756 (mp) cc_final: 0.8433 (tt) REVERT: C 13 MET cc_start: 0.7895 (mtm) cc_final: 0.7527 (ttm) REVERT: C 40 MET cc_start: 0.6897 (tmm) cc_final: 0.6606 (tmm) REVERT: C 119 CYS cc_start: 0.8066 (t) cc_final: 0.7077 (t) REVERT: C 153 ASP cc_start: 0.6749 (OUTLIER) cc_final: 0.6425 (m-30) REVERT: C 204 ARG cc_start: 0.7091 (OUTLIER) cc_final: 0.6380 (ttp80) REVERT: C 225 GLU cc_start: 0.7702 (tp30) cc_final: 0.7428 (tp30) REVERT: C 228 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7581 (mtp85) REVERT: C 232 GLU cc_start: 0.7174 (mp0) cc_final: 0.6934 (mp0) REVERT: C 619 PHE cc_start: 0.8219 (m-80) cc_final: 0.7878 (m-80) REVERT: C 620 VAL cc_start: 0.8743 (p) cc_final: 0.8380 (p) REVERT: C 688 ILE cc_start: 0.9063 (mt) cc_final: 0.8668 (tp) REVERT: C 689 ARG cc_start: 0.8060 (mmm160) cc_final: 0.7779 (mmm160) REVERT: C 694 GLN cc_start: 0.8485 (tt0) cc_final: 0.8237 (tt0) REVERT: C 719 LEU cc_start: 0.8679 (mm) cc_final: 0.8405 (tp) REVERT: C 722 LYS cc_start: 0.8392 (tppt) cc_final: 0.8016 (tppp) REVERT: C 723 VAL cc_start: 0.7896 (OUTLIER) cc_final: 0.7279 (t) REVERT: C 725 LYS cc_start: 0.8924 (mmtt) cc_final: 0.8664 (mmmt) REVERT: C 731 GLU cc_start: 0.6649 (tm-30) cc_final: 0.6369 (tm-30) REVERT: C 736 MET cc_start: 0.8293 (mmm) cc_final: 0.7777 (mmm) REVERT: C 746 ASP cc_start: 0.7660 (m-30) cc_final: 0.7454 (m-30) REVERT: C 756 LYS cc_start: 0.8643 (tttt) cc_final: 0.8222 (ttpt) REVERT: C 760 ARG cc_start: 0.7684 (tpm170) cc_final: 0.6994 (tpm170) REVERT: C 799 LYS cc_start: 0.8751 (tttt) cc_final: 0.8407 (tmtp) REVERT: C 806 MET cc_start: 0.7933 (ttt) cc_final: 0.7297 (tmm) REVERT: C 819 ASN cc_start: 0.8474 (t0) cc_final: 0.8248 (t0) REVERT: C 825 GLU cc_start: 0.8165 (pp20) cc_final: 0.7878 (pp20) REVERT: C 830 GLN cc_start: 0.8641 (tp40) cc_final: 0.8292 (mm-40) REVERT: C 842 GLN cc_start: 0.8624 (tp-100) cc_final: 0.7990 (tp40) REVERT: C 846 GLU cc_start: 0.8649 (tt0) cc_final: 0.8390 (mt-10) REVERT: C 852 LEU cc_start: 0.9246 (tp) cc_final: 0.8976 (mm) REVERT: C 853 LEU cc_start: 0.9033 (tm) cc_final: 0.8704 (tm) REVERT: C 857 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7536 (mm-30) REVERT: C 861 LEU cc_start: 0.8458 (mt) cc_final: 0.8229 (mm) REVERT: C 863 LEU cc_start: 0.8862 (tp) cc_final: 0.8637 (tm) REVERT: C 864 GLU cc_start: 0.8387 (tt0) cc_final: 0.7847 (tp30) REVERT: C 874 THR cc_start: 0.8027 (p) cc_final: 0.7607 (t) REVERT: C 876 GLU cc_start: 0.7929 (pt0) cc_final: 0.7695 (pm20) REVERT: C 878 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7641 (mt-10) REVERT: C 880 MET cc_start: 0.8101 (mmm) cc_final: 0.7774 (mtp) REVERT: C 881 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.8898 (mmmm) REVERT: C 886 LYS cc_start: 0.8575 (mptt) cc_final: 0.8276 (mtpt) REVERT: C 906 GLN cc_start: 0.7860 (pp30) cc_final: 0.7477 (pp30) REVERT: C 924 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8193 (mm) REVERT: C 925 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7834 (mm-30) REVERT: C 961 GLU cc_start: 0.7866 (tp30) cc_final: 0.7559 (tp30) REVERT: D 9 GLU cc_start: 0.8308 (mp0) cc_final: 0.7809 (mp0) REVERT: D 30 LYS cc_start: 0.8617 (mtmt) cc_final: 0.8371 (mtmt) REVERT: D 36 ASP cc_start: 0.7326 (t0) cc_final: 0.7117 (t0) REVERT: D 40 MET cc_start: 0.7473 (pmm) cc_final: 0.7249 (pmm) REVERT: D 45 LEU cc_start: 0.8704 (mt) cc_final: 0.8484 (tt) REVERT: D 59 HIS cc_start: 0.8148 (m90) cc_final: 0.7869 (m-70) REVERT: D 136 LEU cc_start: 0.9013 (tp) cc_final: 0.8769 (tm) REVERT: D 201 SER cc_start: 0.8907 (t) cc_final: 0.8675 (p) REVERT: D 261 LYS cc_start: 0.8781 (tppp) cc_final: 0.8373 (tppt) REVERT: D 629 LYS cc_start: 0.8511 (mmmm) cc_final: 0.8212 (mmmt) REVERT: D 665 ASN cc_start: 0.8655 (m-40) cc_final: 0.8388 (m-40) REVERT: D 691 LEU cc_start: 0.9238 (tp) cc_final: 0.8935 (tm) REVERT: D 694 GLN cc_start: 0.8652 (mm110) cc_final: 0.8168 (mm110) REVERT: D 714 LEU cc_start: 0.8801 (mt) cc_final: 0.8502 (mt) REVERT: D 717 ARG cc_start: 0.7775 (tmm160) cc_final: 0.6969 (tmm160) REVERT: D 749 MET cc_start: 0.8264 (ttp) cc_final: 0.7886 (ttp) REVERT: D 756 LYS cc_start: 0.8609 (tmmm) cc_final: 0.8335 (tptp) REVERT: D 764 LEU cc_start: 0.8681 (tm) cc_final: 0.8271 (tm) REVERT: D 842 GLN cc_start: 0.8135 (tm-30) cc_final: 0.7903 (tm-30) REVERT: D 844 GLN cc_start: 0.8020 (tm-30) cc_final: 0.7732 (tm-30) REVERT: D 846 GLU cc_start: 0.8230 (tt0) cc_final: 0.7487 (OUTLIER) REVERT: D 860 GLU cc_start: 0.7939 (tp30) cc_final: 0.7416 (tp30) REVERT: D 863 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8437 (mt) REVERT: D 864 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7379 (mm-30) REVERT: D 867 GLN cc_start: 0.8114 (pt0) cc_final: 0.7843 (pt0) REVERT: D 868 ASN cc_start: 0.7410 (m110) cc_final: 0.7077 (m-40) REVERT: D 880 MET cc_start: 0.8532 (mmp) cc_final: 0.8053 (mmp) REVERT: D 881 LYS cc_start: 0.8890 (mttt) cc_final: 0.8649 (tttt) REVERT: D 886 LYS cc_start: 0.8761 (tptt) cc_final: 0.8485 (ttpp) REVERT: D 887 GLU cc_start: 0.8073 (tp30) cc_final: 0.7571 (tp30) REVERT: D 903 ASP cc_start: 0.8026 (m-30) cc_final: 0.7496 (t0) REVERT: D 907 LYS cc_start: 0.8641 (mmtt) cc_final: 0.8271 (mmmm) REVERT: D 918 LYS cc_start: 0.8577 (tptt) cc_final: 0.8278 (mttm) REVERT: D 920 ASP cc_start: 0.7875 (t70) cc_final: 0.7635 (t0) REVERT: D 925 GLU cc_start: 0.8102 (tp30) cc_final: 0.7824 (tm-30) REVERT: D 961 GLU cc_start: 0.7972 (tt0) cc_final: 0.7704 (tm-30) REVERT: E 25 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.8050 (tppp) REVERT: E 30 ILE cc_start: 0.8136 (mt) cc_final: 0.7829 (mt) REVERT: E 34 ASP cc_start: 0.8239 (m-30) cc_final: 0.7987 (m-30) REVERT: E 35 ASP cc_start: 0.8034 (m-30) cc_final: 0.7786 (t0) REVERT: E 38 ASP cc_start: 0.7909 (t0) cc_final: 0.7442 (t0) REVERT: E 40 GLU cc_start: 0.7955 (tt0) cc_final: 0.7698 (tt0) REVERT: E 72 GLU cc_start: 0.7984 (tt0) cc_final: 0.7761 (tt0) REVERT: E 82 LYS cc_start: 0.8622 (ttmm) cc_final: 0.8365 (tttm) REVERT: E 93 LYS cc_start: 0.8709 (mttt) cc_final: 0.8403 (mtpp) REVERT: E 106 GLU cc_start: 0.8264 (tt0) cc_final: 0.8039 (tt0) REVERT: E 143 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8755 (mm-30) REVERT: E 144 MET cc_start: 0.8452 (mtt) cc_final: 0.8096 (mtt) REVERT: E 222 ARG cc_start: 0.8511 (mmm-85) cc_final: 0.8137 (mtp180) REVERT: E 249 LYS cc_start: 0.8140 (tptt) cc_final: 0.7644 (tptt) REVERT: F 60 LEU cc_start: 0.7973 (tp) cc_final: 0.7756 (tm) REVERT: F 119 PHE cc_start: 0.7062 (t80) cc_final: 0.6124 (m-80) REVERT: F 126 LEU cc_start: 0.8023 (tp) cc_final: 0.7711 (pp) REVERT: F 144 ASN cc_start: 0.4234 (OUTLIER) cc_final: 0.3994 (t0) REVERT: F 296 PHE cc_start: 0.5584 (t80) cc_final: 0.4423 (t80) outliers start: 164 outliers final: 56 residues processed: 1089 average time/residue: 0.7460 time to fit residues: 959.3725 Evaluate side-chains 988 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 918 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 503 GLN Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 860 PHE Chi-restraints excluded: chain A residue 882 ASN Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1209 LEU Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain A residue 1754 ILE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 829 LYS Chi-restraints excluded: chain B residue 887 CYS Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 204 ARG Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 678 HIS Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 858 VAL Chi-restraints excluded: chain C residue 873 THR Chi-restraints excluded: chain C residue 881 LYS Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 716 ASN Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 771 MET Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 864 GLU Chi-restraints excluded: chain D residue 879 MET Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 175 LYS Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 274 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 129 optimal weight: 0.0020 chunk 82 optimal weight: 0.3980 chunk 241 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 220 optimal weight: 0.0870 chunk 264 optimal weight: 0.8980 chunk 187 optimal weight: 0.0070 chunk 121 optimal weight: 0.9980 chunk 345 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 216 optimal weight: 3.9990 overall best weight: 0.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS A 166 GLN A 275 ASN A 444 ASN ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 GLN ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 763 HIS B 798 HIS B1019 HIS B1503 GLN B1588 GLN ** B1616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 617 HIS ** C 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 763 GLN C 867 GLN D 710 GLN ** D 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 776 HIS D 823 HIS E 179 GLN ** F 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.143656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.119186 restraints weight = 73514.408| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.63 r_work: 0.3594 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 35789 Z= 0.168 Angle : 0.686 11.220 48433 Z= 0.345 Chirality : 0.043 0.167 5550 Planarity : 0.005 0.049 6169 Dihedral : 5.203 58.754 4762 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.09 % Allowed : 18.63 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.03 (0.13), residues: 4311 helix: 1.02 (0.10), residues: 2687 sheet: 0.02 (0.28), residues: 296 loop : 0.42 (0.19), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 721 TYR 0.039 0.002 TYR B 324 PHE 0.030 0.002 PHE B 408 TRP 0.040 0.002 TRP B 441 HIS 0.010 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00377 (35789) covalent geometry : angle 0.68571 (48433) hydrogen bonds : bond 0.04491 ( 2259) hydrogen bonds : angle 5.12024 ( 6642) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1091 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 931 time to evaluate : 1.433 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 119 LEU cc_start: 0.7624 (mt) cc_final: 0.6962 (mt) REVERT: A 123 PHE cc_start: 0.7819 (m-80) cc_final: 0.7339 (m-80) REVERT: A 167 TRP cc_start: 0.6839 (OUTLIER) cc_final: 0.6598 (t60) REVERT: A 168 MET cc_start: 0.7515 (mtp) cc_final: 0.7142 (mmm) REVERT: A 182 ASN cc_start: 0.8180 (m-40) cc_final: 0.7831 (m-40) REVERT: A 186 PHE cc_start: 0.7979 (m-80) cc_final: 0.7475 (m-80) REVERT: A 190 TYR cc_start: 0.7118 (m-80) cc_final: 0.6858 (m-80) REVERT: A 234 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7267 (tp30) REVERT: A 251 GLU cc_start: 0.8052 (mp0) cc_final: 0.7725 (mp0) REVERT: A 275 ASN cc_start: 0.8324 (OUTLIER) cc_final: 0.8077 (t0) REVERT: A 307 HIS cc_start: 0.8238 (m-70) cc_final: 0.7898 (m-70) REVERT: A 325 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7619 (mp10) REVERT: A 340 LEU cc_start: 0.8831 (mt) cc_final: 0.8568 (mt) REVERT: A 392 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7517 (mm-30) REVERT: A 393 GLU cc_start: 0.7850 (pp20) cc_final: 0.7401 (pp20) REVERT: A 405 GLU cc_start: 0.7809 (tt0) cc_final: 0.7289 (tp30) REVERT: A 429 TYR cc_start: 0.8247 (t80) cc_final: 0.7794 (t80) REVERT: A 479 PHE cc_start: 0.7598 (m-80) cc_final: 0.7194 (m-80) REVERT: A 482 GLU cc_start: 0.8086 (tt0) cc_final: 0.7746 (tm-30) REVERT: A 483 GLU cc_start: 0.7757 (mp0) cc_final: 0.7285 (mp0) REVERT: A 499 ASP cc_start: 0.7475 (m-30) cc_final: 0.7167 (m-30) REVERT: A 535 MET cc_start: 0.7994 (mtm) cc_final: 0.7666 (mtp) REVERT: A 622 ARG cc_start: 0.8192 (mpp80) cc_final: 0.7829 (ttm110) REVERT: A 691 ARG cc_start: 0.8506 (ttp80) cc_final: 0.8206 (ttm110) REVERT: A 707 LYS cc_start: 0.8950 (tmtt) cc_final: 0.8639 (ttmm) REVERT: A 712 ARG cc_start: 0.8406 (mtt-85) cc_final: 0.8058 (mmm-85) REVERT: A 715 GLU cc_start: 0.7709 (pm20) cc_final: 0.7478 (pm20) REVERT: A 741 LEU cc_start: 0.8332 (mp) cc_final: 0.8091 (mt) REVERT: A 750 LEU cc_start: 0.8923 (mt) cc_final: 0.8617 (mm) REVERT: A 759 ARG cc_start: 0.8069 (tpt-90) cc_final: 0.7808 (mmt180) REVERT: A 778 ASN cc_start: 0.8591 (m-40) cc_final: 0.8319 (m110) REVERT: A 782 LYS cc_start: 0.8024 (mttt) cc_final: 0.7623 (mppt) REVERT: A 788 MET cc_start: 0.7885 (ttp) cc_final: 0.7619 (ttm) REVERT: A 791 CYS cc_start: 0.8250 (m) cc_final: 0.8030 (m) REVERT: A 798 HIS cc_start: 0.7835 (m-70) cc_final: 0.7622 (m-70) REVERT: A 873 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8656 (tp) REVERT: A 880 LYS cc_start: 0.8531 (mttt) cc_final: 0.8140 (ttmm) REVERT: A 919 ASN cc_start: 0.7820 (m-40) cc_final: 0.7548 (m-40) REVERT: A 1016 LYS cc_start: 0.8293 (mttt) cc_final: 0.7912 (tppt) REVERT: A 1043 LYS cc_start: 0.8388 (tttm) cc_final: 0.8165 (ttpp) REVERT: A 1044 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8203 (ttp-170) REVERT: A 1213 GLU cc_start: 0.7351 (mp0) cc_final: 0.7014 (mp0) REVERT: A 1239 GLU cc_start: 0.7201 (tp30) cc_final: 0.6927 (tp30) REVERT: A 1243 GLU cc_start: 0.6993 (tp30) cc_final: 0.6538 (tp30) REVERT: A 1495 ILE cc_start: 0.8661 (mm) cc_final: 0.8433 (mp) REVERT: A 1528 GLU cc_start: 0.7203 (pp20) cc_final: 0.6798 (pp20) REVERT: A 1529 ARG cc_start: 0.7648 (tpp-160) cc_final: 0.7379 (tpp-160) REVERT: A 1588 GLN cc_start: 0.7531 (tp-100) cc_final: 0.7304 (tp-100) REVERT: A 1602 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7757 (tt0) REVERT: A 1607 THR cc_start: 0.8507 (OUTLIER) cc_final: 0.8212 (t) REVERT: A 1756 GLU cc_start: 0.6700 (pp20) cc_final: 0.6436 (pp20) REVERT: B 60 MET cc_start: 0.8204 (tpp) cc_final: 0.7973 (tpp) REVERT: B 136 LEU cc_start: 0.7641 (mp) cc_final: 0.7398 (mm) REVERT: B 144 LYS cc_start: 0.8730 (mtpt) cc_final: 0.8341 (ttmm) REVERT: B 152 HIS cc_start: 0.7730 (t70) cc_final: 0.7352 (t70) REVERT: B 158 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7404 (mm-30) REVERT: B 167 TRP cc_start: 0.7931 (t60) cc_final: 0.7705 (t60) REVERT: B 186 PHE cc_start: 0.8350 (m-80) cc_final: 0.7522 (m-80) REVERT: B 258 LYS cc_start: 0.8276 (mtpt) cc_final: 0.8062 (mppt) REVERT: B 280 MET cc_start: 0.7452 (mtt) cc_final: 0.7196 (mtp) REVERT: B 345 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8233 (tt) REVERT: B 366 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7615 (tm-30) REVERT: B 380 LEU cc_start: 0.8662 (tp) cc_final: 0.8350 (tp) REVERT: B 424 LEU cc_start: 0.8349 (mp) cc_final: 0.8128 (mm) REVERT: B 426 LEU cc_start: 0.9273 (tp) cc_final: 0.8955 (tm) REVERT: B 430 ARG cc_start: 0.8399 (ttm110) cc_final: 0.8074 (mtt-85) REVERT: B 464 LYS cc_start: 0.8637 (mtpp) cc_final: 0.8224 (mtpp) REVERT: B 467 ASP cc_start: 0.8005 (t70) cc_final: 0.7758 (t0) REVERT: B 470 SER cc_start: 0.8551 (t) cc_final: 0.8101 (p) REVERT: B 471 PHE cc_start: 0.8527 (t80) cc_final: 0.8283 (t80) REVERT: B 510 GLN cc_start: 0.8253 (mt0) cc_final: 0.7535 (tm-30) REVERT: B 511 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8140 (tm) REVERT: B 514 ASP cc_start: 0.7748 (m-30) cc_final: 0.7183 (m-30) REVERT: B 528 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6782 (mm) REVERT: B 553 TYR cc_start: 0.6842 (t80) cc_final: 0.6149 (t80) REVERT: B 557 LEU cc_start: 0.8292 (mt) cc_final: 0.7578 (mt) REVERT: B 576 TYR cc_start: 0.7509 (OUTLIER) cc_final: 0.7095 (m-80) REVERT: B 585 ARG cc_start: 0.8539 (ttp80) cc_final: 0.8280 (ttt180) REVERT: B 628 ARG cc_start: 0.8741 (ptm160) cc_final: 0.8137 (mtm110) REVERT: B 704 LYS cc_start: 0.8568 (mttt) cc_final: 0.8188 (mppt) REVERT: B 707 LYS cc_start: 0.8773 (tttt) cc_final: 0.8404 (ttpp) REVERT: B 757 PHE cc_start: 0.7893 (t80) cc_final: 0.7627 (t80) REVERT: B 759 ARG cc_start: 0.7881 (ptp-110) cc_final: 0.7646 (ptp-110) REVERT: B 761 ASP cc_start: 0.7918 (m-30) cc_final: 0.7591 (m-30) REVERT: B 764 LEU cc_start: 0.8602 (mt) cc_final: 0.8340 (mm) REVERT: B 782 LYS cc_start: 0.8638 (mttt) cc_final: 0.8390 (mttp) REVERT: B 800 CYS cc_start: 0.7680 (p) cc_final: 0.7359 (p) REVERT: B 880 LYS cc_start: 0.8536 (mptt) cc_final: 0.8311 (mptm) REVERT: B 895 MET cc_start: 0.7963 (mmm) cc_final: 0.7743 (mmm) REVERT: B 906 LYS cc_start: 0.8677 (tttm) cc_final: 0.7852 (tttp) REVERT: B 907 ASP cc_start: 0.8036 (p0) cc_final: 0.7713 (p0) REVERT: B 914 LYS cc_start: 0.8968 (tppt) cc_final: 0.8432 (tppt) REVERT: B 917 ARG cc_start: 0.8551 (ttm170) cc_final: 0.7834 (ttp-110) REVERT: B 934 ARG cc_start: 0.7007 (ttt-90) cc_final: 0.6660 (ttt-90) REVERT: B 1017 ASN cc_start: 0.8714 (t0) cc_final: 0.8343 (t0) REVERT: B 1028 ASP cc_start: 0.7989 (t70) cc_final: 0.7443 (t0) REVERT: B 1222 ASP cc_start: 0.7606 (m-30) cc_final: 0.7189 (m-30) REVERT: B 1230 GLU cc_start: 0.8151 (mp0) cc_final: 0.7910 (mp0) REVERT: B 1573 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: B 1590 ASP cc_start: 0.7851 (m-30) cc_final: 0.7648 (m-30) REVERT: B 1602 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7661 (mm-30) REVERT: B 1614 ILE cc_start: 0.8153 (mt) cc_final: 0.7695 (tt) REVERT: B 1639 ARG cc_start: 0.7981 (ptt180) cc_final: 0.7690 (ptt180) REVERT: B 1656 ASP cc_start: 0.7754 (p0) cc_final: 0.7338 (p0) REVERT: B 1756 GLU cc_start: 0.7433 (pp20) cc_final: 0.7019 (pp20) REVERT: C 13 MET cc_start: 0.7803 (mtm) cc_final: 0.7563 (ttm) REVERT: C 19 LEU cc_start: 0.8785 (mt) cc_final: 0.8555 (mt) REVERT: C 40 MET cc_start: 0.6843 (tmm) cc_final: 0.6543 (tmm) REVERT: C 232 GLU cc_start: 0.7226 (mp0) cc_final: 0.6924 (mp0) REVERT: C 261 LYS cc_start: 0.8567 (tmmt) cc_final: 0.8321 (pptt) REVERT: C 272 GLU cc_start: 0.7096 (tm-30) cc_final: 0.6892 (tm-30) REVERT: C 678 HIS cc_start: 0.7075 (OUTLIER) cc_final: 0.6767 (m-70) REVERT: C 688 ILE cc_start: 0.9038 (mt) cc_final: 0.8656 (tp) REVERT: C 689 ARG cc_start: 0.8002 (mmm160) cc_final: 0.7685 (mmp80) REVERT: C 702 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8579 (tt) REVERT: C 722 LYS cc_start: 0.8361 (tppt) cc_final: 0.7991 (tppp) REVERT: C 739 GLN cc_start: 0.6886 (tm-30) cc_final: 0.6633 (tm-30) REVERT: C 746 ASP cc_start: 0.7640 (m-30) cc_final: 0.7417 (m-30) REVERT: C 756 LYS cc_start: 0.8570 (tttt) cc_final: 0.8203 (tmmt) REVERT: C 799 LYS cc_start: 0.8641 (tttt) cc_final: 0.8235 (tmtp) REVERT: C 806 MET cc_start: 0.7921 (ttt) cc_final: 0.6832 (tmm) REVERT: C 807 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8213 (OUTLIER) REVERT: C 810 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.7972 (mp) REVERT: C 819 ASN cc_start: 0.8491 (t0) cc_final: 0.8238 (t0) REVERT: C 825 GLU cc_start: 0.8197 (pp20) cc_final: 0.7989 (pp20) REVERT: C 830 GLN cc_start: 0.8640 (tp40) cc_final: 0.8273 (mm-40) REVERT: C 839 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8224 (tm-30) REVERT: C 842 GLN cc_start: 0.8612 (tp-100) cc_final: 0.7931 (tp40) REVERT: C 845 MET cc_start: 0.8546 (ttt) cc_final: 0.8218 (ttt) REVERT: C 846 GLU cc_start: 0.8535 (tt0) cc_final: 0.8296 (mt-10) REVERT: C 852 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8931 (mm) REVERT: C 861 LEU cc_start: 0.8450 (mt) cc_final: 0.8221 (mm) REVERT: C 863 LEU cc_start: 0.8771 (tp) cc_final: 0.8524 (tm) REVERT: C 864 GLU cc_start: 0.8331 (tt0) cc_final: 0.7803 (tp30) REVERT: C 874 THR cc_start: 0.7765 (p) cc_final: 0.7260 (t) REVERT: C 878 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7618 (mt-10) REVERT: C 880 MET cc_start: 0.8025 (mmm) cc_final: 0.7684 (mtp) REVERT: C 884 TYR cc_start: 0.8547 (t80) cc_final: 0.8227 (t80) REVERT: C 885 ARG cc_start: 0.8493 (mmm160) cc_final: 0.8289 (mmp80) REVERT: C 886 LYS cc_start: 0.8559 (mptt) cc_final: 0.8258 (mtpt) REVERT: C 906 GLN cc_start: 0.7828 (pp30) cc_final: 0.7437 (pp30) REVERT: C 907 LYS cc_start: 0.8483 (mmmm) cc_final: 