Starting phenix.real_space_refine on Sat Aug 8 16:39:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8i03_35093/08_2026/8i03_35093.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i03_35093/08_2026/8i03_35093.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8i03_35093/08_2026/8i03_35093.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8i03_35