0.8257 (mmmm) REVERT: C 924 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8178 (mm) REVERT: C 925 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7663 (mm-30) REVERT: C 959 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7668 (mm-30) REVERT: C 961 GLU cc_start: 0.7851 (tp30) cc_final: 0.7459 (tp30) REVERT: D 9 GLU cc_start: 0.8291 (mp0) cc_final: 0.7858 (mp0) REVERT: D 18 MET cc_start: 0.7972 (tpp) cc_final: 0.7771 (tpp) REVERT: D 30 LYS cc_start: 0.8531 (mtmt) cc_final: 0.8237 (mtmt) REVERT: D 40 MET cc_start: 0.7522 (pmm) cc_final: 0.7266 (pmm) REVERT: D 136 LEU cc_start: 0.9008 (tp) cc_final: 0.8739 (tm) REVERT: D 201 SER cc_start: 0.8910 (t) cc_final: 0.8676 (p) REVERT: D 218 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7695 (pt0) REVERT: D 261 LYS cc_start: 0.8772 (tppp) cc_final: 0.8477 (tppp) REVERT: D 629 LYS cc_start: 0.8463 (mmmm) cc_final: 0.8259 (mmmt) REVERT: D 665 ASN cc_start: 0.8573 (m-40) cc_final: 0.8297 (m-40) REVERT: D 691 LEU cc_start: 0.9171 (tp) cc_final: 0.8812 (tm) REVERT: D 694 GLN cc_start: 0.8603 (mm110) cc_final: 0.8162 (mm-40) REVERT: D 712 HIS cc_start: 0.8404 (OUTLIER) cc_final: 0.7923 (t-90) REVERT: D 714 LEU cc_start: 0.8855 (mt) cc_final: 0.8524 (mt) REVERT: D 717 ARG cc_start: 0.7824 (tmm160) cc_final: 0.7411 (tmm160) REVERT: D 718 ARG cc_start: 0.8802 (ttm110) cc_final: 0.7823 (ttm110) REVERT: D 721 ARG cc_start: 0.8235 (ptp-110) cc_final: 0.7864 (mtm110) REVERT: D 749 MET cc_start: 0.8170 (ttp) cc_final: 0.7772 (ttp) REVERT: D 751 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8828 (tppp) REVERT: D 752 VAL cc_start: 0.8987 (t) cc_final: 0.8734 (p) REVERT: D 756 LYS cc_start: 0.8568 (tmmm) cc_final: 0.8231 (tptp) REVERT: D 806 MET cc_start: 0.7344 (ttt) cc_final: 0.6750 (tpp) REVERT: D 842 GLN cc_start: 0.8174 (tm-30) cc_final: 0.7891 (tm-30) REVERT: D 844 GLN cc_start: 0.8040 (tm-30) cc_final: 0.7206 (tm-30) REVERT: D 846 GLU cc_start: 0.8171 (tt0) cc_final: 0.7452 (tp30) REVERT: D 848 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8568 (mm) REVERT: D 852 LEU cc_start: 0.8700 (tp) cc_final: 0.8438 (tm) REVERT: D 860 GLU cc_start: 0.7850 (tp30) cc_final: 0.7398 (tp30) REVERT: D 863 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8395 (mt) REVERT: D 864 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7278 (mm-30) REVERT: D 867 GLN cc_start: 0.8032 (pt0) cc_final: 0.7723 (pt0) REVERT: D 868 ASN cc_start: 0.7406 (m110) cc_final: 0.6989 (m-40) REVERT: D 880 MET cc_start: 0.8521 (mmp) cc_final: 0.8034 (mmp) REVERT: D 881 LYS cc_start: 0.8844 (mttt) cc_final: 0.8589 (tttt) REVERT: D 886 LYS cc_start: 0.8712 (tptt) cc_final: 0.8424 (ttpp) REVERT: D 887 GLU cc_start: 0.8030 (tp30) cc_final: 0.7432 (tp30) REVERT: D 903 ASP cc_start: 0.7941 (m-30) cc_final: 0.7531 (t0) REVERT: D 907 LYS cc_start: 0.8582 (mmtt) cc_final: 0.8203 (mmmm) REVERT: D 908 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7874 (tpt170) REVERT: D 918 LYS cc_start: 0.8565 (tptt) cc_final: 0.8308 (mttp) REVERT: D 920 ASP cc_start: 0.7870 (t70) cc_final: 0.7623 (t0) REVERT: D 925 GLU cc_start: 0.8092 (tp30) cc_final: 0.7798 (tm-30) REVERT: E 25 LYS cc_start: 0.8230 (tptp) cc_final: 0.7831 (tppp) REVERT: E 30 ILE cc_start: 0.8139 (mt) cc_final: 0.7827 (mt) REVERT: E 34 ASP cc_start: 0.8120 (m-30) cc_final: 0.7828 (m-30) REVERT: E 38 ASP cc_start: 0.7906 (t0) cc_final: 0.7402 (t0) REVERT: E 40 GLU cc_start: 0.7787 (tt0) cc_final: 0.7530 (tt0) REVERT: E 55 TYR cc_start: 0.8436 (m-80) cc_final: 0.8219 (m-10) REVERT: E 72 GLU cc_start: 0.7918 (tt0) cc_final: 0.7682 (tt0) REVERT: E 82 LYS cc_start: 0.8581 (ttmm) cc_final: 0.8329 (tttm) REVERT: E 83 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7578 (mt-10) REVERT: E 93 LYS cc_start: 0.8685 (mttt) cc_final: 0.8414 (mtpp) REVERT: E 144 MET cc_start: 0.8401 (mtt) cc_final: 0.8035 (mtt) REVERT: E 222 ARG cc_start: 0.8504 (mmm-85) cc_final: 0.8111 (mtp180) REVERT: E 249 LYS cc_start: 0.8170 (tptt) cc_final: 0.7633 (tptt) REVERT: F 39 ASP cc_start: 0.8338 (t0) cc_final: 0.7896 (p0) REVERT: F 44 LYS cc_start: 0.7293 (mmmt) cc_final: 0.6896 (mmmt) REVERT: F 61 PHE cc_start: 0.7827 (m-80) cc_final: 0.7622 (m-80) REVERT: F 126 LEU cc_start: 0.8038 (tp) cc_final: 0.7817 (pp) REVERT: F 144 ASN cc_start: 0.4357 (OUTLIER) cc_final: 0.4157 (t0) REVERT: F 232 PHE cc_start: 0.8061 (m-80) cc_final: 0.7827 (t80) REVERT: F 295 LYS cc_start: 0.8310 (tmmt) cc_final: 0.7828 (pptt) REVERT: F 296 PHE cc_start: 0.5145 (t80) cc_final: 0.4256 (t80) outliers start: 160 outliers final: 62 residues processed: 1015 average time/residue: 0.7920 time to fit residues: 945.2075 Evaluate side-chains 974 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 890 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 167 TRP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 275 ASN Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 503 GLN Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 882 ASN Chi-restraints excluded: chain A residue 1044 ARG Chi-restraints excluded: chain A residue 1507 SER Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain A residue 1735 ILE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 576 TYR Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 1223 ILE Chi-restraints excluded: chain B residue 1573 GLU Chi-restraints excluded: chain B residue 1587 CYS Chi-restraints excluded: chain B residue 1638 LYS Chi-restraints excluded: chain B residue 1647 SER Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 678 HIS Chi-restraints excluded: chain C residue 691 LEU Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 763 GLN Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 858 VAL Chi-restraints excluded: chain C residue 873 THR Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 618 HIS Chi-restraints excluded: chain D residue 712 HIS Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 751 LYS Chi-restraints excluded: chain D residue 771 MET Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 848 LEU Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 864 GLU Chi-restraints excluded: chain D residue 879 MET Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 908 ARG Chi-restraints excluded: chain E residue 175 LYS Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 274 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 305 optimal weight: 0.5980 chunk 218 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 214 optimal weight: 0.2980 chunk 378 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 409 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 201 optimal weight: 0.4980 chunk 284 optimal weight: 2.9990 chunk 288 optimal weight: 0.0970 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN A 444 ASN ** A 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1019 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1532 GLN ** A1611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 GLN ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 HIS ** B 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 763 HIS B 798 HIS B 832 HIS ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 HIS B1588 GLN ** B1707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN C 617 HIS ** C 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 617 HIS ** D 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 776 HIS D 891 ASN ** D 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 915 HIS E 179 GLN ** F 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.147600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.123819 restraints weight = 72763.858| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.72 r_work: 0.3595 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 35789 Z= 0.192 Angle : 0.695 14.254 48433 Z= 0.350 Chirality : 0.043 0.218 5550 Planarity : 0.005 0.093 6169 Dihedral : 5.077 59.166 4758 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.19 % Allowed : 19.88 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.08 (0.13), residues: 4311 helix: 1.06 (0.10), residues: 2689 sheet: -0.09 (0.28), residues: 302 loop : 0.48 (0.19), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 691 TYR 0.024 0.002 TYR B 324 PHE 0.033 0.002 PHE B 408 TRP 0.042 0.002 TRP B 441 HIS 0.010 0.001 HIS A 763 Details of bonding type rmsd covalent geometry : bond 0.00436 (35789) covalent geometry : angle 0.69537 (48433) hydrogen bonds : bond 0.04390 ( 2259) hydrogen bonds : angle 5.07598 ( 6642) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1070 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 906 time to evaluate : 1.355 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: A 119 LEU cc_start: 0.7547 (mt) cc_final: 0.7064 (mt) REVERT: A 123 PHE cc_start: 0.7754 (m-80) cc_final: 0.7303 (m-80) REVERT: A 167 TRP cc_start: 0.6811 (OUTLIER) cc_final: 0.6607 (t60) REVERT: A 182 ASN cc_start: 0.8174 (m-40) cc_final: 0.7804 (m-40) REVERT: A 186 PHE cc_start: 0.7948 (m-80) cc_final: 0.7441 (m-80) REVERT: A 190 TYR cc_start: 0.7224 (m-80) cc_final: 0.6980 (m-80) REVERT: A 197 ARG cc_start: 0.7901 (ttm-80) cc_final: 0.7682 (ttp-110) REVERT: A 234 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7329 (tp30) REVERT: A 251 GLU cc_start: 0.8112 (mp0) cc_final: 0.7793 (mp0) REVERT: A 275 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.8237 (t0) REVERT: A 307 HIS cc_start: 0.8274 (m-70) cc_final: 0.7984 (m-70) REVERT: A 325 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7659 (mp10) REVERT: A 340 LEU cc_start: 0.8869 (mt) cc_final: 0.8588 (mt) REVERT: A 392 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7540 (mm-30) REVERT: A 393 GLU cc_start: 0.7906 (pp20) cc_final: 0.7428 (pp20) REVERT: A 405 GLU cc_start: 0.7823 (tt0) cc_final: 0.7443 (tp30) REVERT: A 467 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7750 (t0) REVERT: A 479 PHE cc_start: 0.7766 (m-80) cc_final: 0.7312 (m-80) REVERT: A 482 GLU cc_start: 0.8090 (tt0) cc_final: 0.7791 (tm-30) REVERT: A 483 GLU cc_start: 0.7738 (mp0) cc_final: 0.7279 (mp0) REVERT: A 499 ASP cc_start: 0.7492 (m-30) cc_final: 0.7219 (m-30) REVERT: A 535 MET cc_start: 0.8035 (mtm) cc_final: 0.7641 (mtp) REVERT: A 572 GLN cc_start: 0.8965 (tt0) cc_final: 0.8515 (tm-30) REVERT: A 622 ARG cc_start: 0.8291 (mpp80) cc_final: 0.7923 (ttm110) REVERT: A 691 ARG cc_start: 0.8524 (ttp80) cc_final: 0.8241 (ttm110) REVERT: A 707 LYS cc_start: 0.8908 (tttt) cc_final: 0.8627 (ttmm) REVERT: A 712 ARG cc_start: 0.8395 (mtt-85) cc_final: 0.8092 (mmm-85) REVERT: A 759 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7806 (mmt180) REVERT: A 778 ASN cc_start: 0.8600 (m-40) cc_final: 0.8338 (m110) REVERT: A 779 TYR cc_start: 0.8582 (m-80) cc_final: 0.8365 (m-80) REVERT: A 782 LYS cc_start: 0.8015 (mttt) cc_final: 0.7598 (mppt) REVERT: A 788 MET cc_start: 0.7822 (ttp) cc_final: 0.7519 (ttm) REVERT: A 791 CYS cc_start: 0.8219 (m) cc_final: 0.8015 (m) REVERT: A 804 CYS cc_start: 0.8162 (m) cc_final: 0.7708 (m) REVERT: A 880 LYS cc_start: 0.8624 (mttt) cc_final: 0.8232 (ttmm) REVERT: A 919 ASN cc_start: 0.7833 (m-40) cc_final: 0.7563 (m-40) REVERT: A 1016 LYS cc_start: 0.8239 (mttt) cc_final: 0.7852 (tppt) REVERT: A 1024 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7475 (tm-30) REVERT: A 1043 LYS cc_start: 0.8463 (tttm) cc_final: 0.8220 (tmmm) REVERT: A 1213 GLU cc_start: 0.7402 (mp0) cc_final: 0.7094 (mp0) REVERT: A 1239 GLU cc_start: 0.7356 (tp30) cc_final: 0.6916 (tp30) REVERT: A 1243 GLU cc_start: 0.7024 (tp30) cc_final: 0.6577 (tp30) REVERT: A 1495 ILE cc_start: 0.8698 (mm) cc_final: 0.8487 (mp) REVERT: A 1528 GLU cc_start: 0.7303 (pp20) cc_final: 0.6815 (pp20) REVERT: A 1529 ARG cc_start: 0.7712 (tpp-160) cc_final: 0.7281 (tpp-160) REVERT: A 1580 ARG cc_start: 0.8054 (ptm-80) cc_final: 0.7756 (ttm170) REVERT: A 1588 GLN cc_start: 0.7616 (tp-100) cc_final: 0.6964 (tm-30) REVERT: A 1590 ASP cc_start: 0.7597 (p0) cc_final: 0.6763 (p0) REVERT: A 1602 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7757 (tt0) REVERT: A 1756 GLU cc_start: 0.6803 (pp20) cc_final: 0.6438 (pp20) REVERT: A 1757 GLU cc_start: 0.7366 (tp30) cc_final: 0.7118 (tm-30) REVERT: B 60 MET cc_start: 0.8214 (tpp) cc_final: 0.7951 (tpp) REVERT: B 115 ARG cc_start: 0.7973 (mtm110) cc_final: 0.7726 (mtm110) REVERT: B 136 LEU cc_start: 0.7640 (mp) cc_final: 0.7400 (mm) REVERT: B 144 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8458 (ttmm) REVERT: B 148 ASP cc_start: 0.8373 (m-30) cc_final: 0.7835 (p0) REVERT: B 152 HIS cc_start: 0.7680 (t70) cc_final: 0.7342 (t70) REVERT: B 167 TRP cc_start: 0.7970 (t60) cc_final: 0.7720 (t60) REVERT: B 186 PHE cc_start: 0.8389 (m-80) cc_final: 0.7631 (m-80) REVERT: B 349 TYR cc_start: 0.7686 (m-80) cc_final: 0.7408 (m-80) REVERT: B 360 ILE cc_start: 0.8492 (mt) cc_final: 0.8187 (tt) REVERT: B 366 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7569 (tm-30) REVERT: B 380 LEU cc_start: 0.8654 (tp) cc_final: 0.8345 (tp) REVERT: B 424 LEU cc_start: 0.8303 (mp) cc_final: 0.8067 (mm) REVERT: B 426 LEU cc_start: 0.9227 (tp) cc_final: 0.8974 (tp) REVERT: B 464 LYS cc_start: 0.8604 (mtpp) cc_final: 0.8366 (mtmt) REVERT: B 467 ASP cc_start: 0.7947 (t70) cc_final: 0.7721 (t0) REVERT: B 470 SER cc_start: 0.8626 (t) cc_final: 0.8186 (p) REVERT: B 471 PHE cc_start: 0.8573 (t80) cc_final: 0.8340 (t80) REVERT: B 510 GLN cc_start: 0.8262 (mt0) cc_final: 0.7559 (tm-30) REVERT: B 511 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8103 (tm) REVERT: B 514 ASP cc_start: 0.7732 (m-30) cc_final: 0.7127 (m-30) REVERT: B 528 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6590 (mm) REVERT: B 553 TYR cc_start: 0.6956 (t80) cc_final: 0.6084 (t80) REVERT: B 557 LEU cc_start: 0.8322 (mt) cc_final: 0.7581 (mt) REVERT: B 628 ARG cc_start: 0.8682 (ptm160) cc_final: 0.8151 (mtm110) REVERT: B 704 LYS cc_start: 0.8648 (mttt) cc_final: 0.8227 (mppt) REVERT: B 707 LYS cc_start: 0.8872 (tttt) cc_final: 0.8585 (ttpp) REVERT: B 759 ARG cc_start: 0.8046 (ptp-110) cc_final: 0.7746 (ptp-110) REVERT: B 761 ASP cc_start: 0.7943 (m-30) cc_final: 0.7680 (m-30) REVERT: B 782 LYS cc_start: 0.8771 (mttt) cc_final: 0.8472 (mtmp) REVERT: B 800 CYS cc_start: 0.7689 (p) cc_final: 0.7310 (p) REVERT: B 880 LYS cc_start: 0.8662 (mptt) cc_final: 0.8453 (mptm) REVERT: B 906 LYS cc_start: 0.8675 (tttm) cc_final: 0.7665 (tttm) REVERT: B 907 ASP cc_start: 0.8130 (p0) cc_final: 0.7803 (p0) REVERT: B 914 LYS cc_start: 0.9010 (tppt) cc_final: 0.8542 (tppt) REVERT: B 917 ARG cc_start: 0.8596 (ttm170) cc_final: 0.7948 (ttm110) REVERT: B 1017 ASN cc_start: 0.8741 (t0) cc_final: 0.8345 (t0) REVERT: B 1028 ASP cc_start: 0.8012 (t70) cc_final: 0.7459 (t0) REVERT: B 1222 ASP cc_start: 0.7592 (m-30) cc_final: 0.7204 (m-30) REVERT: B 1230 GLU cc_start: 0.8170 (mp0) cc_final: 0.7931 (mp0) REVERT: B 1573 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7760 (mp0) REVERT: B 1590 ASP cc_start: 0.7884 (m-30) cc_final: 0.7679 (m-30) REVERT: B 1602 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7721 (mm-30) REVERT: B 1639 ARG cc_start: 0.8042 (ptt180) cc_final: 0.7796 (ptt180) REVERT: B 1656 ASP cc_start: 0.7822 (p0) cc_final: 0.7449 (p0) REVERT: B 1745 ARG cc_start: 0.8961 (mtp85) cc_final: 0.8752 (mtp85) REVERT: B 1756 GLU cc_start: 0.7430 (pp20) cc_final: 0.7185 (pp20) REVERT: C 10 LEU cc_start: 0.8815 (mm) cc_final: 0.8554 (mp) REVERT: C 13 MET cc_start: 0.7925 (mtm) cc_final: 0.7567 (ttm) REVERT: C 19 LEU cc_start: 0.8765 (mt) cc_final: 0.8539 (mt) REVERT: C 40 MET cc_start: 0.6744 (tmm) cc_final: 0.6417 (tmm) REVERT: C 232 GLU cc_start: 0.7350 (mp0) cc_final: 0.7008 (mp0) REVERT: C 272 GLU cc_start: 0.7095 (tm-30) cc_final: 0.6783 (tm-30) REVERT: C 605 ASP cc_start: 0.7788 (t70) cc_final: 0.7536 (t0) REVERT: C 678 HIS cc_start: 0.6612 (OUTLIER) cc_final: 0.6350 (m-70) REVERT: C 688 ILE cc_start: 0.9053 (mt) cc_final: 0.8712 (tp) REVERT: C 689 ARG cc_start: 0.7959 (mmm160) cc_final: 0.7633 (mmp80) REVERT: C 722 LYS cc_start: 0.8610 (tppt) cc_final: 0.7652 (tppp) REVERT: C 725 LYS cc_start: 0.8762 (tmmt) cc_final: 0.8355 (tptp) REVERT: C 736 MET cc_start: 0.8336 (mmm) cc_final: 0.8060 (mmm) REVERT: C 737 LYS cc_start: 0.8602 (mttt) cc_final: 0.8350 (mtmm) REVERT: C 739 GLN cc_start: 0.6917 (tm-30) cc_final: 0.6653 (tm-30) REVERT: C 741 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7797 (tmmm) REVERT: C 746 ASP cc_start: 0.7583 (m-30) cc_final: 0.7294 (m-30) REVERT: C 756 LYS cc_start: 0.8575 (tttt) cc_final: 0.8209 (tmmt) REVERT: C 760 ARG cc_start: 0.7541 (tpm170) cc_final: 0.7331 (tpm170) REVERT: C 764 LEU cc_start: 0.8733 (mt) cc_final: 0.8417 (mt) REVERT: C 771 MET cc_start: 0.7950 (ptt) cc_final: 0.7697 (ptt) REVERT: C 799 LYS cc_start: 0.8688 (tttt) cc_final: 0.8270 (tmtp) REVERT: C 806 MET cc_start: 0.7915 (ttt) cc_final: 0.7131 (tmm) REVERT: C 807 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8146 (OUTLIER) REVERT: C 810 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.7974 (mp) REVERT: C 819 ASN cc_start: 0.8462 (t0) cc_final: 0.8212 (t0) REVERT: C 825 GLU cc_start: 0.8247 (pp20) cc_final: 0.8037 (pp20) REVERT: C 830 GLN cc_start: 0.8650 (tp40) cc_final: 0.8298 (mm-40) REVERT: C 842 GLN cc_start: 0.8746 (tp-100) cc_final: 0.8171 (tp40) REVERT: C 846 GLU cc_start: 0.8486 (tt0) cc_final: 0.8222 (mt-10) REVERT: C 852 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8956 (mm) REVERT: C 857 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7559 (mm-30) REVERT: C 861 LEU cc_start: 0.8485 (mt) cc_final: 0.8249 (mm) REVERT: C 863 LEU cc_start: 0.8864 (tp) cc_final: 0.8587 (tm) REVERT: C 864 GLU cc_start: 0.8354 (tt0) cc_final: 0.7830 (tp30) REVERT: C 874 THR cc_start: 0.7735 (p) cc_final: 0.7399 (t) REVERT: C 876 GLU cc_start: 0.7833 (pt0) cc_final: 0.7398 (pm20) REVERT: C 878 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7666 (mt-10) REVERT: C 884 TYR cc_start: 0.8600 (t80) cc_final: 0.8344 (t80) REVERT: C 885 ARG cc_start: 0.8543 (mmm160) cc_final: 0.8325 (mmp80) REVERT: C 886 LYS cc_start: 0.8521 (mptt) cc_final: 0.8285 (mptm) REVERT: C 890 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8797 (ttpp) REVERT: C 906 GLN cc_start: 0.7815 (pp30) cc_final: 0.7370 (pp30) REVERT: C 907 LYS cc_start: 0.8480 (mmmm) cc_final: 0.8215 (mmmm) REVERT: C 924 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8175 (mm) REVERT: C 925 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7844 (mm-30) REVERT: C 959 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7638 (mm-30) REVERT: C 961 GLU cc_start: 0.7808 (tp30) cc_final: 0.7507 (tp30) REVERT: D 9 GLU cc_start: 0.8240 (mp0) cc_final: 0.7823 (mp0) REVERT: D 136 LEU cc_start: 0.9004 (tp) cc_final: 0.8734 (tm) REVERT: D 201 SER cc_start: 0.8920 (t) cc_final: 0.8694 (p) REVERT: D 261 LYS cc_start: 0.8805 (tppp) cc_final: 0.8500 (tppp) REVERT: D 629 LYS cc_start: 0.8381 (mmmm) cc_final: 0.7794 (mmmt) REVERT: D 650 ASP cc_start: 0.8183 (p0) cc_final: 0.7920 (p0) REVERT: D 665 ASN cc_start: 0.8603 (m-40) cc_final: 0.8317 (m-40) REVERT: D 691 LEU cc_start: 0.9136 (tp) cc_final: 0.8797 (tm) REVERT: D 694 GLN cc_start: 0.8532 (mm110) cc_final: 0.8124 (mm-40) REVERT: D 712 HIS cc_start: 0.8406 (OUTLIER) cc_final: 0.7338 (t70) REVERT: D 714 LEU cc_start: 0.8890 (mt) cc_final: 0.8584 (mt) REVERT: D 717 ARG cc_start: 0.7879 (tmm160) cc_final: 0.7506 (tmm160) REVERT: D 718 ARG cc_start: 0.8850 (ttm110) cc_final: 0.7877 (ttm110) REVERT: D 721 ARG cc_start: 0.8346 (ptp-110) cc_final: 0.8003 (ptp-110) REVERT: D 749 MET cc_start: 0.8190 (ttp) cc_final: 0.7814 (ttp) REVERT: D 751 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8892 (tppp) REVERT: D 752 VAL cc_start: 0.8919 (t) cc_final: 0.8680 (p) REVERT: D 756 LYS cc_start: 0.8590 (tmmm) cc_final: 0.8233 (tptp) REVERT: D 806 MET cc_start: 0.7355 (ttt) cc_final: 0.6709 (tpp) REVERT: D 842 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7783 (tm-30) REVERT: D 844 GLN cc_start: 0.8086 (tm-30) cc_final: 0.7255 (tm-30) REVERT: D 846 GLU cc_start: 0.8222 (tt0) cc_final: 0.7429 (tp30) REVERT: D 848 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8515 (mm) REVERT: D 852 LEU cc_start: 0.8710 (tp) cc_final: 0.8449 (tm) REVERT: D 860 GLU cc_start: 0.7910 (tp30) cc_final: 0.7410 (tp30) REVERT: D 863 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8409 (mt) REVERT: D 864 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7330 (mm-30) REVERT: D 867 GLN cc_start: 0.8062 (pt0) cc_final: 0.7722 (pt0) REVERT: D 868 ASN cc_start: 0.7427 (m110) cc_final: 0.7019 (m-40) REVERT: D 880 MET cc_start: 0.8511 (mmp) cc_final: 0.8056 (mmp) REVERT: D 881 LYS cc_start: 0.8834 (mttt) cc_final: 0.8586 (tttt) REVERT: D 886 LYS cc_start: 0.8693 (tptt) cc_final: 0.8418 (ttpp) REVERT: D 887 GLU cc_start: 0.8082 (tp30) cc_final: 0.7453 (tp30) REVERT: D 894 HIS cc_start: 0.8012 (OUTLIER) cc_final: 0.7703 (t-90) REVERT: D 903 ASP cc_start: 0.8031 (m-30) cc_final: 0.7607 (t0) REVERT: D 907 LYS cc_start: 0.8577 (mmtt) cc_final: 0.8204 (mmmm) REVERT: D 908 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7881 (tpt170) REVERT: D 918 LYS cc_start: 0.8559 (tptt) cc_final: 0.8273 (mttp) REVERT: D 920 ASP cc_start: 0.7871 (t70) cc_final: 0.7631 (t0) REVERT: D 925 GLU cc_start: 0.8108 (tp30) cc_final: 0.7823 (tm-30) REVERT: D 945 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7364 (mm-30) REVERT: E 25 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7865 (tppp) REVERT: E 30 ILE cc_start: 0.8131 (mt) cc_final: 0.7798 (mt) REVERT: E 34 ASP cc_start: 0.8153 (m-30) cc_final: 0.7857 (m-30) REVERT: E 38 ASP cc_start: 0.7935 (t0) cc_final: 0.7396 (t0) REVERT: E 40 GLU cc_start: 0.7939 (tt0) cc_final: 0.7666 (tt0) REVERT: E 54 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.7935 (pmm) REVERT: E 72 GLU cc_start: 0.8041 (tt0) cc_final: 0.7806 (tt0) REVERT: E 76 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8276 (tttm) REVERT: E 82 LYS cc_start: 0.8583 (ttmm) cc_final: 0.8351 (tttm) REVERT: E 83 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7642 (mt-10) REVERT: E 93 LYS cc_start: 0.8713 (mttt) cc_final: 0.8455 (mtpp) REVERT: E 144 MET cc_start: 0.8411 (mtt) cc_final: 0.7970 (mtt) REVERT: E 194 MET cc_start: 0.7319 (tmm) cc_final: 0.7006 (tmm) REVERT: E 217 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8196 (mm-30) REVERT: E 241 GLU cc_start: 0.7092 (tp30) cc_final: 0.6574 (tp30) REVERT: E 249 LYS cc_start: 0.8183 (tptt) cc_final: 0.7694 (tptt) REVERT: F 39 ASP cc_start: 0.8218 (t0) cc_final: 0.7835 (p0) REVERT: F 42 LYS cc_start: 0.6927 (ttmt) cc_final: 0.6667 (ttmt) REVERT: F 61 PHE cc_start: 0.7833 (m-80) cc_final: 0.7585 (m-80) REVERT: F 119 PHE cc_start: 0.6949 (t80) cc_final: 0.5999 (m-80) REVERT: F 126 LEU cc_start: 0.7913 (tp) cc_final: 0.7677 (pp) REVERT: F 295 LYS cc_start: 0.8350 (tmmt) cc_final: 0.8078 (tmmt) outliers start: 164 outliers final: 74 residues processed: 998 average time/residue: 0.7826 time to fit residues: 919.9954 Evaluate side-chains 975 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 878 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 167 TRP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 275 ASN Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 503 GLN Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 759 ARG Chi-restraints excluded: chain A residue 803 GLN Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 882 ASN Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1209 LEU Chi-restraints excluded: chain A residue 1754 ILE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 435 HIS Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 622 ARG Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 788 MET Chi-restraints excluded: chain B residue 1206 THR Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1573 GLU Chi-restraints excluded: chain B residue 1587 CYS Chi-restraints excluded: chain B residue 1647 SER Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 675 ASP Chi-restraints excluded: chain C residue 678 HIS Chi-restraints excluded: chain C residue 691 LEU Chi-restraints excluded: chain C residue 741 LYS Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 858 VAL Chi-restraints excluded: chain C residue 873 THR Chi-restraints excluded: chain C residue 890 LYS Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 646 MET Chi-restraints excluded: chain D residue 712 HIS Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 751 LYS Chi-restraints excluded: chain D residue 771 MET Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 826 LEU Chi-restraints excluded: chain D residue 848 LEU Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 864 GLU Chi-restraints excluded: chain D residue 879 MET Chi-restraints excluded: chain D residue 894 HIS Chi-restraints excluded: chain D residue 908 ARG Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 274 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 28 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 301 optimal weight: 0.9990 chunk 419 optimal weight: 7.9990 chunk 409 optimal weight: 7.9990 chunk 90 optimal weight: 0.5980 chunk 229 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 192 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1019 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1503 GLN ** A1611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 ASN B 695 GLN B 763 HIS B 798 HIS ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 HIS B1536 GLN B1588 GLN ** B1707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 617 HIS ** C 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 763 GLN ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 617 HIS D 776 HIS ** D 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 915 HIS E 179 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.144617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.119934 restraints weight = 73059.711| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.69 r_work: 0.3579 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 35789 Z= 0.235 Angle : 0.719 13.004 48433 Z= 0.361 Chirality : 0.044 0.195 5550 Planarity : 0.005 0.064 6169 Dihedral : 4.969 52.334 4755 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.34 % Allowed : 20.90 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.03 (0.13), residues: 4311 helix: 1.04 (0.10), residues: 2687 sheet: -0.26 (0.27), residues: 302 loop : 0.43 (0.20), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 208 TYR 0.032 0.002 TYR E 55 PHE 0.034 0.002 PHE B 408 TRP 0.053 0.003 TRP B 441 HIS 0.012 0.001 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00522 (35789) covalent geometry : angle 0.71903 (48433) hydrogen bonds : bond 0.04399 ( 2259) hydrogen bonds : angle 5.09247 ( 6642) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1067 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 897 time to evaluate : 1.400 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: A 119 LEU cc_start: 0.7592 (mt) cc_final: 0.7077 (mt) REVERT: A 122 LEU cc_start: 0.8606 (tm) cc_final: 0.8324 (mm) REVERT: A 123 PHE cc_start: 0.7795 (m-80) cc_final: 0.7284 (m-80) REVERT: A 165 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.7147 (mm) REVERT: A 182 ASN cc_start: 0.8081 (m-40) cc_final: 0.7696 (m-40) REVERT: A 186 PHE cc_start: 0.7964 (m-80) cc_final: 0.7420 (m-80) REVERT: A 190 TYR cc_start: 0.7089 (m-80) cc_final: 0.6864 (m-80) REVERT: A 234 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7351 (tp30) REVERT: A 251 GLU cc_start: 0.8131 (mp0) cc_final: 0.7807 (mp0) REVERT: A 275 ASN cc_start: 0.8370 (t0) cc_final: 0.8107 (t0) REVERT: A 281 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7576 (mm-30) REVERT: A 288 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7197 (t0) REVERT: A 307 HIS cc_start: 0.8326 (m-70) cc_final: 0.8017 (m-70) REVERT: A 325 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7551 (mm-40) REVERT: A 340 LEU cc_start: 0.8874 (mt) cc_final: 0.8552 (mt) REVERT: A 375 LEU cc_start: 0.8390 (mt) cc_final: 0.8170 (mp) REVERT: A 392 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7549 (mm-30) REVERT: A 393 GLU cc_start: 0.7917 (pp20) cc_final: 0.7424 (pp20) REVERT: A 405 GLU cc_start: 0.7863 (tt0) cc_final: 0.7418 (tp30) REVERT: A 467 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7740 (t0) REVERT: A 479 PHE cc_start: 0.7834 (m-80) cc_final: 0.7383 (m-80) REVERT: A 482 GLU cc_start: 0.8101 (tt0) cc_final: 0.7763 (tm-30) REVERT: A 483 GLU cc_start: 0.7736 (mp0) cc_final: 0.7251 (mp0) REVERT: A 498 GLU cc_start: 0.7532 (pp20) cc_final: 0.7296 (pp20) REVERT: A 499 ASP cc_start: 0.7471 (m-30) cc_final: 0.7146 (m-30) REVERT: A 535 MET cc_start: 0.8029 (mtm) cc_final: 0.7555 (mtp) REVERT: A 572 GLN cc_start: 0.8896 (tt0) cc_final: 0.8559 (tm-30) REVERT: A 622 ARG cc_start: 0.8303 (mpp80) cc_final: 0.8033 (mmm-85) REVERT: A 691 ARG cc_start: 0.8514 (ttp80) cc_final: 0.8231 (ttm110) REVERT: A 707 LYS cc_start: 0.9006 (tttt) cc_final: 0.8729 (ttmm) REVERT: A 712 ARG cc_start: 0.8465 (mtt-85) cc_final: 0.8216 (mmm-85) REVERT: A 715 GLU cc_start: 0.7868 (pm20) cc_final: 0.7644 (pm20) REVERT: A 759 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7834 (mmt90) REVERT: A 778 ASN cc_start: 0.8651 (m-40) cc_final: 0.8383 (m110) REVERT: A 779 TYR cc_start: 0.8502 (m-80) cc_final: 0.8297 (m-80) REVERT: A 782 LYS cc_start: 0.8048 (mttt) cc_final: 0.7615 (mppt) REVERT: A 788 MET cc_start: 0.7868 (ttp) cc_final: 0.7558 (ttm) REVERT: A 804 CYS cc_start: 0.8196 (m) cc_final: 0.7722 (m) REVERT: A 880 LYS cc_start: 0.8657 (mttt) cc_final: 0.8281 (ttmm) REVERT: A 919 ASN cc_start: 0.7816 (m-40) cc_final: 0.7497 (m-40) REVERT: A 1016 LYS cc_start: 0.8285 (mttt) cc_final: 0.7899 (tppt) REVERT: A 1024 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7524 (tm-30) REVERT: A 1043 LYS cc_start: 0.8520 (tttm) cc_final: 0.8226 (tmmm) REVERT: A 1239 GLU cc_start: 0.7388 (tp30) cc_final: 0.6896 (tp30) REVERT: A 1243 GLU cc_start: 0.7018 (tp30) cc_final: 0.6559 (tp30) REVERT: A 1495 ILE cc_start: 0.8709 (mm) cc_final: 0.8505 (mp) REVERT: A 1523 GLU cc_start: 0.7655 (pp20) cc_final: 0.7440 (pp20) REVERT: A 1528 GLU cc_start: 0.7344 (pp20) cc_final: 0.6824 (pp20) REVERT: A 1529 ARG cc_start: 0.7669 (tpp-160) cc_final: 0.7242 (tpp-160) REVERT: A 1591 LYS cc_start: 0.8356 (mmmm) cc_final: 0.8013 (mmmm) REVERT: A 1602 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7792 (tt0) REVERT: A 1744 LEU cc_start: 0.8653 (tp) cc_final: 0.8382 (tt) REVERT: B 60 MET cc_start: 0.8269 (tpp) cc_final: 0.8004 (tpp) REVERT: B 136 LEU cc_start: 0.7692 (mp) cc_final: 0.7466 (mm) REVERT: B 144 LYS cc_start: 0.8835 (mtpt) cc_final: 0.8418 (ttmm) REVERT: B 148 ASP cc_start: 0.8395 (m-30) cc_final: 0.7647 (p0) REVERT: B 152 HIS cc_start: 0.7741 (t70) cc_final: 0.7354 (t70) REVERT: B 167 TRP cc_start: 0.7977 (t-100) cc_final: 0.7717 (t60) REVERT: B 186 PHE cc_start: 0.8410 (m-80) cc_final: 0.7689 (m-80) REVERT: B 360 ILE cc_start: 0.8553 (mt) cc_final: 0.8222 (tt) REVERT: B 366 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7598 (tm-30) REVERT: B 380 LEU cc_start: 0.8684 (tp) cc_final: 0.8371 (tp) REVERT: B 451 ARG cc_start: 0.7734 (tpt90) cc_final: 0.7425 (tpt90) REVERT: B 467 ASP cc_start: 0.7970 (t70) cc_final: 0.7735 (t70) REVERT: B 470 SER cc_start: 0.8731 (t) cc_final: 0.8288 (p) REVERT: B 471 PHE cc_start: 0.8700 (t80) cc_final: 0.8463 (t80) REVERT: B 510 GLN cc_start: 0.8305 (mt0) cc_final: 0.7624 (tm-30) REVERT: B 511 LEU cc_start: 0.8738 (tt) cc_final: 0.8259 (tm) REVERT: B 514 ASP cc_start: 0.7720 (m-30) cc_final: 0.7188 (m-30) REVERT: B 528 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6761 (mm) REVERT: B 553 TYR cc_start: 0.7071 (t80) cc_final: 0.6217 (t80) REVERT: B 557 LEU cc_start: 0.8399 (mt) cc_final: 0.7631 (mt) REVERT: B 576 TYR cc_start: 0.7663 (OUTLIER) cc_final: 0.7318 (m-80) REVERT: B 628 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8095 (mtm110) REVERT: B 691 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7794 (mtm-85) REVERT: B 704 LYS cc_start: 0.8673 (mttt) cc_final: 0.8279 (mppt) REVERT: B 761 ASP cc_start: 0.7924 (m-30) cc_final: 0.7605 (m-30) REVERT: B 782 LYS cc_start: 0.8694 (mttt) cc_final: 0.8414 (mtmp) REVERT: B 800 CYS cc_start: 0.7656 (p) cc_final: 0.7376 (p) REVERT: B 880 LYS cc_start: 0.8660 (mptt) cc_final: 0.8423 (mptm) REVERT: B 906 LYS cc_start: 0.8704 (tttm) cc_final: 0.7934 (tttm) REVERT: B 907 ASP cc_start: 0.8010 (p0) cc_final: 0.7711 (p0) REVERT: B 914 LYS cc_start: 0.8967 (tppt) cc_final: 0.8572 (tppt) REVERT: B 917 ARG cc_start: 0.8620 (ttm170) cc_final: 0.7805 (ttm110) REVERT: B 934 ARG cc_start: 0.7141 (ttt-90) cc_final: 0.6751 (ttt-90) REVERT: B 1017 ASN cc_start: 0.8739 (t0) cc_final: 0.8313 (t0) REVERT: B 1028 ASP cc_start: 0.8038 (t70) cc_final: 0.7539 (t0) REVERT: B 1222 ASP cc_start: 0.7866 (m-30) cc_final: 0.7531 (m-30) REVERT: B 1230 GLU cc_start: 0.8167 (mp0) cc_final: 0.7931 (mp0) REVERT: B 1573 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7744 (mp0) REVERT: B 1602 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7699 (mm-30) REVERT: B 1639 ARG cc_start: 0.8022 (ptt180) cc_final: 0.7797 (ptt180) REVERT: B 1656 ASP cc_start: 0.7853 (p0) cc_final: 0.7470 (p0) REVERT: B 1756 GLU cc_start: 0.7583 (pp20) cc_final: 0.7265 (pp20) REVERT: C 13 MET cc_start: 0.7899 (mtm) cc_final: 0.7563 (ttm) REVERT: C 19 LEU cc_start: 0.8778 (mt) cc_final: 0.8533 (mt) REVERT: C 40 MET cc_start: 0.6535 (tmm) cc_final: 0.6304 (tmm) REVERT: C 100 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7678 (tp40) REVERT: C 142 MET cc_start: 0.7720 (mtp) cc_final: 0.7519 (mtm) REVERT: C 232 GLU cc_start: 0.7303 (mp0) cc_final: 0.6934 (mp0) REVERT: C 272 GLU cc_start: 0.7101 (tm-30) cc_final: 0.6706 (tm-30) REVERT: C 605 ASP cc_start: 0.7804 (t70) cc_final: 0.7565 (t0) REVERT: C 688 ILE cc_start: 0.9011 (mt) cc_final: 0.8727 (tp) REVERT: C 689 ARG cc_start: 0.8041 (mmm160) cc_final: 0.7726 (mmm160) REVERT: C 722 LYS cc_start: 0.8472 (tppt) cc_final: 0.7991 (tppp) REVERT: C 725 LYS cc_start: 0.8664 (tmmt) cc_final: 0.8348 (tptp) REVERT: C 736 MET cc_start: 0.8288 (mmm) cc_final: 0.7992 (mmm) REVERT: C 739 GLN cc_start: 0.6924 (tm-30) cc_final: 0.6556 (tm-30) REVERT: C 741 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7824 (tmmm) REVERT: C 746 ASP cc_start: 0.7661 (m-30) cc_final: 0.7401 (m-30) REVERT: C 756 LYS cc_start: 0.8501 (tttt) cc_final: 0.8210 (tmmt) REVERT: C 760 ARG cc_start: 0.7575 (tpm170) cc_final: 0.7336 (tpm170) REVERT: C 799 LYS cc_start: 0.8699 (tttt) cc_final: 0.8227 (tmtp) REVERT: C 806 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7002 (tmm) REVERT: C 807 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.8077 (OUTLIER) REVERT: C 810 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.7917 (mp) REVERT: C 819 ASN cc_start: 0.8438 (t0) cc_final: 0.8156 (t0) REVERT: C 825 GLU cc_start: 0.8284 (pp20) cc_final: 0.8083 (pp20) REVERT: C 830 GLN cc_start: 0.8651 (tp40) cc_final: 0.8312 (mm-40) REVERT: C 842 GLN cc_start: 0.8730 (tp-100) cc_final: 0.8135 (tp40) REVERT: C 846 GLU cc_start: 0.8592 (tt0) cc_final: 0.8214 (mt-10) REVERT: C 852 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8947 (mm) REVERT: C 854 VAL cc_start: 0.8834 (t) cc_final: 0.8616 (p) REVERT: C 857 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7525 (mm-30) REVERT: C 861 LEU cc_start: 0.8495 (mt) cc_final: 0.8258 (mm) REVERT: C 863 LEU cc_start: 0.8825 (tp) cc_final: 0.8538 (tm) REVERT: C 864 GLU cc_start: 0.8344 (tt0) cc_final: 0.7825 (tp30) REVERT: C 874 THR cc_start: 0.7722 (p) cc_final: 0.7307 (t) REVERT: C 878 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7654 (mt-10) REVERT: C 884 TYR cc_start: 0.8602 (t80) cc_final: 0.8332 (t80) REVERT: C 885 ARG cc_start: 0.8538 (mmm160) cc_final: 0.8299 (mmp80) REVERT: C 886 LYS cc_start: 0.8504 (mptt) cc_final: 0.8279 (mmtt) REVERT: C 890 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8793 (ttpp) REVERT: C 906 GLN cc_start: 0.7840 (pp30) cc_final: 0.7459 (pp30) REVERT: C 907 LYS cc_start: 0.8486 (mmmm) cc_final: 0.8233 (mmmm) REVERT: C 924 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8129 (mm) REVERT: C 925 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7811 (mm-30) REVERT: C 961 GLU cc_start: 0.7806 (tp30) cc_final: 0.7449 (tp30) REVERT: D 9 GLU cc_start: 0.8389 (mp0) cc_final: 0.7941 (mp0) REVERT: D 29 PHE cc_start: 0.8579 (t80) cc_final: 0.8175 (t80) REVERT: D 136 LEU cc_start: 0.8988 (tp) cc_final: 0.8744 (tm) REVERT: D 201 SER cc_start: 0.8902 (t) cc_final: 0.8698 (p) REVERT: D 261 LYS cc_start: 0.8796 (tppp) cc_final: 0.8539 (tppp) REVERT: D 629 LYS cc_start: 0.8475 (mmmm) cc_final: 0.8247 (mmmt) REVERT: D 665 ASN cc_start: 0.8585 (m-40) cc_final: 0.8297 (m-40) REVERT: D 691 LEU cc_start: 0.9130 (tp) cc_final: 0.8808 (tm) REVERT: D 694 GLN cc_start: 0.8553 (mm110) cc_final: 0.8121 (mm-40) REVERT: D 712 HIS cc_start: 0.8464 (OUTLIER) cc_final: 0.7304 (t70) REVERT: D 714 LEU cc_start: 0.8910 (mt) cc_final: 0.8602 (mt) REVERT: D 717 ARG cc_start: 0.7920 (tmm160) cc_final: 0.7434 (tmm160) REVERT: D 718 ARG cc_start: 0.8881 (ttm110) cc_final: 0.7963 (ttm110) REVERT: D 721 ARG cc_start: 0.8370 (ptp-110) cc_final: 0.7967 (ptp-110) REVERT: D 749 MET cc_start: 0.8174 (ttp) cc_final: 0.7742 (ttp) REVERT: D 751 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8936 (tppp) REVERT: D 752 VAL cc_start: 0.8925 (t) cc_final: 0.8612 (p) REVERT: D 756 LYS cc_start: 0.8626 (tmmm) cc_final: 0.8203 (tptp) REVERT: D 806 MET cc_start: 0.7397 (ttt) cc_final: 0.6773 (tpp) REVERT: D 842 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7968 (tm-30) REVERT: D 844 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7404 (tm-30) REVERT: D 846 GLU cc_start: 0.8231 (tt0) cc_final: 0.7481 (tp30) REVERT: D 848 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8468 (mt) REVERT: D 852 LEU cc_start: 0.8720 (tp) cc_final: 0.8452 (tm) REVERT: D 857 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: D 860 GLU cc_start: 0.7931 (tp30) cc_final: 0.7411 (tp30) REVERT: D 863 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8415 (mt) REVERT: D 864 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7206 (mm-30) REVERT: D 867 GLN cc_start: 0.8070 (pt0) cc_final: 0.7695 (pt0) REVERT: D 868 ASN cc_start: 0.7411 (m110) cc_final: 0.6888 (m-40) REVERT: D 880 MET cc_start: 0.8413 (mmp) cc_final: 0.7936 (mmp) REVERT: D 886 LYS cc_start: 0.8763 (tptt) cc_final: 0.8461 (ttpp) REVERT: D 887 GLU cc_start: 0.8126 (tp30) cc_final: 0.7473 (tp30) REVERT: D 894 HIS cc_start: 0.7988 (OUTLIER) cc_final: 0.7688 (t-90) REVERT: D 903 ASP cc_start: 0.7986 (m-30) cc_final: 0.7603 (t0) REVERT: D 907 LYS cc_start: 0.8592 (mmtt) cc_final: 0.8236 (mmmm) REVERT: D 908 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7904 (tpt170) REVERT: D 918 LYS cc_start: 0.8589 (tptt) cc_final: 0.8283 (mttm) REVERT: D 920 ASP cc_start: 0.7894 (t70) cc_final: 0.7658 (t0) REVERT: D 925 GLU cc_start: 0.8106 (tp30) cc_final: 0.7802 (tm-30) REVERT: E 25 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7717 (tppp) REVERT: E 30 ILE cc_start: 0.8172 (mt) cc_final: 0.7845 (mt) REVERT: E 34 ASP cc_start: 0.8163 (m-30) cc_final: 0.7876 (m-30) REVERT: E 38 ASP cc_start: 0.7919 (t0) cc_final: 0.7407 (t0) REVERT: E 40 GLU cc_start: 0.7893 (tt0) cc_final: 0.7615 (tt0) REVERT: E 54 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8133 (pmt) REVERT: E 72 GLU cc_start: 0.8014 (tt0) cc_final: 0.7785 (tt0) REVERT: E 79 MET cc_start: 0.7930 (ttp) cc_final: 0.7295 (tmt) REVERT: E 82 LYS cc_start: 0.8589 (ttmm) cc_final: 0.8359 (tttm) REVERT: E 83 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7665 (mt-10) REVERT: E 93 LYS cc_start: 0.8699 (mttt) cc_final: 0.8433 (mtpp) REVERT: E 144 MET cc_start: 0.8451 (mtt) cc_final: 0.8014 (mtt) REVERT: E 159 VAL cc_start: 0.8148 (t) cc_final: 0.7916 (m) REVERT: E 194 MET cc_start: 0.7507 (tmm) cc_final: 0.7200 (tmm) REVERT: E 241 GLU cc_start: 0.7123 (tp30) cc_final: 0.6651 (tp30) REVERT: E 249 LYS cc_start: 0.8139 (tptt) cc_final: 0.7617 (tptt) REVERT: E 258 LYS cc_start: 0.7308 (pttm) cc_final: 0.7106 (pttm) REVERT: F 39 ASP cc_start: 0.8181 (t0) cc_final: 0.7793 (p0) REVERT: F 42 LYS cc_start: 0.7014 (ttmt) cc_final: 0.6714 (ttmt) REVERT: F 61 PHE cc_start: 0.7915 (m-80) cc_final: 0.7659 (m-80) REVERT: F 126 LEU cc_start: 0.7970 (tp) cc_final: 0.7717 (pp) REVERT: F 144 ASN cc_start: 0.3980 (OUTLIER) cc_final: 0.3622 (t0) REVERT: F 264 LYS cc_start: 0.7555 (tptt) cc_final: 0.7177 (tppt) REVERT: F 295 LYS cc_start: 0.8364 (tmmt) cc_final: 0.8040 (tmmt) outliers start: 170 outliers final: 85 residues processed: 990 average time/residue: 0.7650 time to fit residues: 892.9641 Evaluate side-chains 969 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 859 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 503 GLN Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 759 ARG Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 803 GLN Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 882 ASN Chi-restraints excluded: chain A residue 1019 HIS Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1209 LEU Chi-restraints excluded: chain A residue 1585 LYS Chi-restraints excluded: chain A residue 1677 ASP Chi-restraints excluded: chain A residue 1754 ILE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 435 HIS Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 576 TYR Chi-restraints excluded: chain B residue 628 ARG Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 788 MET Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 887 CYS Chi-restraints excluded: chain B residue 1206 THR Chi-restraints excluded: chain B residue 1223 ILE Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1573 GLU Chi-restraints excluded: chain B residue 1647 SER Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 617 HIS Chi-restraints excluded: chain C residue 691 LEU Chi-restraints excluded: chain C residue 741 LYS Chi-restraints excluded: chain C residue 773 THR Chi-restraints excluded: chain C residue 806 MET Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 858 VAL Chi-restraints excluded: chain C residue 873 THR Chi-restraints excluded: chain C residue 890 LYS Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 617 HIS Chi-restraints excluded: chain D residue 646 MET Chi-restraints excluded: chain D residue 712 HIS Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 751 LYS Chi-restraints excluded: chain D residue 771 MET Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 826 LEU Chi-restraints excluded: chain D residue 848 LEU Chi-restraints excluded: chain D residue 857 GLU Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 864 GLU Chi-restraints excluded: chain D residue 879 MET Chi-restraints excluded: chain D residue 894 HIS Chi-restraints excluded: chain D residue 908 ARG Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain F residue 25 PHE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain F residue 274 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 38 optimal weight: 0.5980 chunk 425 optimal weight: 0.9990 chunk 97 optimal weight: 0.4980 chunk 80 optimal weight: 0.4980 chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 275 optimal weight: 0.5980 chunk 131 optimal weight: 0.1980 chunk 85 optimal weight: 0.0970 chunk 392 optimal weight: 0.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN A 444 ASN A 597 HIS A 627 HIS ** A 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1019 HIS ** A1611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 763 HIS B 798 HIS ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 HIS B1588 GLN ** B1681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 617 HIS ** C 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 617 HIS D 776 HIS ** D 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 915 HIS E 179 GLN ** E 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.145780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.121320 restraints weight = 73239.352| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.70 r_work: 0.3591 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 35789 Z= 0.181 Angle : 0.716 12.981 48433 Z= 0.356 Chirality : 0.043 0.184 5550 Planarity : 0.004 0.055 6169 Dihedral : 4.832 50.734 4753 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.14 % Allowed : 22.44 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.12 (0.13), residues: 4311 helix: 1.13 (0.10), residues: 2689 sheet: -0.33 (0.27), residues: 314 loop : 0.47 (0.20), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 115 TYR 0.026 0.002 TYR A 779 PHE 0.032 0.002 PHE B 297 TRP 0.032 0.002 TRP C 103 HIS 0.014 0.001 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00413 (35789) covalent geometry : angle 0.71574 (48433) hydrogen bonds : bond 0.04213 ( 2259) hydrogen bonds : angle 5.01767 ( 6642) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1041 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 879 time to evaluate : 1.394 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: A 119 LEU cc_start: 0.7640 (mt) cc_final: 0.7105 (mt) REVERT: A 122 LEU cc_start: 0.8651 (tm) cc_final: 0.8323 (mm) REVERT: A 123 PHE cc_start: 0.7797 (m-80) cc_final: 0.7323 (m-80) REVERT: A 168 MET cc_start: 0.7778 (mmm) cc_final: 0.7372 (mmm) REVERT: A 182 ASN cc_start: 0.8079 (m-40) cc_final: 0.7695 (m-40) REVERT: A 186 PHE cc_start: 0.7912 (m-80) cc_final: 0.7379 (m-80) REVERT: A 190 TYR cc_start: 0.7057 (m-80) cc_final: 0.6799 (m-80) REVERT: A 197 ARG cc_start: 0.7894 (ttp-110) cc_final: 0.7537 (ttp80) REVERT: A 201 MET cc_start: 0.8039 (ptt) cc_final: 0.7725 (ptt) REVERT: A 234 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7225 (tp30) REVERT: A 251 GLU cc_start: 0.8134 (mp0) cc_final: 0.7812 (mp0) REVERT: A 275 ASN cc_start: 0.8247 (OUTLIER) cc_final: 0.7948 (t0) REVERT: A 282 ASP cc_start: 0.8064 (t0) cc_final: 0.7810 (p0) REVERT: A 307 HIS cc_start: 0.8293 (m-70) cc_final: 0.7972 (m-70) REVERT: A 325 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7538 (mm-40) REVERT: A 340 LEU cc_start: 0.8859 (mt) cc_final: 0.8582 (mt) REVERT: A 392 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7554 (mm-30) REVERT: A 393 GLU cc_start: 0.7960 (pp20) cc_final: 0.7433 (pp20) REVERT: A 405 GLU cc_start: 0.7890 (tt0) cc_final: 0.7405 (tp30) REVERT: A 467 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7709 (t0) REVERT: A 479 PHE cc_start: 0.7820 (m-80) cc_final: 0.7348 (m-80) REVERT: A 482 GLU cc_start: 0.8083 (tt0) cc_final: 0.7699 (tm-30) REVERT: A 483 GLU cc_start: 0.7744 (mp0) cc_final: 0.7273 (mp0) REVERT: A 498 GLU cc_start: 0.7504 (pp20) cc_final: 0.7284 (pp20) REVERT: A 499 ASP cc_start: 0.7389 (m-30) cc_final: 0.7101 (m-30) REVERT: A 517 GLU cc_start: 0.7402 (tm-30) cc_final: 0.7198 (tp30) REVERT: A 535 MET cc_start: 0.7973 (mtm) cc_final: 0.7463 (mtp) REVERT: A 572 GLN cc_start: 0.8894 (tt0) cc_final: 0.8693 (tm-30) REVERT: A 596 LEU cc_start: 0.8896 (tp) cc_final: 0.8554 (tp) REVERT: A 608 SER cc_start: 0.8969 (OUTLIER) cc_final: 0.8684 (p) REVERT: A 622 ARG cc_start: 0.8318 (mpp80) cc_final: 0.8061 (mmm-85) REVERT: A 691 ARG cc_start: 0.8547 (ttp80) cc_final: 0.8259 (ttm110) REVERT: A 707 LYS cc_start: 0.9011 (tttt) cc_final: 0.8738 (ttmm) REVERT: A 712 ARG cc_start: 0.8462 (mtt-85) cc_final: 0.8213 (mmm-85) REVERT: A 715 GLU cc_start: 0.7820 (pm20) cc_final: 0.7586 (pm20) REVERT: A 759 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7798 (mmt90) REVERT: A 778 ASN cc_start: 0.8603 (m-40) cc_final: 0.8323 (m110) REVERT: A 779 TYR cc_start: 0.8477 (m-80) cc_final: 0.8241 (m-80) REVERT: A 782 LYS cc_start: 0.8006 (mttt) cc_final: 0.7600 (mppt) REVERT: A 788 MET cc_start: 0.7859 (ttp) cc_final: 0.7646 (ttm) REVERT: A 793 GLU cc_start: 0.7557 (tp30) cc_final: 0.7270 (tp30) REVERT: A 804 CYS cc_start: 0.8220 (m) cc_final: 0.7702 (m) REVERT: A 880 LYS cc_start: 0.8622 (mttt) cc_final: 0.8253 (ttmm) REVERT: A 919 ASN cc_start: 0.7828 (m-40) cc_final: 0.7572 (m-40) REVERT: A 1016 LYS cc_start: 0.8330 (mttt) cc_final: 0.7919 (tppt) REVERT: A 1024 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7492 (tm-30) REVERT: A 1043 LYS cc_start: 0.8500 (tttm) cc_final: 0.8190 (tmmm) REVERT: A 1213 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: A 1231 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8432 (mm) REVERT: A 1239 GLU cc_start: 0.7352 (tp30) cc_final: 0.6913 (tp30) REVERT: A 1243 GLU cc_start: 0.6970 (tp30) cc_final: 0.6599 (tp30) REVERT: A 1495 ILE cc_start: 0.8688 (mm) cc_final: 0.8487 (mp) REVERT: A 1528 GLU cc_start: 0.7359 (pp20) cc_final: 0.6813 (pp20) REVERT: A 1529 ARG cc_start: 0.7666 (tpp-160) cc_final: 0.7296 (tpp-160) REVERT: A 1588 GLN cc_start: 0.7507 (tm-30) cc_final: 0.7296 (tm-30) REVERT: A 1602 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7760 (tt0) REVERT: A 1679 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7937 (mm-30) REVERT: A 1744 LEU cc_start: 0.8604 (tp) cc_final: 0.8398 (tp) REVERT: A 1756 GLU cc_start: 0.6768 (pp20) cc_final: 0.6479 (pp20) REVERT: B 60 MET cc_start: 0.8216 (tpp) cc_final: 0.7976 (tpp) REVERT: B 106 LYS cc_start: 0.8356 (mtpp) cc_final: 0.7945 (mmmm) REVERT: B 136 LEU cc_start: 0.7679 (mp) cc_final: 0.7476 (mm) REVERT: B 141 GLU cc_start: 0.7666 (tp30) cc_final: 0.7153 (tp30) REVERT: B 144 LYS cc_start: 0.8814 (mtpt) cc_final: 0.8388 (ttmm) REVERT: B 148 ASP cc_start: 0.8407 (m-30) cc_final: 0.7643 (p0) REVERT: B 152 HIS cc_start: 0.7719 (t70) cc_final: 0.7281 (t70) REVERT: B 167 TRP cc_start: 0.7924 (t-100) cc_final: 0.7660 (t60) REVERT: B 186 PHE cc_start: 0.8466 (m-80) cc_final: 0.7676 (m-80) REVERT: B 258 LYS cc_start: 0.8257 (mppt) cc_final: 0.8011 (mttt) REVERT: B 278 HIS cc_start: 0.7457 (t70) cc_final: 0.7079 (t70) REVERT: B 327 MET cc_start: 0.6516 (mmp) cc_final: 0.6154 (mmt) REVERT: B 360 ILE cc_start: 0.8532 (mt) cc_final: 0.8075 (tp) REVERT: B 366 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7582 (tm-30) REVERT: B 380 LEU cc_start: 0.8673 (tp) cc_final: 0.8361 (tp) REVERT: B 426 LEU cc_start: 0.9322 (tp) cc_final: 0.9054 (tm) REVERT: B 467 ASP cc_start: 0.7891 (t70) cc_final: 0.7672 (t0) REVERT: B 470 SER cc_start: 0.8610 (t) cc_final: 0.8207 (p) REVERT: B 471 PHE cc_start: 0.8635 (t80) cc_final: 0.8422 (t80) REVERT: B 510 GLN cc_start: 0.8163 (mt0) cc_final: 0.7522 (tm-30) REVERT: B 511 LEU cc_start: 0.8629 (tt) cc_final: 0.8188 (tm) REVERT: B 514 ASP cc_start: 0.7590 (m-30) cc_final: 0.7085 (m-30) REVERT: B 528 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6738 (mm) REVERT: B 553 TYR cc_start: 0.7043 (t80) cc_final: 0.6164 (t80) REVERT: B 557 LEU cc_start: 0.8400 (mt) cc_final: 0.7616 (mt) REVERT: B 576 TYR cc_start: 0.7701 (OUTLIER) cc_final: 0.7344 (m-80) REVERT: B 585 ARG cc_start: 0.8528 (ttp80) cc_final: 0.8273 (ttp80) REVERT: B 595 GLN cc_start: 0.7788 (tp40) cc_final: 0.7463 (tp-100) REVERT: B 628 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8032 (mtm110) REVERT: B 691 ARG cc_start: 0.8080 (ttm-80) cc_final: 0.7743 (mtm-85) REVERT: B 704 LYS cc_start: 0.8628 (mttt) cc_final: 0.8229 (mppt) REVERT: B 761 ASP cc_start: 0.7911 (m-30) cc_final: 0.7592 (m-30) REVERT: B 762 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8484 (tt) REVERT: B 782 LYS cc_start: 0.8737 (mttt) cc_final: 0.8429 (mtmp) REVERT: B 815 MET cc_start: 0.8814 (mtm) cc_final: 0.8492 (ptp) REVERT: B 880 LYS cc_start: 0.8641 (mptt) cc_final: 0.8432 (mptm) REVERT: B 906 LYS cc_start: 0.8646 (tttm) cc_final: 0.7629 (tttm) REVERT: B 907 ASP cc_start: 0.8116 (p0) cc_final: 0.7717 (p0) REVERT: B 914 LYS cc_start: 0.9007 (tppt) cc_final: 0.8599 (tppt) REVERT: B 917 ARG cc_start: 0.8630 (ttm170) cc_final: 0.7899 (ttm110) REVERT: B 934 ARG cc_start: 0.7075 (ttt-90) cc_final: 0.6800 (ttt-90) REVERT: B 1017 ASN cc_start: 0.8765 (t0) cc_final: 0.8334 (t0) REVERT: B 1028 ASP cc_start: 0.8051 (t70) cc_final: 0.7564 (t0) REVERT: B 1222 ASP cc_start: 0.7892 (m-30) cc_final: 0.7600 (m-30) REVERT: B 1230 GLU cc_start: 0.8157 (mp0) cc_final: 0.7900 (mp0) REVERT: B 1573 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: B 1602 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7675 (mm-30) REVERT: B 1639 ARG cc_start: 0.7963 (ptt180) cc_final: 0.7683 (ptt180) REVERT: B 1656 ASP cc_start: 0.7875 (p0) cc_final: 0.7515 (p0) REVERT: B 1756 GLU cc_start: 0.7543 (pp20) cc_final: 0.7188 (pp20) REVERT: C 10 LEU cc_start: 0.8844 (mm) cc_final: 0.8618 (mp) REVERT: C 13 MET cc_start: 0.7894 (mtm) cc_final: 0.7558 (ttm) REVERT: C 232 GLU cc_start: 0.7328 (mp0) cc_final: 0.6976 (mp0) REVERT: C 272 GLU cc_start: 0.7026 (tm-30) cc_final: 0.6623 (tm-30) REVERT: C 688 ILE cc_start: 0.8988 (mt) cc_final: 0.8610 (tp) REVERT: C 689 ARG cc_start: 0.7996 (mmm160) cc_final: 0.7558 (mmp80) REVERT: C 722 LYS cc_start: 0.8475 (tppt) cc_final: 0.8155 (tppp) REVERT: C 725 LYS cc_start: 0.8665 (tmmt) cc_final: 0.8365 (tptp) REVERT: C 736 MET cc_start: 0.8238 (mmm) cc_final: 0.7939 (mmm) REVERT: C 739 GLN cc_start: 0.6940 (tm-30) cc_final: 0.6685 (tm-30) REVERT: C 741 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7798 (tmmm) REVERT: C 746 ASP cc_start: 0.7653 (m-30) cc_final: 0.7362 (m-30) REVERT: C 750 TRP cc_start: 0.6952 (m100) cc_final: 0.6689 (m100) REVERT: C 756 LYS cc_start: 0.8478 (tttt) cc_final: 0.8169 (tmmt) REVERT: C 799 LYS cc_start: 0.8744 (tttt) cc_final: 0.8324 (tmtp) REVERT: C 806 MET cc_start: 0.8142 (ttt) cc_final: 0.6965 (tmm) REVERT: C 807 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.8039 (OUTLIER) REVERT: C 810 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.7864 (mp) REVERT: C 819 ASN cc_start: 0.8464 (t0) cc_final: 0.8187 (t0) REVERT: C 830 GLN cc_start: 0.8673 (tp40) cc_final: 0.8356 (mm-40) REVERT: C 842 GLN cc_start: 0.8723 (tp-100) cc_final: 0.8165 (tp40) REVERT: C 846 GLU cc_start: 0.8587 (tt0) cc_final: 0.8181 (mt-10) REVERT: C 852 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8952 (mm) REVERT: C 854 VAL cc_start: 0.8838 (t) cc_final: 0.8630 (p) REVERT: C 857 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7530 (mm-30) REVERT: C 861 LEU cc_start: 0.8495 (mt) cc_final: 0.8250 (mm) REVERT: C 863 LEU cc_start: 0.8828 (tp) cc_final: 0.8554 (tm) REVERT: C 864 GLU cc_start: 0.8351 (tt0) cc_final: 0.7829 (tp30) REVERT: C 874 THR cc_start: 0.7649 (p) cc_final: 0.7222 (t) REVERT: C 878 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7611 (mt-10) REVERT: C 880 MET cc_start: 0.8177 (mtp) cc_final: 0.7943 (mtm) REVERT: C 884 TYR cc_start: 0.8566 (t80) cc_final: 0.8328 (t80) REVERT: C 885 ARG cc_start: 0.8542 (mmm160) cc_final: 0.8298 (mmp80) REVERT: C 886 LYS cc_start: 0.8499 (mptt) cc_final: 0.8282 (mmtt) REVERT: C 890 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8840 (ttpp) REVERT: C 906 GLN cc_start: 0.7778 (pp30) cc_final: 0.7369 (pp30) REVERT: C 907 LYS cc_start: 0.8497 (mmmm) cc_final: 0.8231 (mmmm) REVERT: C 924 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8112 (mm) REVERT: C 925 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7816 (mm-30) REVERT: C 961 GLU cc_start: 0.7832 (tp30) cc_final: 0.7387 (tp30) REVERT: D 9 GLU cc_start: 0.8382 (mp0) cc_final: 0.7918 (mp0) REVERT: D 29 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.8162 (t80) REVERT: D 75 ARG cc_start: 0.7867 (tpp-160) cc_final: 0.7345 (mmp80) REVERT: D 136 LEU cc_start: 0.8971 (tp) cc_final: 0.8722 (tm) REVERT: D 261 LYS cc_start: 0.8790 (tppp) cc_final: 0.8389 (tppt) REVERT: D 646 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7713 (tmm) REVERT: D 650 ASP cc_start: 0.8216 (p0) cc_final: 0.7427 (p0) REVERT: D 665 ASN cc_start: 0.8601 (m-40) cc_final: 0.8292 (m-40) REVERT: D 691 LEU cc_start: 0.9107 (tp) cc_final: 0.8799 (tm) REVERT: D 694 GLN cc_start: 0.8513 (mm110) cc_final: 0.8089 (mm-40) REVERT: D 712 HIS cc_start: 0.8436 (OUTLIER) cc_final: 0.7281 (t70) REVERT: D 714 LEU cc_start: 0.8891 (mt) cc_final: 0.8579 (mt) REVERT: D 717 ARG cc_start: 0.7948 (tmm160) cc_final: 0.7360 (tmm160) REVERT: D 721 ARG cc_start: 0.8420 (ptp-110) cc_final: 0.7936 (ptp-110) REVERT: D 749 MET cc_start: 0.8122 (ttp) cc_final: 0.7716 (ttp) REVERT: D 751 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8254 (tppt) REVERT: D 752 VAL cc_start: 0.8859 (t) cc_final: 0.8590 (p) REVERT: D 756 LYS cc_start: 0.8577 (tmmm) cc_final: 0.8206 (tptp) REVERT: D 806 MET cc_start: 0.7353 (ttt) cc_final: 0.6754 (tpp) REVERT: D 842 GLN cc_start: 0.8299 (tm-30) cc_final: 0.7859 (tm-30) REVERT: D 844 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7441 (tm-30) REVERT: D 846 GLU cc_start: 0.8208 (tt0) cc_final: 0.7455 (tp30) REVERT: D 848 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8426 (mt) REVERT: D 852 LEU cc_start: 0.8728 (tp) cc_final: 0.8463 (tm) REVERT: D 860 GLU cc_start: 0.7946 (tp30) cc_final: 0.7425 (tp30) REVERT: D 863 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8412 (mt) REVERT: D 864 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7229 (mm-30) REVERT: D 867 GLN cc_start: 0.8041 (pt0) cc_final: 0.7634 (pt0) REVERT: D 868 ASN cc_start: 0.7384 (m110) cc_final: 0.6767 (m-40) REVERT: D 879 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8452 (tpp) REVERT: D 880 MET cc_start: 0.8403 (mmp) cc_final: 0.7914 (mmp) REVERT: D 886 LYS cc_start: 0.8738 (tptt) cc_final: 0.8454 (ttpp) REVERT: D 887 GLU cc_start: 0.8121 (tp30) cc_final: 0.7455 (tp30) REVERT: D 894 HIS cc_start: 0.7996 (OUTLIER) cc_final: 0.7705 (t-90) REVERT: D 903 ASP cc_start: 0.7924 (m-30) cc_final: 0.7557 (t0) REVERT: D 907 LYS cc_start: 0.8585 (mmtt) cc_final: 0.8239 (mmmm) REVERT: D 908 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7894 (tpt170) REVERT: D 918 LYS cc_start: 0.8577 (tptt) cc_final: 0.8289 (mttp) REVERT: D 920 ASP cc_start: 0.7894 (t70) cc_final: 0.7637 (t0) REVERT: D 925 GLU cc_start: 0.8077 (tp30) cc_final: 0.7822 (tm-30) REVERT: E 30 ILE cc_start: 0.8120 (mt) cc_final: 0.7790 (mt) REVERT: E 34 ASP cc_start: 0.8146 (m-30) cc_final: 0.7870 (m-30) REVERT: E 38 ASP cc_start: 0.7879 (t0) cc_final: 0.7381 (t0) REVERT: E 40 GLU cc_start: 0.7857 (tt0) cc_final: 0.7596 (tt0) REVERT: E 72 GLU cc_start: 0.8017 (tt0) cc_final: 0.7772 (tt0) REVERT: E 79 MET cc_start: 0.7902 (ttp) cc_final: 0.7221 (tmt) REVERT: E 82 LYS cc_start: 0.8575 (ttmm) cc_final: 0.8363 (tttm) REVERT: E 83 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7619 (mt-10) REVERT: E 93 LYS cc_start: 0.8751 (mttt) cc_final: 0.8487 (mtpp) REVERT: E 144 MET cc_start: 0.8396 (mtt) cc_final: 0.7983 (mtt) REVERT: E 159 VAL cc_start: 0.8131 (t) cc_final: 0.7916 (m) REVERT: E 194 MET cc_start: 0.7473 (tmm) cc_final: 0.7186 (tmm) REVERT: E 241 GLU cc_start: 0.7119 (tp30) cc_final: 0.6656 (tp30) REVERT: E 249 LYS cc_start: 0.8172 (tptt) cc_final: 0.7679 (tptt) REVERT: F 42 LYS cc_start: 0.7148 (ttmt) cc_final: 0.6799 (ttmt) REVERT: F 61 PHE cc_start: 0.7938 (m-80) cc_final: 0.7674 (m-80) REVERT: F 126 LEU cc_start: 0.7999 (tp) cc_final: 0.7780 (pp) REVERT: F 144 ASN cc_start: 0.4057 (OUTLIER) cc_final: 0.3699 (t0) REVERT: F 264 LYS cc_start: 0.7764 (tptt) cc_final: 0.7458 (mmmt) REVERT: F 295 LYS cc_start: 0.8535 (tmmt) cc_final: 0.8180 (tmmt) outliers start: 162 outliers final: 79 residues processed: 963 average time/residue: 0.7595 time to fit residues: 863.6096 Evaluate side-chains 961 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 855 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 275 ASN Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 503 GLN Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 759 ARG Chi-restraints excluded: chain A residue 803 GLN Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 882 ASN Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1209 LEU Chi-restraints excluded: chain A residue 1213 GLU Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain A residue 1559 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 435 HIS Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 576 TYR Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 628 ARG Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 788 MET Chi-restraints excluded: chain B residue 887 CYS Chi-restraints excluded: chain B residue 1206 THR Chi-restraints excluded: chain B residue 1223 ILE Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1573 GLU Chi-restraints excluded: chain B residue 1587 CYS Chi-restraints excluded: chain B residue 1647 SER Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 71 HIS Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 675 ASP Chi-restraints excluded: chain C residue 691 LEU Chi-restraints excluded: chain C residue 741 LYS Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 826 LEU Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 858 VAL Chi-restraints excluded: chain C residue 873 THR Chi-restraints excluded: chain C residue 890 LYS Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 646 MET Chi-restraints excluded: chain D residue 712 HIS Chi-restraints excluded: chain D residue 751 LYS Chi-restraints excluded: chain D residue 771 MET Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 823 HIS Chi-restraints excluded: chain D residue 826 LEU Chi-restraints excluded: chain D residue 827 LEU Chi-restraints excluded: chain D residue 848 LEU Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 864 GLU Chi-restraints excluded: chain D residue 879 MET Chi-restraints excluded: chain D residue 894 HIS Chi-restraints excluded: chain D residue 908 ARG Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 175 LYS Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain F residue 25 PHE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain F residue 274 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 314 optimal weight: 0.9980 chunk 204 optimal weight: 0.4980 chunk 347 optimal weight: 0.6980 chunk 403 optimal weight: 0.9990 chunk 306 optimal weight: 0.9980 chunk 206 optimal weight: 0.0770 chunk 50 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 177 optimal weight: 0.4980 chunk 47 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN A 444 ASN ** A 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1019 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 GLN B 486 ASN B 763 HIS B 798 HIS ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 HIS B1588 GLN ** B1681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 617 HIS ** C 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 HIS D 617 HIS D 694 GLN ** D 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 776 HIS D 823 HIS D 915 HIS E 179 GLN ** E 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.145295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.120561 restraints weight = 73408.853| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.70 r_work: 0.3582 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 35789 Z= 0.200 Angle : 0.730 13.481 48433 Z= 0.363 Chirality : 0.044 0.214 5550 Planarity : 0.004 0.056 6169 Dihedral : 4.737 50.755 4750 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.01 % Allowed : 23.61 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.10 (0.13), residues: 4311 helix: 1.12 (0.10), residues: 2690 sheet: -0.44 (0.27), residues: 312 loop : 0.48 (0.20), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 208 TYR 0.024 0.002 TYR A 779 PHE 0.031 0.002 PHE B1606 TRP 0.036 0.003 TRP C 103 HIS 0.017 0.001 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00452 (35789) covalent geometry : angle 0.72976 (48433) hydrogen bonds : bond 0.04197 ( 2259) hydrogen bonds : angle 5.01723 ( 6642) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 883 time to evaluate : 1.496 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: A 119 LEU cc_start: 0.7670 (mt) cc_final: 0.7159 (mt) REVERT: A 122 LEU cc_start: 0.8634 (tm) cc_final: 0.8218 (mm) REVERT: A 123 PHE cc_start: 0.7818 (m-80) cc_final: 0.7359 (m-80) REVERT: A 165 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7222 (mm) REVERT: A 182 ASN cc_start: 0.8104 (m-40) cc_final: 0.7720 (m-40) REVERT: A 186 PHE cc_start: 0.7922 (m-80) cc_final: 0.7384 (m-80) REVERT: A 190 TYR cc_start: 0.7078 (m-80) cc_final: 0.6832 (m-80) REVERT: A 216 GLU cc_start: 0.7992 (tt0) cc_final: 0.7292 (tp30) REVERT: A 234 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7387 (tp30) REVERT: A 251 GLU cc_start: 0.8162 (mp0) cc_final: 0.7836 (mp0) REVERT: A 275 ASN cc_start: 0.8054 (OUTLIER) cc_final: 0.7801 (t0) REVERT: A 279 LEU cc_start: 0.8268 (mt) cc_final: 0.7673 (mt) REVERT: A 282 ASP cc_start: 0.8049 (t0) cc_final: 0.7698 (p0) REVERT: A 307 HIS cc_start: 0.8294 (m-70) cc_final: 0.7974 (m-70) REVERT: A 325 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7625 (mp10) REVERT: A 340 LEU cc_start: 0.8890 (mt) cc_final: 0.8644 (mt) REVERT: A 392 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7559 (mm-30) REVERT: A 393 GLU cc_start: 0.7981 (pp20) cc_final: 0.7487 (pp20) REVERT: A 405 GLU cc_start: 0.7919 (tt0) cc_final: 0.7445 (tp30) REVERT: A 467 ASP cc_start: 0.8075 (t70) cc_final: 0.7860 (p0) REVERT: A 482 GLU cc_start: 0.8114 (tt0) cc_final: 0.7725 (tm-30) REVERT: A 483 GLU cc_start: 0.7758 (mp0) cc_final: 0.7278 (mp0) REVERT: A 498 GLU cc_start: 0.7518 (pp20) cc_final: 0.7230 (pp20) REVERT: A 499 ASP cc_start: 0.7372 (m-30) cc_final: 0.7060 (m-30) REVERT: A 535 MET cc_start: 0.7986 (mtm) cc_final: 0.7514 (mtp) REVERT: A 596 LEU cc_start: 0.8884 (tp) cc_final: 0.8538 (tp) REVERT: A 608 SER cc_start: 0.8991 (OUTLIER) cc_final: 0.8676 (p) REVERT: A 622 ARG cc_start: 0.8356 (mpp80) cc_final: 0.8094 (mmm-85) REVERT: A 691 ARG cc_start: 0.8563 (ttp80) cc_final: 0.8296 (ttm110) REVERT: A 707 LYS cc_start: 0.9022 (tttt) cc_final: 0.8654 (ttmm) REVERT: A 715 GLU cc_start: 0.7836 (pm20) cc_final: 0.7583 (pm20) REVERT: A 741 LEU cc_start: 0.8081 (mp) cc_final: 0.7863 (mt) REVERT: A 759 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7819 (mmt90) REVERT: A 778 ASN cc_start: 0.8591 (m-40) cc_final: 0.8327 (m110) REVERT: A 779 TYR cc_start: 0.8453 (m-80) cc_final: 0.8239 (m-80) REVERT: A 782 LYS cc_start: 0.8043 (mttt) cc_final: 0.7638 (mppt) REVERT: A 788 MET cc_start: 0.7835 (ttp) cc_final: 0.7624 (ttm) REVERT: A 804 CYS cc_start: 0.8226 (m) cc_final: 0.7746 (m) REVERT: A 880 LYS cc_start: 0.8663 (mttt) cc_final: 0.8305 (ttmm) REVERT: A 919 ASN cc_start: 0.7853 (m-40) cc_final: 0.7549 (m-40) REVERT: A 1016 LYS cc_start: 0.8381 (mttt) cc_final: 0.7972 (tppt) REVERT: A 1024 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7491 (tm-30) REVERT: A 1037 ASN cc_start: 0.8378 (m-40) cc_final: 0.8016 (m-40) REVERT: A 1043 LYS cc_start: 0.8494 (tttm) cc_final: 0.8137 (ttpp) REVERT: A 1231 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8435 (mm) REVERT: A 1239 GLU cc_start: 0.7352 (tp30) cc_final: 0.6987 (tp30) REVERT: A 1243 GLU cc_start: 0.6946 (tp30) cc_final: 0.6619 (tp30) REVERT: A 1528 GLU cc_start: 0.7384 (pp20) cc_final: 0.6829 (pp20) REVERT: A 1529 ARG cc_start: 0.7675 (tpp-160) cc_final: 0.7308 (tpp-160) REVERT: A 1580 ARG cc_start: 0.8130 (ptm-80) cc_final: 0.7792 (ttm170) REVERT: A 1588 GLN cc_start: 0.7545 (tm-30) cc_final: 0.7344 (tm-30) REVERT: A 1602 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7748 (tt0) REVERT: A 1679 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7979 (mm-30) REVERT: A 1744 LEU cc_start: 0.8567 (tp) cc_final: 0.8192 (tt) REVERT: A 1756 GLU cc_start: 0.6835 (pp20) cc_final: 0.6471 (pp20) REVERT: B 60 MET cc_start: 0.8238 (tpp) cc_final: 0.7970 (tpp) REVERT: B 74 GLU cc_start: 0.6243 (OUTLIER) cc_final: 0.3594 (mt-10) REVERT: B 136 LEU cc_start: 0.7710 (mp) cc_final: 0.7499 (mm) REVERT: B 144 LYS cc_start: 0.8752 (mtpt) cc_final: 0.8344 (ttmm) REVERT: B 148 ASP cc_start: 0.8400 (m-30) cc_final: 0.7587 (p0) REVERT: B 151 ARG cc_start: 0.7909 (ptm160) cc_final: 0.6864 (ptm160) REVERT: B 152 HIS cc_start: 0.7708 (t70) cc_final: 0.7259 (t70) REVERT: B 167 TRP cc_start: 0.7857 (t-100) cc_final: 0.7576 (t60) REVERT: B 186 PHE cc_start: 0.8526 (m-80) cc_final: 0.7755 (m-80) REVERT: B 258 LYS cc_start: 0.8269 (mppt) cc_final: 0.8058 (ptpt) REVERT: B 278 HIS cc_start: 0.7553 (t70) cc_final: 0.7143 (t70) REVERT: B 360 ILE cc_start: 0.8550 (mt) cc_final: 0.8121 (tp) REVERT: B 366 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7594 (tm-30) REVERT: B 380 LEU cc_start: 0.8652 (tp) cc_final: 0.8347 (tp) REVERT: B 426 LEU cc_start: 0.9303 (tp) cc_final: 0.9017 (tm) REVERT: B 451 ARG cc_start: 0.7447 (tpt90) cc_final: 0.7151 (tpt90) REVERT: B 467 ASP cc_start: 0.7866 (t70) cc_final: 0.7659 (t70) REVERT: B 470 SER cc_start: 0.8639 (t) cc_final: 0.8241 (p) REVERT: B 471 PHE cc_start: 0.8675 (t80) cc_final: 0.8461 (t80) REVERT: B 510 GLN cc_start: 0.8194 (mt0) cc_final: 0.7565 (tm-30) REVERT: B 511 LEU cc_start: 0.8572 (tt) cc_final: 0.8116 (tm) REVERT: B 514 ASP cc_start: 0.7538 (m-30) cc_final: 0.7026 (m-30) REVERT: B 528 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6574 (mm) REVERT: B 553 TYR cc_start: 0.7047 (t80) cc_final: 0.6225 (t80) REVERT: B 557 LEU cc_start: 0.8362 (mt) cc_final: 0.7551 (mt) REVERT: B 576 TYR cc_start: 0.7767 (OUTLIER) cc_final: 0.7275 (m-80) REVERT: B 585 ARG cc_start: 0.8589 (ttp80) cc_final: 0.8291 (ttp80) REVERT: B 595 GLN cc_start: 0.7731 (tp40) cc_final: 0.7396 (tp-100) REVERT: B 628 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8056 (mtm110) REVERT: B 691 ARG cc_start: 0.8084 (ttm-80) cc_final: 0.7779 (mtm-85) REVERT: B 704 LYS cc_start: 0.8624 (mttt) cc_final: 0.8244 (mppt) REVERT: B 757 PHE cc_start: 0.7870 (t80) cc_final: 0.7630 (t80) REVERT: B 761 ASP cc_start: 0.7919 (m-30) cc_final: 0.7588 (m-30) REVERT: B 762 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8489 (tt) REVERT: B 782 LYS cc_start: 0.8743 (mttt) cc_final: 0.8447 (mtmp) REVERT: B 800 CYS cc_start: 0.7644 (p) cc_final: 0.7406 (p) REVERT: B 815 MET cc_start: 0.8798 (mtm) cc_final: 0.8485 (ptp) REVERT: B 880 LYS cc_start: 0.8674 (mptt) cc_final: 0.8466 (mptm) REVERT: B 906 LYS cc_start: 0.8661 (tttm) cc_final: 0.7565 (tttp) REVERT: B 907 ASP cc_start: 0.8122 (p0) cc_final: 0.7691 (p0) REVERT: B 914 LYS cc_start: 0.9008 (tppt) cc_final: 0.8630 (tppt) REVERT: B 917 ARG cc_start: 0.8687 (ttm170) cc_final: 0.7881 (ttm110) REVERT: B 919 ASN cc_start: 0.8347 (m-40) cc_final: 0.7904 (m110) REVERT: B 934 ARG cc_start: 0.7105 (ttt-90) cc_final: 0.6836 (ttt-90) REVERT: B 1017 ASN cc_start: 0.8714 (t0) cc_final: 0.8298 (t0) REVERT: B 1028 ASP cc_start: 0.8055 (t70) cc_final: 0.7603 (t0) REVERT: B 1222 ASP cc_start: 0.7917 (m-30) cc_final: 0.7627 (m-30) REVERT: B 1230 GLU cc_start: 0.8164 (mp0) cc_final: 0.7911 (mp0) REVERT: B 1573 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7829 (mp0) REVERT: B 1602 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7709 (mm-30) REVERT: B 1639 ARG cc_start: 0.7970 (ptt180) cc_final: 0.7677 (ptt180) REVERT: B 1656 ASP cc_start: 0.7902 (p0) cc_final: 0.7535 (p0) REVERT: B 1756 GLU cc_start: 0.7590 (pp20) cc_final: 0.7208 (pp20) REVERT: C 13 MET cc_start: 0.7883 (mtm) cc_final: 0.7540 (ttm) REVERT: C 223 MET cc_start: 0.7857 (ttm) cc_final: 0.7633 (mtp) REVERT: C 232 GLU cc_start: 0.7345 (mp0) cc_final: 0.6987 (mp0) REVERT: C 272 GLU cc_start: 0.7101 (tm-30) cc_final: 0.6671 (tm-30) REVERT: C 688 ILE cc_start: 0.8997 (mt) cc_final: 0.8587 (tp) REVERT: C 689 ARG cc_start: 0.8012 (mmm160) cc_final: 0.7563 (mmp80) REVERT: C 722 LYS cc_start: 0.8574 (tppt) cc_final: 0.8243 (tppp) REVERT: C 736 MET cc_start: 0.8211 (mmm) cc_final: 0.7936 (mmm) REVERT: C 739 GLN cc_start: 0.6968 (tm-30) cc_final: 0.6712 (tm-30) REVERT: C 741 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7786 (tmmm) REVERT: C 746 ASP cc_start: 0.7645 (m-30) cc_final: 0.7350 (m-30) REVERT: C 750 TRP cc_start: 0.6821 (m100) cc_final: 0.6587 (m100) REVERT: C 756 LYS cc_start: 0.8487 (tttt) cc_final: 0.8188 (tmmt) REVERT: C 799 LYS cc_start: 0.8763 (tttt) cc_final: 0.8337 (tmtp) REVERT: C 806 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.6856 (tmm) REVERT: C 807 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.8008 (OUTLIER) REVERT: C 810 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.7226 (mm) REVERT: C 819 ASN cc_start: 0.8499 (t0) cc_final: 0.8235 (t0) REVERT: C 825 GLU cc_start: 0.8114 (pp20) cc_final: 0.7841 (pp20) REVERT: C 830 GLN cc_start: 0.8701 (tp40) cc_final: 0.8406 (mm-40) REVERT: C 842 GLN cc_start: 0.8730 (tp-100) cc_final: 0.8149 (tp40) REVERT: C 846 GLU cc_start: 0.8575 (tt0) cc_final: 0.8198 (mt-10) REVERT: C 852 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8972 (mm) REVERT: C 854 VAL cc_start: 0.8859 (t) cc_final: 0.8653 (p) REVERT: C 857 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7549 (mm-30) REVERT: C 861 LEU cc_start: 0.8513 (mt) cc_final: 0.8270 (mm) REVERT: C 863 LEU cc_start: 0.8849 (tp) cc_final: 0.8570 (tm) REVERT: C 864 GLU cc_start: 0.8394 (tt0) cc_final: 0.7863 (tp30) REVERT: C 874 THR cc_start: 0.7665 (p) cc_final: 0.7258 (t) REVERT: C 878 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7636 (mt-10) REVERT: C 884 TYR cc_start: 0.8580 (t80) cc_final: 0.8338 (t80) REVERT: C 885 ARG cc_start: 0.8560 (mmm160) cc_final: 0.8317 (mmp80) REVERT: C 890 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8799 (ttpp) REVERT: C 906 GLN cc_start: 0.7788 (pp30) cc_final: 0.7442 (pp30) REVERT: C 907 LYS cc_start: 0.8503 (mmmm) cc_final: 0.8220 (mmmm) REVERT: C 924 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8122 (mm) REVERT: C 925 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7852 (mm-30) REVERT: C 961 GLU cc_start: 0.7821 (tp30) cc_final: 0.7370 (tp30) REVERT: D 9 GLU cc_start: 0.8407 (mp0) cc_final: 0.7990 (mp0) REVERT: D 29 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.8151 (t80) REVERT: D 64 LEU cc_start: 0.7735 (tp) cc_final: 0.7409 (tp) REVERT: D 136 LEU cc_start: 0.8944 (tp) cc_final: 0.8711 (tm) REVERT: D 261 LYS cc_start: 0.8787 (tppp) cc_final: 0.8481 (tppp) REVERT: D 629 LYS cc_start: 0.8469 (mmmt) cc_final: 0.7812 (mmmt) REVERT: D 646 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7705 (tmm) REVERT: D 650 ASP cc_start: 0.8150 (p0) cc_final: 0.7307 (p0) REVERT: D 665 ASN cc_start: 0.8584 (m-40) cc_final: 0.8265 (m-40) REVERT: D 691 LEU cc_start: 0.9128 (tp) cc_final: 0.8827 (tm) REVERT: D 694 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8099 (mm-40) REVERT: D 705 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8158 (tm-30) REVERT: D 712 HIS cc_start: 0.8421 (OUTLIER) cc_final: 0.7290 (t70) REVERT: D 714 LEU cc_start: 0.8888 (mt) cc_final: 0.8592 (mt) REVERT: D 717 ARG cc_start: 0.7953 (tmm160) cc_final: 0.7350 (tmm160) REVERT: D 721 ARG cc_start: 0.8448 (ptp-110) cc_final: 0.7937 (ptp-110) REVERT: D 749 MET cc_start: 0.8142 (ttp) cc_final: 0.7709 (ttp) REVERT: D 751 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8327 (tppt) REVERT: D 752 VAL cc_start: 0.8845 (t) cc_final: 0.8562 (p) REVERT: D 756 LYS cc_start: 0.8587 (tmmm) cc_final: 0.8205 (tptp) REVERT: D 766 GLU cc_start: 0.8451 (tm-30) cc_final: 0.7992 (tm-30) REVERT: D 806 MET cc_start: 0.7279 (ttt) cc_final: 0.6724 (tpp) REVERT: D 842 GLN cc_start: 0.8280 (tm-30) cc_final: 0.7953 (tm-30) REVERT: D 844 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7453 (tm-30) REVERT: D 846 GLU cc_start: 0.8221 (tt0) cc_final: 0.7480 (tp30) REVERT: D 848 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8473 (mt) REVERT: D 852 LEU cc_start: 0.8747 (tp) cc_final: 0.8484 (tm) REVERT: D 857 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7790 (mm-30) REVERT: D 860 GLU cc_start: 0.7950 (tp30) cc_final: 0.7626 (tp30) REVERT: D 863 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8445 (mt) REVERT: D 864 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7241 (mm-30) REVERT: D 867 GLN cc_start: 0.8031 (pt0) cc_final: 0.7640 (pt0) REVERT: D 868 ASN cc_start: 0.7386 (m110) cc_final: 0.6870 (m-40) REVERT: D 880 MET cc_start: 0.8421 (mmp) cc_final: 0.8074 (mmp) REVERT: D 885 ARG cc_start: 0.7642 (mtp85) cc_final: 0.7376 (mtp85) REVERT: D 886 LYS cc_start: 0.8744 (tptt) cc_final: 0.8464 (ttpp) REVERT: D 887 GLU cc_start: 0.8124 (tp30) cc_final: 0.7483 (tp30) REVERT: D 903 ASP cc_start: 0.7933 (m-30) cc_final: 0.7571 (t0) REVERT: D 907 LYS cc_start: 0.8599 (mmtt) cc_final: 0.8256 (mmmm) REVERT: D 918 LYS cc_start: 0.8569 (tptt) cc_final: 0.8295 (mttp) REVERT: D 920 ASP cc_start: 0.7900 (t70) cc_final: 0.7656 (t0) REVERT: D 925 GLU cc_start: 0.8112 (tp30) cc_final: 0.7853 (tm-30) REVERT: D 961 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7784 (pp20) REVERT: E 30 ILE cc_start: 0.8147 (mt) cc_final: 0.7825 (mt) REVERT: E 34 ASP cc_start: 0.8162 (m-30) cc_final: 0.7908 (m-30) REVERT: E 38 ASP cc_start: 0.7923 (t0) cc_final: 0.7429 (t0) REVERT: E 40 GLU cc_start: 0.7910 (tt0) cc_final: 0.7647 (tt0) REVERT: E 72 GLU cc_start: 0.8068 (tt0) cc_final: 0.7835 (tt0) REVERT: E 79 MET cc_start: 0.7920 (ttp) cc_final: 0.7281 (tmt) REVERT: E 82 LYS cc_start: 0.8597 (ttmm) cc_final: 0.8396 (tttm) REVERT: E 83 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7651 (mt-10) REVERT: E 93 LYS cc_start: 0.8712 (mttt) cc_final: 0.8443 (mtpp) REVERT: E 144 MET cc_start: 0.8427 (mtt) cc_final: 0.7988 (mtt) REVERT: E 159 VAL cc_start: 0.8161 (t) cc_final: 0.7946 (m) REVERT: E 194 MET cc_start: 0.7553 (tmm) cc_final: 0.7291 (tmm) REVERT: E 241 GLU cc_start: 0.7151 (tp30) cc_final: 0.6701 (tp30) REVERT: E 249 LYS cc_start: 0.8177 (tptt) cc_final: 0.7676 (tptt) REVERT: E 251 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7768 (tpt) REVERT: F 29 MET cc_start: 0.6844 (tpt) cc_final: 0.6549 (tpp) REVERT: F 42 LYS cc_start: 0.7231 (ttmt) cc_final: 0.6909 (ttmt) REVERT: F 61 PHE cc_start: 0.7986 (m-80) cc_final: 0.7766 (m-80) REVERT: F 126 LEU cc_start: 0.7994 (tp) cc_final: 0.7775 (pp) REVERT: F 144 ASN cc_start: 0.4051 (OUTLIER) cc_final: 0.3698 (t0) REVERT: F 264 LYS cc_start: 0.7840 (tptt) cc_final: 0.7434 (mmmt) REVERT: F 295 LYS cc_start: 0.8578 (tmmt) cc_final: 0.8238 (tmmt) outliers start: 157 outliers final: 95 residues processed: 963 average time/residue: 0.7859 time to fit residues: 894.9011 Evaluate side-chains 971 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 848 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 275 ASN Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 503 GLN Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 759 ARG Chi-restraints excluded: chain A residue 803 GLN Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 882 ASN Chi-restraints excluded: chain A residue 1019 HIS Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1209 LEU Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain A residue 1559 LEU Chi-restraints excluded: chain A residue 1754 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 435 HIS Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 576 TYR Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 628 ARG Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 788 MET Chi-restraints excluded: chain B residue 803 GLN Chi-restraints excluded: chain B residue 887 CYS Chi-restraints excluded: chain B residue 1206 THR Chi-restraints excluded: chain B residue 1223 ILE Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1573 GLU Chi-restraints excluded: chain B residue 1587 CYS Chi-restraints excluded: chain B residue 1647 SER Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 71 HIS Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 617 HIS Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 675 ASP Chi-restraints excluded: chain C residue 691 LEU Chi-restraints excluded: chain C residue 741 LYS Chi-restraints excluded: chain C residue 805 ASN Chi-restraints excluded: chain C residue 806 MET Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 826 LEU Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 858 VAL Chi-restraints excluded: chain C residue 873 THR Chi-restraints excluded: chain C residue 890 LYS Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 224 MET Chi-restraints excluded: chain D residue 646 MET Chi-restraints excluded: chain D residue 705 GLU Chi-restraints excluded: chain D residue 712 HIS Chi-restraints excluded: chain D residue 751 LYS Chi-restraints excluded: chain D residue 771 MET Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 827 LEU Chi-restraints excluded: chain D residue 848 LEU Chi-restraints excluded: chain D residue 857 GLU Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 864 GLU Chi-restraints excluded: chain D residue 879 MET Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 208 LYS Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain F residue 25 PHE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain F residue 274 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 162 optimal weight: 1.9990 chunk 220 optimal weight: 0.4980 chunk 306 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 124 optimal weight: 0.5980 chunk 184 optimal weight: 0.7980 chunk 298 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 404 optimal weight: 0.3980 chunk 353 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN A 444 ASN ** A 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1019 HIS ** A1192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 GLN B 486 ASN B 763 HIS B 794 GLN B 798 HIS ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 HIS B1588 GLN ** B1681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS C 617 HIS ** C 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 617 HIS ** D 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 776 HIS D 915 HIS E 179 GLN ** E 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 249 HIS F 311 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.145380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.120829 restraints weight = 73353.589| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.69 r_work: 0.3581 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 35789 Z= 0.215 Angle : 0.762 12.725 48433 Z= 0.379 Chirality : 0.045 0.196 5550 Planarity : 0.005 0.058 6169 Dihedral : 4.748 49.994 4750 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.34 % Allowed : 24.10 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.04 (0.13), residues: 4311 helix: 1.08 (0.10), residues: 2690 sheet: -0.47 (0.27), residues: 312 loop : 0.45 (0.20), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 934 TYR 0.023 0.002 TYR A 779 PHE 0.031 0.002 PHE E 49 TRP 0.044 0.003 TRP C 103 HIS 0.025 0.001 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00487 (35789) covalent geometry : angle 0.76151 (48433) hydrogen bonds : bond 0.04243 ( 2259) hydrogen bonds : angle 5.03743 ( 6642) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1037 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 867 time to evaluate : 1.415 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: A 119 LEU cc_start: 0.7725 (mt) cc_final: 0.7212 (mt) REVERT: A 122 LEU cc_start: 0.8624 (tm) cc_final: 0.8242 (mm) REVERT: A 123 PHE cc_start: 0.7828 (m-80) cc_final: 0.7412 (m-80) REVERT: A 182 ASN cc_start: 0.8115 (m-40) cc_final: 0.7732 (m-40) REVERT: A 186 PHE cc_start: 0.7919 (m-80) cc_final: 0.7387 (m-80) REVERT: A 190 TYR cc_start: 0.7048 (m-80) cc_final: 0.6789 (m-80) REVERT: A 216 GLU cc_start: 0.7970 (tt0) cc_final: 0.7266 (tp30) REVERT: A 234 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7362 (tp30) REVERT: A 251 GLU cc_start: 0.8170 (mp0) cc_final: 0.7851 (mp0) REVERT: A 279 LEU cc_start: 0.8308 (mt) cc_final: 0.7718 (mt) REVERT: A 282 ASP cc_start: 0.8058 (t0) cc_final: 0.7760 (p0) REVERT: A 307 HIS cc_start: 0.8326 (m-70) cc_final: 0.8028 (m-70) REVERT: A 325 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7674 (mp10) REVERT: A 340 LEU cc_start: 0.8880 (mt) cc_final: 0.8614 (mt) REVERT: A 392 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7529 (mm-30) REVERT: A 393 GLU cc_start: 0.7976 (pp20) cc_final: 0.7479 (pp20) REVERT: A 405 GLU cc_start: 0.7877 (tt0) cc_final: 0.7436 (tp30) REVERT: A 482 GLU cc_start: 0.8105 (tt0) cc_final: 0.7705 (tm-30) REVERT: A 483 GLU cc_start: 0.7792 (mp0) cc_final: 0.7308 (mp0) REVERT: A 498 GLU cc_start: 0.7527 (pp20) cc_final: 0.7198 (pp20) REVERT: A 499 ASP cc_start: 0.7396 (m-30) cc_final: 0.6976 (m-30) REVERT: A 535 MET cc_start: 0.7992 (mtm) cc_final: 0.7499 (mtp) REVERT: A 596 LEU cc_start: 0.8874 (tp) cc_final: 0.8538 (tp) REVERT: A 608 SER cc_start: 0.9040 (OUTLIER) cc_final: 0.8708 (p) REVERT: A 622 ARG cc_start: 0.8307 (mpp80) cc_final: 0.8041 (mmm-85) REVERT: A 691 ARG cc_start: 0.8546 (ttp80) cc_final: 0.8278 (ttm110) REVERT: A 707 LYS cc_start: 0.9006 (tttt) cc_final: 0.8716 (ttmm) REVERT: A 778 ASN cc_start: 0.8620 (m-40) cc_final: 0.8341 (m110) REVERT: A 782 LYS cc_start: 0.8013 (mttt) cc_final: 0.7619 (mppt) REVERT: A 788 MET cc_start: 0.7857 (ttp) cc_final: 0.7614 (ttm) REVERT: A 793 GLU cc_start: 0.7621 (tp30) cc_final: 0.7418 (tp30) REVERT: A 804 CYS cc_start: 0.8221 (m) cc_final: 0.7710 (m) REVERT: A 873 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8674 (tp) REVERT: A 880 LYS cc_start: 0.8588 (mttt) cc_final: 0.8200 (ttmm) REVERT: A 919 ASN cc_start: 0.7878 (m-40) cc_final: 0.7560 (m-40) REVERT: A 1016 LYS cc_start: 0.8367 (mttt) cc_final: 0.7937 (tppt) REVERT: A 1024 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7440 (tm-30) REVERT: A 1043 LYS cc_start: 0.8502 (tttm) cc_final: 0.8133 (ttpp) REVERT: A 1213 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: A 1231 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8056 (mm) REVERT: A 1239 GLU cc_start: 0.7333 (tp30) cc_final: 0.7029 (tp30) REVERT: A 1243 GLU cc_start: 0.6953 (tp30) cc_final: 0.6637 (tp30) REVERT: A 1528 GLU cc_start: 0.7367 (pp20) cc_final: 0.6791 (pp20) REVERT: A 1529 ARG cc_start: 0.7685 (tpp-160) cc_final: 0.7293 (tpp-160) REVERT: A 1580 ARG cc_start: 0.8204 (ptm-80) cc_final: 0.7848 (ttm170) REVERT: A 1602 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7777 (tt0) REVERT: A 1679 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8052 (mm-30) REVERT: A 1744 LEU cc_start: 0.8570 (tp) cc_final: 0.8260 (tp) REVERT: A 1756 GLU cc_start: 0.6860 (pp20) cc_final: 0.6483 (pp20) REVERT: B 60 MET cc_start: 0.8227 (tpp) cc_final: 0.7985 (tpp) REVERT: B 63 GLN cc_start: 0.8110 (mm-40) cc_final: 0.7781 (mm110) REVERT: B 136 LEU cc_start: 0.7740 (mp) cc_final: 0.7500 (mm) REVERT: B 141 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7214 (tp30) REVERT: B 144 LYS cc_start: 0.8852 (mtpt) cc_final: 0.8461 (ttmm) REVERT: B 148 ASP cc_start: 0.8430 (m-30) cc_final: 0.7584 (p0) REVERT: B 151 ARG cc_start: 0.7924 (ptm160) cc_final: 0.6898 (ptm160) REVERT: B 152 HIS cc_start: 0.7739 (t70) cc_final: 0.7285 (t70) REVERT: B 157 GLU cc_start: 0.7505 (mp0) cc_final: 0.7187 (mm-30) REVERT: B 167 TRP cc_start: 0.7913 (t-100) cc_final: 0.7603 (t60) REVERT: B 186 PHE cc_start: 0.8591 (m-80) cc_final: 0.7829 (m-80) REVERT: B 258 LYS cc_start: 0.8343 (mppt) cc_final: 0.8098 (ptpt) REVERT: B 278 HIS cc_start: 0.7363 (t70) cc_final: 0.6861 (t70) REVERT: B 309 LEU cc_start: 0.7317 (mm) cc_final: 0.7090 (mp) REVERT: B 327 MET cc_start: 0.6420 (mmp) cc_final: 0.6028 (mmt) REVERT: B 349 TYR cc_start: 0.7546 (m-80) cc_final: 0.7273 (m-80) REVERT: B 360 ILE cc_start: 0.8516 (mt) cc_final: 0.8089 (tp) REVERT: B 366 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7589 (tm-30) REVERT: B 380 LEU cc_start: 0.8669 (tp) cc_final: 0.8362 (tp) REVERT: B 426 LEU cc_start: 0.9306 (tp) cc_final: 0.8946 (tm) REVERT: B 451 ARG cc_start: 0.7456 (tpt90) cc_final: 0.7112 (tpt90) REVERT: B 470 SER cc_start: 0.8674 (t) cc_final: 0.8246 (p) REVERT: B 471 PHE cc_start: 0.8652 (t80) cc_final: 0.8442 (t80) REVERT: B 510 GLN cc_start: 0.8233 (mt0) cc_final: 0.7621 (tm-30) REVERT: B 511 LEU cc_start: 0.8636 (tt) cc_final: 0.8202 (tm) REVERT: B 514 ASP cc_start: 0.7563 (m-30) cc_final: 0.7040 (m-30) REVERT: B 528 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6628 (mm) REVERT: B 557 LEU cc_start: 0.8396 (mt) cc_final: 0.8118 (mt) REVERT: B 576 TYR cc_start: 0.7810 (OUTLIER) cc_final: 0.7312 (m-80) REVERT: B 585 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8422 (ttp80) REVERT: B 595 GLN cc_start: 0.7749 (tp40) cc_final: 0.7430 (tp-100) REVERT: B 628 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8132 (mtm110) REVERT: B 691 ARG cc_start: 0.8162 (ttm-80) cc_final: 0.7849 (mtm-85) REVERT: B 704 LYS cc_start: 0.8518 (mttt) cc_final: 0.8170 (mppt) REVERT: B 757 PHE cc_start: 0.7920 (t80) cc_final: 0.7686 (t80) REVERT: B 761 ASP cc_start: 0.7896 (m-30) cc_final: 0.7553 (m-30) REVERT: B 762 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8479 (tt) REVERT: B 782 LYS cc_start: 0.8770 (mttt) cc_final: 0.8469 (mtmp) REVERT: B 815 MET cc_start: 0.8820 (mtm) cc_final: 0.8439 (ptp) REVERT: B 880 LYS cc_start: 0.8717 (mptt) cc_final: 0.8506 (mptm) REVERT: B 906 LYS cc_start: 0.8697 (tttm) cc_final: 0.7558 (tttp) REVERT: B 907 ASP cc_start: 0.8139 (p0) cc_final: 0.7760 (p0) REVERT: B 914 LYS cc_start: 0.9027 (tppt) cc_final: 0.8665 (tppt) REVERT: B 917 ARG cc_start: 0.8705 (ttm170) cc_final: 0.7915 (ttm110) REVERT: B 919 ASN cc_start: 0.8347 (m-40) cc_final: 0.7899 (m110) REVERT: B 1017 ASN cc_start: 0.8774 (t0) cc_final: 0.8336 (t0) REVERT: B 1028 ASP cc_start: 0.8062 (t70) cc_final: 0.7559 (t0) REVERT: B 1222 ASP cc_start: 0.7901 (m-30) cc_final: 0.7606 (m-30) REVERT: B 1230 GLU cc_start: 0.8259 (mp0) cc_final: 0.8016 (mp0) REVERT: B 1559 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8360 (mm) REVERT: B 1573 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7820 (mp0) REVERT: B 1602 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7754 (mm-30) REVERT: B 1639 ARG cc_start: 0.8024 (ptt180) cc_final: 0.7722 (ptt180) REVERT: B 1656 ASP cc_start: 0.7843 (p0) cc_final: 0.7483 (p0) REVERT: B 1756 GLU cc_start: 0.7583 (pp20) cc_final: 0.7190 (pp20) REVERT: C 13 MET cc_start: 0.7893 (mtm) cc_final: 0.7557 (ttm) REVERT: C 223 MET cc_start: 0.7947 (ttm) cc_final: 0.7658 (mtp) REVERT: C 232 GLU cc_start: 0.7399 (mp0) cc_final: 0.7020 (mp0) REVERT: C 272 GLU cc_start: 0.7109 (tm-30) cc_final: 0.6651 (tm-30) REVERT: C 688 ILE cc_start: 0.8995 (mt) cc_final: 0.8585 (tp) REVERT: C 689 ARG cc_start: 0.8049 (mmm160) cc_final: 0.7586 (mmp80) REVERT: C 722 LYS cc_start: 0.8668 (tppt) cc_final: 0.8309 (tppp) REVERT: C 736 MET cc_start: 0.8253 (mmm) cc_final: 0.7965 (mmm) REVERT: C 741 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7713 (tmmm) REVERT: C 746 ASP cc_start: 0.7639 (m-30) cc_final: 0.7361 (m-30) REVERT: C 756 LYS cc_start: 0.8465 (tttt) cc_final: 0.8172 (tmmt) REVERT: C 799 LYS cc_start: 0.8753 (tttt) cc_final: 0.8295 (tmtp) REVERT: C 806 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.6967 (tmm) REVERT: C 807 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.8090 (OUTLIER) REVERT: C 819 ASN cc_start: 0.8484 (t0) cc_final: 0.8238 (t0) REVERT: C 825 GLU cc_start: 0.8135 (pp20) cc_final: 0.7855 (pp20) REVERT: C 830 GLN cc_start: 0.8663 (tp40) cc_final: 0.8373 (mm-40) REVERT: C 839 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8187 (tp30) REVERT: C 842 GLN cc_start: 0.8744 (tp-100) cc_final: 0.8160 (tp40) REVERT: C 845 MET cc_start: 0.8382 (ttt) cc_final: 0.8172 (ttm) REVERT: C 846 GLU cc_start: 0.8473 (tt0) cc_final: 0.8179 (mt-10) REVERT: C 852 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8965 (mm) REVERT: C 854 VAL cc_start: 0.8854 (t) cc_final: 0.8653 (p) REVERT: C 857 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7532 (mm-30) REVERT: C 861 LEU cc_start: 0.8501 (mt) cc_final: 0.8256 (mm) REVERT: C 863 LEU cc_start: 0.8874 (tp) cc_final: 0.8602 (tm) REVERT: C 864 GLU cc_start: 0.8328 (tt0) cc_final: 0.7821 (tp30) REVERT: C 874 THR cc_start: 0.7769 (p) cc_final: 0.7343 (t) REVERT: C 878 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7638 (mt-10) REVERT: C 884 TYR cc_start: 0.8580 (t80) cc_final: 0.8341 (t80) REVERT: C 885 ARG cc_start: 0.8550 (mmm160) cc_final: 0.8319 (mmp80) REVERT: C 890 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8843 (ttpp) REVERT: C 906 GLN cc_start: 0.7779 (pp30) cc_final: 0.7439 (pp30) REVERT: C 907 LYS cc_start: 0.8490 (mmmm) cc_final: 0.8219 (mmmm) REVERT: C 924 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8117 (mm) REVERT: C 925 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7832 (mm-30) REVERT: C 961 GLU cc_start: 0.7813 (tp30) cc_final: 0.7506 (tp30) REVERT: D 9 GLU cc_start: 0.8329 (mp0) cc_final: 0.7920 (mp0) REVERT: D 29 PHE cc_start: 0.8586 (OUTLIER) cc_final: 0.8132 (t80) REVERT: D 30 LYS cc_start: 0.8527 (mtmt) cc_final: 0.8273 (mtmt) REVERT: D 136 LEU cc_start: 0.8923 (tp) cc_final: 0.8678 (tm) REVERT: D 261 LYS cc_start: 0.8790 (tppp) cc_final: 0.8403 (tppp) REVERT: D 629 LYS cc_start: 0.8437 (mmmt) cc_final: 0.8103 (mmmt) REVERT: D 650 ASP cc_start: 0.8117 (p0) cc_final: 0.7782 (p0) REVERT: D 665 ASN cc_start: 0.8617 (m-40) cc_final: 0.8273 (m-40) REVERT: D 691 LEU cc_start: 0.9162 (tp) cc_final: 0.8841 (tm) REVERT: D 694 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8105 (mm-40) REVERT: D 705 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8201 (tm-30) REVERT: D 712 HIS cc_start: 0.8449 (OUTLIER) cc_final: 0.7289 (t70) REVERT: D 714 LEU cc_start: 0.8900 (mt) cc_final: 0.8593 (mt) REVERT: D 717 ARG cc_start: 0.7943 (tmm160) cc_final: 0.7279 (tmm160) REVERT: D 721 ARG cc_start: 0.8413 (ptp-110) cc_final: 0.7901 (ptp-110) REVERT: D 749 MET cc_start: 0.8145 (ttp) cc_final: 0.7805 (ttp) REVERT: D 751 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.9008 (tppp) REVERT: D 756 LYS cc_start: 0.8575 (tmmm) cc_final: 0.8205 (tptp) REVERT: D 806 MET cc_start: 0.7274 (ttt) cc_final: 0.6771 (tpp) REVERT: D 842 GLN cc_start: 0.8415 (tm-30) cc_final: 0.8013 (tm-30) REVERT: D 844 GLN cc_start: 0.8161 (tm-30) cc_final: 0.7636 (tm-30) REVERT: D 846 GLU cc_start: 0.8229 (tt0) cc_final: 0.7499 (tp30) REVERT: D 848 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8440 (mt) REVERT: D 852 LEU cc_start: 0.8727 (tp) cc_final: 0.8465 (tm) REVERT: D 860 GLU cc_start: 0.7970 (tp30) cc_final: 0.7638 (tp30) REVERT: D 863 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8456 (mt) REVERT: D 864 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7218 (mm-30) REVERT: D 867 GLN cc_start: 0.8043 (pt0) cc_final: 0.7628 (pt0) REVERT: D 868 ASN cc_start: 0.7402 (m110) cc_final: 0.6783 (m-40) REVERT: D 886 LYS cc_start: 0.8682 (tptt) cc_final: 0.8435 (ttpp) REVERT: D 887 GLU cc_start: 0.8168 (tp30) cc_final: 0.7552 (tp30) REVERT: D 903 ASP cc_start: 0.7957 (m-30) cc_final: 0.7599 (t0) REVERT: D 907 LYS cc_start: 0.8586 (mmtt) cc_final: 0.8247 (mmmm) REVERT: D 918 LYS cc_start: 0.8572 (tptt) cc_final: 0.8283 (mttp) REVERT: D 920 ASP cc_start: 0.7875 (t70) cc_final: 0.7633 (t0) REVERT: D 925 GLU cc_start: 0.8084 (tp30) cc_final: 0.7825 (tm-30) REVERT: D 961 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7814 (pp20) REVERT: E 30 ILE cc_start: 0.8155 (mt) cc_final: 0.7834 (mt) REVERT: E 34 ASP cc_start: 0.8193 (m-30) cc_final: 0.7945 (m-30) REVERT: E 38 ASP cc_start: 0.7941 (t0) cc_final: 0.7449 (t0) REVERT: E 40 GLU cc_start: 0.7920 (tt0) cc_final: 0.7645 (tt0) REVERT: E 72 GLU cc_start: 0.8095 (tt0) cc_final: 0.7855 (tt0) REVERT: E 79 MET cc_start: 0.7908 (ttp) cc_final: 0.7251 (tmt) REVERT: E 83 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7674 (mt-10) REVERT: E 93 LYS cc_start: 0.8720 (mttt) cc_final: 0.8448 (mtpp) REVERT: E 144 MET cc_start: 0.8389 (mtt) cc_final: 0.8036 (mtt) REVERT: E 159 VAL cc_start: 0.8148 (t) cc_final: 0.7931 (m) REVERT: E 172 GLN cc_start: 0.7382 (tm130) cc_final: 0.6992 (tm130) REVERT: E 194 MET cc_start: 0.7556 (tmm) cc_final: 0.7319 (tmm) REVERT: E 241 GLU cc_start: 0.7175 (tp30) cc_final: 0.6733 (tp30) REVERT: E 249 LYS cc_start: 0.8204 (tptt) cc_final: 0.7719 (tptt) REVERT: E 251 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7737 (tpt) REVERT: F 29 MET cc_start: 0.6888 (tpt) cc_final: 0.6515 (tpp) REVERT: F 42 LYS cc_start: 0.7371 (ttmt) cc_final: 0.7006 (ttmt) REVERT: F 61 PHE cc_start: 0.8035 (m-80) cc_final: 0.7771 (m-80) REVERT: F 144 ASN cc_start: 0.4206 (OUTLIER) cc_final: 0.3838 (t0) REVERT: F 264 LYS cc_start: 0.7743 (tptt) cc_final: 0.7178 (mmmt) REVERT: F 295 LYS cc_start: 0.8524 (tmmt) cc_final: 0.8208 (tmmt) outliers start: 170 outliers final: 91 residues processed: 957 average time/residue: 0.7731 time to fit residues: 873.8842 Evaluate side-chains 952 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 836 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 503 GLN Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 803 GLN Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 882 ASN Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1209 LEU Chi-restraints excluded: chain A residue 1213 GLU Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain A residue 1559 LEU Chi-restraints excluded: chain A residue 1717 LEU Chi-restraints excluded: chain A residue 1754 ILE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 435 HIS Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 576 TYR Chi-restraints excluded: chain B residue 585 ARG Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 628 ARG Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 803 GLN Chi-restraints excluded: chain B residue 887 CYS Chi-restraints excluded: chain B residue 1206 THR Chi-restraints excluded: chain B residue 1223 ILE Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1559 LEU Chi-restraints excluded: chain B residue 1573 GLU Chi-restraints excluded: chain B residue 1587 CYS Chi-restraints excluded: chain B residue 1647 SER Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 71 HIS Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 675 ASP Chi-restraints excluded: chain C residue 691 LEU Chi-restraints excluded: chain C residue 741 LYS Chi-restraints excluded: chain C residue 747 ILE Chi-restraints excluded: chain C residue 773 THR Chi-restraints excluded: chain C residue 805 ASN Chi-restraints excluded: chain C residue 806 MET Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain C residue 826 LEU Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 858 VAL Chi-restraints excluded: chain C residue 873 THR Chi-restraints excluded: chain C residue 890 LYS Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain C residue 924 LEU Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 646 MET Chi-restraints excluded: chain D residue 705 GLU Chi-restraints excluded: chain D residue 712 HIS Chi-restraints excluded: chain D residue 751 LYS Chi-restraints excluded: chain D residue 771 MET Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 827 LEU Chi-restraints excluded: chain D residue 848 LEU Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 864 GLU Chi-restraints excluded: chain D residue 879 MET Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 208 LYS Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain F residue 274 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 145 optimal weight: 0.1980 chunk 273 optimal weight: 0.2980 chunk 302 optimal weight: 0.9980 chunk 260 optimal weight: 0.7980 chunk 183 optimal weight: 0.5980 chunk 5 optimal weight: 0.0870 chunk 130 optimal weight: 0.0770 chunk 103 optimal weight: 0.4980 chunk 158 optimal weight: 0.2980 chunk 107 optimal weight: 0.9980 chunk 213 optimal weight: 0.6980 overall best weight: 0.1916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN A 444 ASN ** A 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 GLN B 763 HIS B 794 GLN B 798 HIS ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 HIS B1588 GLN ** B1707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 617 HIS ** C 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 617 HIS ** D 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 823 HIS D 915 HIS E 179 GLN ** E 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.147670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.123683 restraints weight = 73221.620| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.70 r_work: 0.3601 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 35789 Z= 0.158 Angle : 0.769 12.819 48433 Z= 0.380 Chirality : 0.043 0.190 5550 Planarity : 0.004 0.055 6169 Dihedral : 4.705 51.304 4750 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.42 % Allowed : 25.50 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.15 (0.13), residues: 4311 helix: 1.19 (0.10), residues: 2681 sheet: -0.59 (0.27), residues: 307 loop : 0.48 (0.20), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 245 TYR 0.021 0.002 TYR C 271 PHE 0.038 0.002 PHE B 297 TRP 0.049 0.003 TRP C 103 HIS 0.019 0.001 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00365 (35789) covalent geometry : angle 0.76915 (48433) hydrogen bonds : bond 0.04077 ( 2259) hydrogen bonds : angle 4.95544 ( 6642) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1006 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 872 time to evaluate : 1.446 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: A 119 LEU cc_start: 0.7610 (mt) cc_final: 0.7026 (mt) REVERT: A 122 LEU cc_start: 0.8602 (tm) cc_final: 0.8206 (mm) REVERT: A 123 PHE cc_start: 0.7772 (m-80) cc_final: 0.7321 (m-80) REVERT: A 182 ASN cc_start: 0.8108 (m-40) cc_final: 0.7725 (m-40) REVERT: A 186 PHE cc_start: 0.7890 (m-80) cc_final: 0.7357 (m-80) REVERT: A 190 TYR cc_start: 0.7071 (m-80) cc_final: 0.6825 (m-80) REVERT: A 216 GLU cc_start: 0.7905 (tt0) cc_final: 0.7244 (tp30) REVERT: A 234 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7303 (tp30) REVERT: A 251 GLU cc_start: 0.8092 (mp0) cc_final: 0.7787 (mp0) REVERT: A 279 LEU cc_start: 0.8225 (mt) cc_final: 0.7646 (mt) REVERT: A 282 ASP cc_start: 0.8056 (t0) cc_final: 0.7723 (p0) REVERT: A 307 HIS cc_start: 0.8279 (m-70) cc_final: 0.7912 (m-70) REVERT: A 325 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7635 (mp10) REVERT: A 340 LEU cc_start: 0.8847 (mt) cc_final: 0.8579 (mt) REVERT: A 392 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7555 (mm-30) REVERT: A 393 GLU cc_start: 0.7991 (pp20) cc_final: 0.7483 (pp20) REVERT: A 405 GLU cc_start: 0.7843 (tt0) cc_final: 0.7388 (tp30) REVERT: A 482 GLU cc_start: 0.8086 (tt0) cc_final: 0.7615 (tm-30) REVERT: A 483 GLU cc_start: 0.7833 (mp0) cc_final: 0.7356 (mp0) REVERT: A 498 GLU cc_start: 0.7479 (pp20) cc_final: 0.7117 (pp20) REVERT: A 499 ASP cc_start: 0.7386 (m-30) cc_final: 0.6976 (m-30) REVERT: A 517 GLU cc_start: 0.7361 (tp30) cc_final: 0.7137 (mm-30) REVERT: A 535 MET cc_start: 0.7934 (mtm) cc_final: 0.7475 (mtp) REVERT: A 596 LEU cc_start: 0.8843 (tp) cc_final: 0.8522 (tt) REVERT: A 608 SER cc_start: 0.9071 (OUTLIER) cc_final: 0.8736 (p) REVERT: A 622 ARG cc_start: 0.8325 (mpp80) cc_final: 0.8074 (mmm-85) REVERT: A 691 ARG cc_start: 0.8512 (ttp80) cc_final: 0.8239 (ttm110) REVERT: A 707 LYS cc_start: 0.8993 (tttt) cc_final: 0.8430 (ttmm) REVERT: A 782 LYS cc_start: 0.8026 (mttt) cc_final: 0.7679 (mppt) REVERT: A 793 GLU cc_start: 0.7499 (tp30) cc_final: 0.7299 (tp30) REVERT: A 804 CYS cc_start: 0.8224 (m) cc_final: 0.7735 (m) REVERT: A 873 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8639 (tp) REVERT: A 880 LYS cc_start: 0.8488 (mttt) cc_final: 0.8171 (ttmm) REVERT: A 919 ASN cc_start: 0.7819 (m-40) cc_final: 0.7520 (m-40) REVERT: A 1016 LYS cc_start: 0.8351 (mttt) cc_final: 0.7907 (tppt) REVERT: A 1024 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7436 (tm-30) REVERT: A 1037 ASN cc_start: 0.8293 (m-40) cc_final: 0.7909 (m-40) REVERT: A 1043 LYS cc_start: 0.8434 (tttm) cc_final: 0.8134 (ttpp) REVERT: A 1213 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.7044 (mt-10) REVERT: A 1231 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8335 (mm) REVERT: A 1239 GLU cc_start: 0.7341 (tp30) cc_final: 0.7080 (tp30) REVERT: A 1243 GLU cc_start: 0.6911 (tp30) cc_final: 0.6580 (tp30) REVERT: A 1528 GLU cc_start: 0.7354 (pp20) cc_final: 0.6788 (pp20) REVERT: A 1529 ARG cc_start: 0.7635 (tpp-160) cc_final: 0.7176 (tpp-160) REVERT: A 1580 ARG cc_start: 0.8073 (ptm-80) cc_final: 0.7719 (ttm170) REVERT: A 1602 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7751 (tt0) REVERT: A 1679 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8112 (mm-30) REVERT: A 1744 LEU cc_start: 0.8500 (tp) cc_final: 0.8241 (tp) REVERT: A 1756 GLU cc_start: 0.6898 (pp20) cc_final: 0.6634 (pp20) REVERT: B 60 MET cc_start: 0.8221 (tpp) cc_final: 0.8008 (tpp) REVERT: B 74 GLU cc_start: 0.6289 (OUTLIER) cc_final: 0.4135 (mt-10) REVERT: B 136 LEU cc_start: 0.7584 (mp) cc_final: 0.7336 (mm) REVERT: B 141 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7159 (tp30) REVERT: B 144 LYS cc_start: 0.8800 (mtpt) cc_final: 0.8362 (ttmm) REVERT: B 148 ASP cc_start: 0.8404 (m-30) cc_final: 0.7562 (p0) REVERT: B 151 ARG cc_start: 0.7901 (ptm160) cc_final: 0.6915 (ptm160) REVERT: B 152 HIS cc_start: 0.7701 (t70) cc_final: 0.7327 (t70) REVERT: B 167 TRP cc_start: 0.7782 (t-100) cc_final: 0.7490 (t60) REVERT: B 186 PHE cc_start: 0.8486 (m-80) cc_final: 0.7749 (m-80) REVERT: B 258 LYS cc_start: 0.8286 (mppt) cc_final: 0.8021 (ptpt) REVERT: B 278 HIS cc_start: 0.7236 (t70) cc_final: 0.6941 (t70) REVERT: B 327 MET cc_start: 0.6301 (mmp) cc_final: 0.5977 (mmt) REVERT: B 349 TYR cc_start: 0.7439 (m-80) cc_final: 0.7218 (m-10) REVERT: B 360 ILE cc_start: 0.8471 (mt) cc_final: 0.7937 (tt) REVERT: B 364 ILE cc_start: 0.8950 (mp) cc_final: 0.8678 (mp) REVERT: B 366 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7538 (tm-30) REVERT: B 380 LEU cc_start: 0.8718 (tp) cc_final: 0.8407 (tp) REVERT: B 426 LEU cc_start: 0.9283 (tp) cc_final: 0.8992 (tm) REVERT: B 451 ARG cc_start: 0.7397 (tpt90) cc_final: 0.6990 (tpt90) REVERT: B 471 PHE cc_start: 0.8620 (t80) cc_final: 0.8406 (t80) REVERT: B 510 GLN cc_start: 0.8099 (mt0) cc_final: 0.7553 (tm-30) REVERT: B 511 LEU cc_start: 0.8629 (tt) cc_final: 0.8208 (tm) REVERT: B 514 ASP cc_start: 0.7576 (m-30) cc_final: 0.7061 (m-30) REVERT: B 557 LEU cc_start: 0.8418 (mt) cc_final: 0.8123 (mt) REVERT: B 585 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8367 (ttp80) REVERT: B 595 GLN cc_start: 0.7661 (tp40) cc_final: 0.7378 (tp-100) REVERT: B 628 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8054 (mtm110) REVERT: B 691 ARG cc_start: 0.8000 (ttm-80) cc_final: 0.7735 (mtm-85) REVERT: B 704 LYS cc_start: 0.8437 (mttt) cc_final: 0.8136 (mppt) REVERT: B 757 PHE cc_start: 0.7912 (t80) cc_final: 0.7688 (t80) REVERT: B 761 ASP cc_start: 0.7894 (m-30) cc_final: 0.7613 (m-30) REVERT: B 762 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8411 (tt) REVERT: B 782 LYS cc_start: 0.8702 (mttt) cc_final: 0.8437 (mppt) REVERT: B 800 CYS cc_start: 0.7664 (p) cc_final: 0.7318 (p) REVERT: B 880 LYS cc_start: 0.8587 (mptt) cc_final: 0.8371 (mptm) REVERT: B 899 ARG cc_start: 0.8324 (ptp-170) cc_final: 0.8051 (ptp-170) REVERT: B 906 LYS cc_start: 0.8644 (tttm) cc_final: 0.8307 (tttm) REVERT: B 907 ASP cc_start: 0.8071 (p0) cc_final: 0.7855 (p0) REVERT: B 914 LYS cc_start: 0.9004 (tppt) cc_final: 0.8648 (tppt) REVERT: B 917 ARG cc_start: 0.8638 (ttm170) cc_final: 0.7854 (ttm110) REVERT: B 919 ASN cc_start: 0.8312 (m-40) cc_final: 0.7878 (m110) REVERT: B 1016 LYS cc_start: 0.8782 (tppt) cc_final: 0.8551 (mptt) REVERT: B 1017 ASN cc_start: 0.8699 (t0) cc_final: 0.8188 (t0) REVERT: B 1028 ASP cc_start: 0.8061 (t70) cc_final: 0.7579 (t0) REVERT: B 1222 ASP cc_start: 0.7872 (m-30) cc_final: 0.7584 (m-30) REVERT: B 1230 GLU cc_start: 0.8223 (mp0) cc_final: 0.7994 (mp0) REVERT: B 1559 LEU cc_start: 0.8788 (tm) cc_final: 0.8389 (mm) REVERT: B 1573 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7859 (mp0) REVERT: B 1602 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7682 (mm-30) REVERT: B 1639 ARG cc_start: 0.7967 (ptt180) cc_final: 0.7669 (ptt180) REVERT: B 1656 ASP cc_start: 0.7865 (p0) cc_final: 0.7515 (p0) REVERT: B 1756 GLU cc_start: 0.7553 (pp20) cc_final: 0.7182 (pp20) REVERT: C 10 LEU cc_start: 0.8796 (mp) cc_final: 0.8367 (tp) REVERT: C 11 LEU cc_start: 0.8692 (mt) cc_final: 0.8467 (mm) REVERT: C 13 MET cc_start: 0.7847 (mtm) cc_final: 0.7498 (ttm) REVERT: C 210 LYS cc_start: 0.8750 (mmpt) cc_final: 0.8545 (mmmm) REVERT: C 223 MET cc_start: 0.7918 (ttm) cc_final: 0.7685 (mtp) REVERT: C 232 GLU cc_start: 0.7181 (mp0) cc_final: 0.6928 (mp0) REVERT: C 272 GLU cc_start: 0.7063 (tm-30) cc_final: 0.6627 (tm-30) REVERT: C 688 ILE cc_start: 0.8974 (mt) cc_final: 0.8579 (tp) REVERT: C 689 ARG cc_start: 0.8013 (mmm160) cc_final: 0.7553 (mmp80) REVERT: C 722 LYS cc_start: 0.8513 (tppt) cc_final: 0.8197 (tppp) REVERT: C 736 MET cc_start: 0.8227 (mmm) cc_final: 0.7954 (mmm) REVERT: C 741 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7802 (tmmm) REVERT: C 746 ASP cc_start: 0.7633 (m-30) cc_final: 0.7333 (m-30) REVERT: C 756 LYS cc_start: 0.8413 (tttt) cc_final: 0.8118 (tmmt) REVERT: C 799 LYS cc_start: 0.8837 (tttt) cc_final: 0.8422 (tmtp) REVERT: C 806 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.6769 (tmm) REVERT: C 807 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.8046 (OUTLIER) REVERT: C 810 LEU cc_start: 0.8544 (mm) cc_final: 0.7693 (mm) REVERT: C 819 ASN cc_start: 0.8446 (t0) cc_final: 0.8147 (t0) REVERT: C 825 GLU cc_start: 0.8217 (pp20) cc_final: 0.7905 (pp20) REVERT: C 830 GLN cc_start: 0.8638 (tp40) cc_final: 0.8320 (mm-40) REVERT: C 844 GLN cc_start: 0.7347 (tm-30) cc_final: 0.7025 (tm-30) REVERT: C 845 MET cc_start: 0.8310 (ttt) cc_final: 0.7956 (ttm) REVERT: C 852 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8932 (mm) REVERT: C 861 LEU cc_start: 0.8517 (mt) cc_final: 0.8273 (mm) REVERT: C 863 LEU cc_start: 0.8853 (tp) cc_final: 0.8577 (tm) REVERT: C 864 GLU cc_start: 0.8277 (tt0) cc_final: 0.7784 (tp30) REVERT: C 874 THR cc_start: 0.7590 (p) cc_final: 0.7356 (t) REVERT: C 876 GLU cc_start: 0.7970 (pt0) cc_final: 0.7384 (pm20) REVERT: C 878 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7573 (mt-10) REVERT: C 884 TYR cc_start: 0.8586 (t80) cc_final: 0.8269 (t80) REVERT: C 885 ARG cc_start: 0.8520 (mmm160) cc_final: 0.8256 (mmp80) REVERT: C 890 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8821 (ttpp) REVERT: C 906 GLN cc_start: 0.7751 (pp30) cc_final: 0.7356 (pp30) REVERT: C 907 LYS cc_start: 0.8445 (mmmm) cc_final: 0.8209 (mmmm) REVERT: C 924 LEU cc_start: 0.8506 (tt) cc_final: 0.8146 (mm) REVERT: C 925 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7794 (mm-30) REVERT: C 961 GLU cc_start: 0.7783 (tp30) cc_final: 0.7473 (tp30) REVERT: D 9 GLU cc_start: 0.8310 (mp0) cc_final: 0.7901 (mp0) REVERT: D 18 MET cc_start: 0.7988 (tpp) cc_final: 0.7757 (tmm) REVERT: D 29 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.8133 (t80) REVERT: D 51 GLU cc_start: 0.7352 (tm-30) cc_final: 0.7105 (pp20) REVERT: D 136 LEU cc_start: 0.8890 (tp) cc_final: 0.8623 (tm) REVERT: D 261 LYS cc_start: 0.8741 (tppp) cc_final: 0.8351 (tppp) REVERT: D 629 LYS cc_start: 0.8428 (mmmt) cc_final: 0.8040 (mmmt) REVERT: D 646 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7614 (tmm) REVERT: D 650 ASP cc_start: 0.8121 (p0) cc_final: 0.7155 (p0) REVERT: D 665 ASN cc_start: 0.8489 (m-40) cc_final: 0.8152 (m-40) REVERT: D 691 LEU cc_start: 0.9113 (tp) cc_final: 0.8804 (tm) REVERT: D 694 GLN cc_start: 0.8408 (mm-40) cc_final: 0.8009 (mm-40) REVERT: D 705 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8212 (tm-30) REVERT: D 714 LEU cc_start: 0.8858 (mt) cc_final: 0.8571 (mt) REVERT: D 717 ARG cc_start: 0.7832 (tmm160) cc_final: 0.7076 (tmm160) REVERT: D 718 ARG cc_start: 0.8827 (ttm110) cc_final: 0.7926 (ttm110) REVERT: D 721 ARG cc_start: 0.8304 (ptp-110) cc_final: 0.7935 (ptp-110) REVERT: D 749 MET cc_start: 0.8096 (ttp) cc_final: 0.7739 (ttp) REVERT: D 751 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8962 (tppp) REVERT: D 756 LYS cc_start: 0.8553 (tmmm) cc_final: 0.8193 (tptp) REVERT: D 806 MET cc_start: 0.7332 (ttt) cc_final: 0.6765 (tpp) REVERT: D 842 GLN cc_start: 0.8413 (tm-30) cc_final: 0.7971 (tm-30) REVERT: D 844 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7557 (tm-30) REVERT: D 845 MET cc_start: 0.8306 (tmt) cc_final: 0.7914 (tmt) REVERT: D 846 GLU cc_start: 0.8171 (tt0) cc_final: 0.7395 (tp30) REVERT: D 848 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8458 (mt) REVERT: D 852 LEU cc_start: 0.8742 (tp) cc_final: 0.8486 (tm) REVERT: D 857 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7775 (mm-30) REVERT: D 860 GLU cc_start: 0.7909 (tp30) cc_final: 0.7592 (tp30) REVERT: D 863 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8442 (mt) REVERT: D 864 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7207 (mm-30) REVERT: D 867 GLN cc_start: 0.7938 (pt0) cc_final: 0.7553 (pt0) REVERT: D 868 ASN cc_start: 0.7375 (m110) cc_final: 0.6870 (m-40) REVERT: D 880 MET cc_start: 0.8159 (tmm) cc_final: 0.7806 (tmm) REVERT: D 886 LYS cc_start: 0.8726 (tptt) cc_final: 0.8441 (ttpp) REVERT: D 887 GLU cc_start: 0.8133 (tp30) cc_final: 0.7486 (tp30) REVERT: D 903 ASP cc_start: 0.7959 (m-30) cc_final: 0.7542 (t0) REVERT: D 907 LYS cc_start: 0.8558 (mmtt) cc_final: 0.8217 (mmmm) REVERT: D 918 LYS cc_start: 0.8523 (tptt) cc_final: 0.8245 (mttp) REVERT: D 920 ASP cc_start: 0.7861 (t70) cc_final: 0.7596 (t0) REVERT: D 925 GLU cc_start: 0.8073 (tp30) cc_final: 0.7858 (tm-30) REVERT: D 961 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7854 (pp20) REVERT: E 25 LYS cc_start: 0.8223 (tppp) cc_final: 0.7903 (tppp) REVERT: E 30 ILE cc_start: 0.8110 (mt) cc_final: 0.7778 (mt) REVERT: E 34 ASP cc_start: 0.8165 (m-30) cc_final: 0.7913 (m-30) REVERT: E 38 ASP cc_start: 0.7915 (t0) cc_final: 0.7372 (t0) REVERT: E 40 GLU cc_start: 0.7773 (tt0) cc_final: 0.7549 (tt0) REVERT: E 72 GLU cc_start: 0.7963 (tt0) cc_final: 0.7733 (tt0) REVERT: E 79 MET cc_start: 0.7967 (ttp) cc_final: 0.7317 (tmt) REVERT: E 82 LYS cc_start: 0.8618 (ttmm) cc_final: 0.8399 (tttm) REVERT: E 83 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7681 (mt-10) REVERT: E 93 LYS cc_start: 0.8742 (mttt) cc_final: 0.8479 (mtpp) REVERT: E 144 MET cc_start: 0.8429 (mtt) cc_final: 0.8009 (mtt) REVERT: E 159 VAL cc_start: 0.8142 (t) cc_final: 0.7918 (m) REVERT: E 172 GLN cc_start: 0.7354 (tm130) cc_final: 0.6979 (tm130) REVERT: E 194 MET cc_start: 0.7565 (tmm) cc_final: 0.7317 (tmm) REVERT: E 241 GLU cc_start: 0.7128 (tp30) cc_final: 0.6632 (tp30) REVERT: E 249 LYS cc_start: 0.8125 (tptt) cc_final: 0.7609 (tptt) REVERT: F 29 MET cc_start: 0.6753 (tpt) cc_final: 0.6393 (tpp) REVERT: F 42 LYS cc_start: 0.7171 (ttmt) cc_final: 0.6857 (ttmt) REVERT: F 59 MET cc_start: 0.2935 (pmm) cc_final: 0.2579 (ppp) REVERT: F 61 PHE cc_start: 0.8029 (m-80) cc_final: 0.7789 (m-80) REVERT: F 144 ASN cc_start: 0.3996 (OUTLIER) cc_final: 0.3626 (t0) REVERT: F 264 LYS cc_start: 0.7878 (tptt) cc_final: 0.7317 (mmmt) REVERT: F 295 LYS cc_start: 0.8586 (tmmt) cc_final: 0.8257 (tmmt) outliers start: 134 outliers final: 73 residues processed: 944 average time/residue: 0.7676 time to fit residues: 857.2087 Evaluate side-chains 937 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 842 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 503 GLN Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 882 ASN Chi-restraints excluded: chain A residue 1019 HIS Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1213 GLU Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain A residue 1495 ILE Chi-restraints excluded: chain A residue 1559 LEU Chi-restraints excluded: chain A residue 1733 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 435 HIS Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 585 ARG Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 628 ARG Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 887 CYS Chi-restraints excluded: chain B residue 1206 THR Chi-restraints excluded: chain B residue 1223 ILE Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1573 GLU Chi-restraints excluded: chain B residue 1587 CYS Chi-restraints excluded: chain B residue 1588 GLN Chi-restraints excluded: chain B residue 1647 SER Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 675 ASP Chi-restraints excluded: chain C residue 691 LEU Chi-restraints excluded: chain C residue 741 LYS Chi-restraints excluded: chain C residue 798 THR Chi-restraints excluded: chain C residue 805 ASN Chi-restraints excluded: chain C residue 806 MET Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 858 VAL Chi-restraints excluded: chain C residue 873 THR Chi-restraints excluded: chain C residue 890 LYS Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 646 MET Chi-restraints excluded: chain D residue 705 GLU Chi-restraints excluded: chain D residue 751 LYS Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 827 LEU Chi-restraints excluded: chain D residue 848 LEU Chi-restraints excluded: chain D residue 857 GLU Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 864 GLU Chi-restraints excluded: chain D residue 879 MET Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 208 LYS Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain F residue 274 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 129 optimal weight: 0.4980 chunk 74 optimal weight: 0.9980 chunk 248 optimal weight: 0.7980 chunk 295 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 125 optimal weight: 0.3980 chunk 364 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN ** A 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 GLN B 486 ASN B 763 HIS B 778 ASN B 794 GLN B 798 HIS ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 HIS B1588 GLN ** B1681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 HIS ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 617 HIS ** C 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 823 HIS D 212 ASN D 617 HIS ** D 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 915 HIS E 191 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.144977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.120294 restraints weight = 73303.236| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.67 r_work: 0.3575 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 35789 Z= 0.234 Angle : 0.822 14.077 48433 Z= 0.409 Chirality : 0.046 0.259 5550 Planarity : 0.005 0.082 6169 Dihedral : 4.788 52.044 4750 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.91 % Allowed : 26.73 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.02 (0.13), residues: 4311 helix: 1.06 (0.10), residues: 2676 sheet: -0.61 (0.27), residues: 306 loop : 0.47 (0.19), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 751 TYR 0.027 0.002 TYR A1569 PHE 0.030 0.002 PHE B 860 TRP 0.051 0.003 TRP C 103 HIS 0.011 0.001 HIS C 823 Details of bonding type rmsd covalent geometry : bond 0.00532 (35789) covalent geometry : angle 0.82239 (48433) hydrogen bonds : bond 0.04257 ( 2259) hydrogen bonds : angle 5.05395 ( 6642) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8622 Ramachandran restraints generated. 4311 Oldfield, 0 Emsley, 4311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 855 time to evaluate : 1.392 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 119 LEU cc_start: 0.7684 (mt) cc_final: 0.7170 (mt) REVERT: A 122 LEU cc_start: 0.8632 (tm) cc_final: 0.8194 (mm) REVERT: A 123 PHE cc_start: 0.7831 (m-80) cc_final: 0.7396 (m-80) REVERT: A 182 ASN cc_start: 0.8120 (m-40) cc_final: 0.7727 (m-40) REVERT: A 186 PHE cc_start: 0.7927 (m-80) cc_final: 0.7380 (m-80) REVERT: A 190 TYR cc_start: 0.7070 (m-80) cc_final: 0.6846 (m-80) REVERT: A 216 GLU cc_start: 0.7983 (tt0) cc_final: 0.7280 (tp30) REVERT: A 234 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7353 (tp30) REVERT: A 251 GLU cc_start: 0.8130 (mp0) cc_final: 0.7830 (mp0) REVERT: A 279 LEU cc_start: 0.8289 (mt) cc_final: 0.7682 (mt) REVERT: A 282 ASP cc_start: 0.8048 (t0) cc_final: 0.7743 (p0) REVERT: A 307 HIS cc_start: 0.8314 (m-70) cc_final: 0.7970 (m-70) REVERT: A 325 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7640 (mp10) REVERT: A 340 LEU cc_start: 0.8881 (mt) cc_final: 0.8606 (mt) REVERT: A 392 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7515 (mm-30) REVERT: A 393 GLU cc_start: 0.8012 (pp20) cc_final: 0.7516 (pp20) REVERT: A 405 GLU cc_start: 0.7882 (tt0) cc_final: 0.7420 (tp30) REVERT: A 482 GLU cc_start: 0.8078 (tt0) cc_final: 0.7578 (tm-30) REVERT: A 483 GLU cc_start: 0.7794 (mp0) cc_final: 0.7292 (mp0) REVERT: A 489 VAL cc_start: 0.8532 (t) cc_final: 0.8318 (t) REVERT: A 498 GLU cc_start: 0.7509 (pp20) cc_final: 0.7179 (pp20) REVERT: A 517 GLU cc_start: 0.7388 (tp30) cc_final: 0.7094 (mm-30) REVERT: A 535 MET cc_start: 0.7987 (mtm) cc_final: 0.7475 (mtp) REVERT: A 596 LEU cc_start: 0.8855 (tp) cc_final: 0.8546 (tt) REVERT: A 608 SER cc_start: 0.9069 (OUTLIER) cc_final: 0.8811 (p) REVERT: A 622 ARG cc_start: 0.8309 (mpp80) cc_final: 0.8042 (mmm-85) REVERT: A 691 ARG cc_start: 0.8597 (ttp80) cc_final: 0.8319 (ttm110) REVERT: A 707 LYS cc_start: 0.9027 (tttt) cc_final: 0.8703 (ttmm) REVERT: A 782 LYS cc_start: 0.8055 (mttt) cc_final: 0.7655 (mppt) REVERT: A 804 CYS cc_start: 0.8169 (m) cc_final: 0.7658 (m) REVERT: A 880 LYS cc_start: 0.8612 (mttt) cc_final: 0.8249 (ttmm) REVERT: A 919 ASN cc_start: 0.7838 (m-40) cc_final: 0.7576 (m-40) REVERT: A 1016 LYS cc_start: 0.8373 (mttt) cc_final: 0.7927 (tppt) REVERT: A 1024 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7516 (tm-30) REVERT: A 1037 ASN cc_start: 0.8362 (m-40) cc_final: 0.7984 (m-40) REVERT: A 1043 LYS cc_start: 0.8481 (tttm) cc_final: 0.8120 (ttpp) REVERT: A 1213 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7108 (mt-10) REVERT: A 1231 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8360 (mm) REVERT: A 1239 GLU cc_start: 0.7360 (tp30) cc_final: 0.7103 (tp30) REVERT: A 1243 GLU cc_start: 0.6949 (tp30) cc_final: 0.6648 (tp30) REVERT: A 1528 GLU cc_start: 0.7386 (pp20) cc_final: 0.6802 (pp20) REVERT: A 1529 ARG cc_start: 0.7666 (tpp-160) cc_final: 0.7145 (tpp-160) REVERT: A 1580 ARG cc_start: 0.8269 (ptm-80) cc_final: 0.7909 (ttm170) REVERT: A 1602 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7783 (tt0) REVERT: A 1679 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8116 (mm-30) REVERT: A 1744 LEU cc_start: 0.8534 (tp) cc_final: 0.8146 (tt) REVERT: A 1756 GLU cc_start: 0.6903 (pp20) cc_final: 0.6641 (pp20) REVERT: B 60 MET cc_start: 0.8240 (tpp) cc_final: 0.7993 (tpp) REVERT: B 74 GLU cc_start: 0.6306 (OUTLIER) cc_final: 0.3814 (mt-10) REVERT: B 136 LEU cc_start: 0.7692 (mp) cc_final: 0.7450 (mm) REVERT: B 141 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7271 (tp30) REVERT: B 144 LYS cc_start: 0.8834 (mtpt) cc_final: 0.8415 (ttmm) REVERT: B 148 ASP cc_start: 0.8435 (m-30) cc_final: 0.7587 (p0) REVERT: B 151 ARG cc_start: 0.7913 (ptm160) cc_final: 0.6909 (ptm160) REVERT: B 152 HIS cc_start: 0.7728 (t70) cc_final: 0.7377 (t70) REVERT: B 157 GLU cc_start: 0.7600 (mp0) cc_final: 0.7323 (mm-30) REVERT: B 167 TRP cc_start: 0.7860 (t-100) cc_final: 0.7539 (t60) REVERT: B 186 PHE cc_start: 0.8531 (m-80) cc_final: 0.7775 (m-80) REVERT: B 278 HIS cc_start: 0.7200 (t70) cc_final: 0.6903 (t70) REVERT: B 327 MET cc_start: 0.6379 (mmp) cc_final: 0.5898 (mmt) REVERT: B 360 ILE cc_start: 0.8549 (mt) cc_final: 0.8062 (tt) REVERT: B 364 ILE cc_start: 0.8999 (mp) cc_final: 0.8747 (mp) REVERT: B 366 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7585 (tm-30) REVERT: B 380 LEU cc_start: 0.8667 (tp) cc_final: 0.8360 (tp) REVERT: B 426 LEU cc_start: 0.9269 (tp) cc_final: 0.8963 (tm) REVERT: B 451 ARG cc_start: 0.7720 (tpt90) cc_final: 0.7311 (tpt90) REVERT: B 471 PHE cc_start: 0.8716 (t80) cc_final: 0.8509 (t80) REVERT: B 510 GLN cc_start: 0.8174 (mt0) cc_final: 0.7678 (tm-30) REVERT: B 511 LEU cc_start: 0.8574 (tt) cc_final: 0.8153 (tm) REVERT: B 514 ASP cc_start: 0.7497 (m-30) cc_final: 0.6721 (m-30) REVERT: B 557 LEU cc_start: 0.8458 (mt) cc_final: 0.8152 (mt) REVERT: B 574 LYS cc_start: 0.8244 (ptmt) cc_final: 0.7970 (ptmm) REVERT: B 585 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8382 (ttp80) REVERT: B 595 GLN cc_start: 0.7704 (tp40) cc_final: 0.7413 (tp-100) REVERT: B 628 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8041 (mtm110) REVERT: B 691 ARG cc_start: 0.8105 (ttm-80) cc_final: 0.7820 (mtm-85) REVERT: B 704 LYS cc_start: 0.8492 (mttt) cc_final: 0.8160 (mppt) REVERT: B 761 ASP cc_start: 0.7859 (m-30) cc_final: 0.7531 (m-30) REVERT: B 762 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8479 (tt) REVERT: B 782 LYS cc_start: 0.8774 (mttt) cc_final: 0.8395 (mppt) REVERT: B 906 LYS cc_start: 0.8659 (tttm) cc_final: 0.8354 (tttm) REVERT: B 907 ASP cc_start: 0.8054 (p0) cc_final: 0.7838 (p0) REVERT: B 914 LYS cc_start: 0.9039 (tppt) cc_final: 0.8661 (tppt) REVERT: B 917 ARG cc_start: 0.8685 (ttm170) cc_final: 0.7910 (ttm110) REVERT: B 919 ASN cc_start: 0.8312 (m-40) cc_final: 0.7868 (m110) REVERT: B 1016 LYS cc_start: 0.8762 (tppt) cc_final: 0.8538 (mptt) REVERT: B 1017 ASN cc_start: 0.8735 (t0) cc_final: 0.8289 (t0) REVERT: B 1028 ASP cc_start: 0.8060 (t70) cc_final: 0.7540 (t0) REVERT: B 1222 ASP cc_start: 0.7903 (m-30) cc_final: 0.7626 (m-30) REVERT: B 1230 GLU cc_start: 0.8203 (mp0) cc_final: 0.7987 (mp0) REVERT: B 1573 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7835 (mp0) REVERT: B 1602 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7732 (mm-30) REVERT: B 1639 ARG cc_start: 0.7984 (ptt180) cc_final: 0.7673 (ptt180) REVERT: B 1656 ASP cc_start: 0.7888 (p0) cc_final: 0.7529 (p0) REVERT: B 1756 GLU cc_start: 0.7606 (pp20) cc_final: 0.7240 (pp20) REVERT: C 7 VAL cc_start: 0.8950 (t) cc_final: 0.8735 (m) REVERT: C 10 LEU cc_start: 0.8811 (mp) cc_final: 0.8399 (tp) REVERT: C 11 LEU cc_start: 0.8699 (mt) cc_final: 0.8484 (mm) REVERT: C 13 MET cc_start: 0.7918 (mtm) cc_final: 0.7597 (ttm) REVERT: C 232 GLU cc_start: 0.7459 (mp0) cc_final: 0.7063 (mp0) REVERT: C 255 VAL cc_start: 0.8630 (m) cc_final: 0.8401 (p) REVERT: C 272 GLU cc_start: 0.7082 (tm-30) cc_final: 0.6637 (tm-30) REVERT: C 688 ILE cc_start: 0.8990 (mt) cc_final: 0.8580 (tp) REVERT: C 689 ARG cc_start: 0.8034 (mmm160) cc_final: 0.7559 (mmp80) REVERT: C 722 LYS cc_start: 0.8458 (tppt) cc_final: 0.8159 (tppp) REVERT: C 736 MET cc_start: 0.8241 (mmm) cc_final: 0.7944 (mmm) REVERT: C 741 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7764 (tmmm) REVERT: C 746 ASP cc_start: 0.7677 (m-30) cc_final: 0.7215 (m-30) REVERT: C 756 LYS cc_start: 0.8404 (tttt) cc_final: 0.8096 (tmmt) REVERT: C 799 LYS cc_start: 0.8861 (tttt) cc_final: 0.8524 (tmtp) REVERT: C 806 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7262 (tmm) REVERT: C 810 LEU cc_start: 0.8583 (mm) cc_final: 0.8020 (mt) REVERT: C 813 GLU cc_start: 0.7889 (pp20) cc_final: 0.7668 (pp20) REVERT: C 819 ASN cc_start: 0.8448 (t0) cc_final: 0.8157 (t0) REVERT: C 825 GLU cc_start: 0.8214 (pp20) cc_final: 0.7898 (pp20) REVERT: C 830 GLN cc_start: 0.8692 (tp40) cc_final: 0.8377 (mm-40) REVERT: C 844 GLN cc_start: 0.7346 (tm-30) cc_final: 0.6986 (tm-30) REVERT: C 845 MET cc_start: 0.8397 (ttt) cc_final: 0.8081 (ttm) REVERT: C 852 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8949 (mm) REVERT: C 857 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7435 (mm-30) REVERT: C 861 LEU cc_start: 0.8497 (mt) cc_final: 0.8251 (mm) REVERT: C 863 LEU cc_start: 0.8870 (tp) cc_final: 0.8594 (tm) REVERT: C 864 GLU cc_start: 0.8357 (tt0) cc_final: 0.7840 (tp30) REVERT: C 874 THR cc_start: 0.7756 (p) cc_final: 0.7428 (t) REVERT: C 878 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7633 (mt-10) REVERT: C 884 TYR cc_start: 0.8636 (t80) cc_final: 0.8169 (t80) REVERT: C 890 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8756 (ttpp) REVERT: C 906 GLN cc_start: 0.7769 (pp30) cc_final: 0.7385 (pp30) REVERT: C 907 LYS cc_start: 0.8482 (mmmm) cc_final: 0.8225 (mmmm) REVERT: C 925 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7848 (mm-30) REVERT: C 961 GLU cc_start: 0.7804 (tp30) cc_final: 0.7395 (tp30) REVERT: D 9 GLU cc_start: 0.8400 (mp0) cc_final: 0.7961 (mp0) REVERT: D 18 MET cc_start: 0.8113 (tpp) cc_final: 0.7893 (tmm) REVERT: D 29 PHE cc_start: 0.8556 (t80) cc_final: 0.8248 (t80) REVERT: D 51 GLU cc_start: 0.7426 (tm-30) cc_final: 0.7134 (pp20) REVERT: D 59 HIS cc_start: 0.7867 (m90) cc_final: 0.7659 (m-70) REVERT: D 64 LEU cc_start: 0.8004 (tp) cc_final: 0.7599 (tp) REVERT: D 136 LEU cc_start: 0.8861 (tp) cc_final: 0.8624 (tm) REVERT: D 261 LYS cc_start: 0.8760 (tppp) cc_final: 0.8373 (tppp) REVERT: D 629 LYS cc_start: 0.8450 (mmmt) cc_final: 0.8061 (mmmt) REVERT: D 646 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7676 (tmm) REVERT: D 650 ASP cc_start: 0.8094 (p0) cc_final: 0.7108 (p0) REVERT: D 665 ASN cc_start: 0.8664 (m-40) cc_final: 0.8344 (m-40) REVERT: D 691 LEU cc_start: 0.9155 (tp) cc_final: 0.8871 (tm) REVERT: D 694 GLN cc_start: 0.8535 (mm-40) cc_final: 0.8096 (mm-40) REVERT: D 705 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8177 (tm-30) REVERT: D 712 HIS cc_start: 0.8407 (OUTLIER) cc_final: 0.7231 (t70) REVERT: D 714 LEU cc_start: 0.8877 (mt) cc_final: 0.8571 (mt) REVERT: D 717 ARG cc_start: 0.7986 (tmm160) cc_final: 0.7163 (tmm160) REVERT: D 718 ARG cc_start: 0.8893 (ttm110) cc_final: 0.8047 (ttm110) REVERT: D 721 ARG cc_start: 0.8421 (ptp-110) cc_final: 0.8091 (ptp-110) REVERT: D 749 MET cc_start: 0.8158 (ttp) cc_final: 0.7815 (ttp) REVERT: D 751 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8988 (tppp) REVERT: D 756 LYS cc_start: 0.8590 (tmmm) cc_final: 0.8187 (tptp) REVERT: D 806 MET cc_start: 0.7271 (ttt) cc_final: 0.6759 (tpp) REVERT: D 842 GLN cc_start: 0.8445 (tm-30) cc_final: 0.8005 (tm-30) REVERT: D 844 GLN cc_start: 0.8192 (tm-30) cc_final: 0.7565 (tm-30) REVERT: D 845 MET cc_start: 0.8355 (tmt) cc_final: 0.7955 (tmt) REVERT: D 846 GLU cc_start: 0.8219 (tt0) cc_final: 0.7446 (tp30) REVERT: D 848 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8464 (mt) REVERT: D 852 LEU cc_start: 0.8728 (tp) cc_final: 0.8466 (tm) REVERT: D 857 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7776 (mm-30) REVERT: D 860 GLU cc_start: 0.7960 (tp30) cc_final: 0.7639 (tp30) REVERT: D 864 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7244 (mm-30) REVERT: D 867 GLN cc_start: 0.8024 (pt0) cc_final: 0.7634 (pt0) REVERT: D 868 ASN cc_start: 0.7412 (m110) cc_final: 0.6889 (m-40) REVERT: D 886 LYS cc_start: 0.8721 (tptt) cc_final: 0.8449 (ttpp) REVERT: D 887 GLU cc_start: 0.8181 (tp30) cc_final: 0.7473 (tp30) REVERT: D 903 ASP cc_start: 0.8317 (m-30) cc_final: 0.7923 (t0) REVERT: D 907 LYS cc_start: 0.8548 (mmtt) cc_final: 0.8225 (mmmm) REVERT: D 918 LYS cc_start: 0.8599 (tptt) cc_final: 0.8291 (mttm) REVERT: D 920 ASP cc_start: 0.7846 (t70) cc_final: 0.7593 (t0) REVERT: D 925 GLU cc_start: 0.8061 (tp30) cc_final: 0.7803 (tm-30) REVERT: D 961 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7939 (pp20) REVERT: E 30 ILE cc_start: 0.8133 (mt) cc_final: 0.7812 (mt) REVERT: E 34 ASP cc_start: 0.8163 (m-30) cc_final: 0.7913 (m-30) REVERT: E 38 ASP cc_start: 0.7927 (t0) cc_final: 0.7441 (t0) REVERT: E 40 GLU cc_start: 0.7895 (tt0) cc_final: 0.7658 (tt0) REVERT: E 54 MET cc_start: 0.8472 (pmm) cc_final: 0.8128 (pmm) REVERT: E 72 GLU cc_start: 0.8056 (tt0) cc_final: 0.7806 (tt0) REVERT: E 79 MET cc_start: 0.7928 (ttp) cc_final: 0.7252 (tmt) REVERT: E 82 LYS cc_start: 0.8619 (ttmm) cc_final: 0.8387 (tttm) REVERT: E 93 LYS cc_start: 0.8698 (mttt) cc_final: 0.8427 (mtpp) REVERT: E 144 MET cc_start: 0.8474 (mtt) cc_final: 0.8053 (mtt) REVERT: E 159 VAL cc_start: 0.8135 (t) cc_final: 0.7921 (m) REVERT: E 172 GLN cc_start: 0.7395 (tm130) cc_final: 0.7017 (tm130) REVERT: E 191 HIS cc_start: 0.5833 (OUTLIER) cc_final: 0.5549 (t-170) REVERT: E 194 MET cc_start: 0.7599 (tmm) cc_final: 0.7332 (tmm) REVERT: E 241 GLU cc_start: 0.7216 (tp30) cc_final: 0.6696 (tp30) REVERT: E 249 LYS cc_start: 0.8111 (tptt) cc_final: 0.7583 (tptt) REVERT: E 251 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7762 (tmt) REVERT: E 277 LYS cc_start: 0.8176 (mtmt) cc_final: 0.7888 (mtmm) REVERT: F 29 MET cc_start: 0.6886 (tpt) cc_final: 0.6659 (tpp) REVERT: F 42 LYS cc_start: 0.7251 (ttmt) cc_final: 0.6932 (ttmt) REVERT: F 61 PHE cc_start: 0.8076 (m-80) cc_final: 0.7705 (m-80) REVERT: F 63 CYS cc_start: 0.8089 (p) cc_final: 0.7825 (p) REVERT: F 144 ASN cc_start: 0.4029 (OUTLIER) cc_final: 0.3675 (t0) REVERT: F 232 PHE cc_start: 0.7924 (t80) cc_final: 0.7681 (t80) REVERT: F 264 LYS cc_start: 0.7900 (tptt) cc_final: 0.7340 (mmmt) REVERT: F 295 LYS cc_start: 0.8547 (tmmt) cc_final: 0.8188 (tmmt) outliers start: 114 outliers final: 64 residues processed: 912 average time/residue: 0.8042 time to fit residues: 864.6562 Evaluate side-chains 927 residues out of total 3916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 841 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 503 GLN Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 882 ASN Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1213 GLU Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain A residue 1559 LEU Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 435 HIS Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 585 ARG Chi-restraints excluded: chain B residue 628 ARG Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 887 CYS Chi-restraints excluded: chain B residue 1206 THR Chi-restraints excluded: chain B residue 1573 GLU Chi-restraints excluded: chain B residue 1588 GLN Chi-restraints excluded: chain B residue 1647 SER Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 71 HIS Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 617 HIS Chi-restraints excluded: chain C residue 691 LEU Chi-restraints excluded: chain C residue 741 LYS Chi-restraints excluded: chain C residue 805 ASN Chi-restraints excluded: chain C residue 806 MET Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain C residue 823 HIS Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 858 VAL Chi-restraints excluded: chain C residue 873 THR Chi-restraints excluded: chain C residue 890 LYS Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain D residue 646 MET Chi-restraints excluded: chain D residue 705 GLU Chi-restraints excluded: chain D residue 712 HIS Chi-restraints excluded: chain D residue 751 LYS Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 827 LEU Chi-restraints excluded: chain D residue 848 LEU Chi-restraints excluded: chain D residue 857 GLU Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 864 GLU Chi-restraints excluded: chain D residue 879 MET Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 191 HIS Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 208 LYS Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain F residue 274 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 77 optimal weight: 0.9990 chunk 368 optimal weight: 0.6980 chunk 13 optimal weight: 0.0070 chunk 140 optimal weight: 0.8980 chunk 43 optimal weight: 0.2980 chunk 379 optimal weight: 0.0870 chunk 195 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 405 optimal weight: 4.9990 chunk 234 optimal weight: 0.2980 overall best weight: 0.2776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN ** A 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1019 HIS ** A1611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 GLN B 763 HIS B 778 ASN B 794 GLN B 798 HIS ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 HIS B1588 GLN ** B1681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 617 HIS C 743 GLN C 823 HIS D 617 HIS D 823 HIS ** D 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 915 HIS E 191 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.146705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.122270 restraints weight = 73055.765| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.69 r_work: 0.3600 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35789 Z= 0.174 Angle : 0.812 13.778 48433 Z= 0.401 Chirality : 0.044 0.245 5550 Planarity : 0.005 0.095 6169 Dihedral : 4.677 51.279 4745 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.68 % Allowed : 27.29 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.04 (0.13), residues: 4311 helix: 1.08 (0.10), residues: 2678 sheet: -0.61 (0.27), residues: 308 loop : 0.47 (0.19), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG D 706 TYR 0.036 0.002 TYR D 884 PHE 0.032 0.002 PHE E 49 TRP 0.054 0.003 TRP C 103 HIS 0.023 0.001 HIS E 191 Details of bonding type rmsd covalent geometry : bond 0.00404 (35789) covalent geometry : angle 0.81190 (48433) hydrogen bonds : bond 0.04141 ( 2259) hydrogen bonds : angle 5.02157 ( 6642) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20154.78 seconds wall clock time: 343 minutes 1.99 seconds (20581.99 seconds total)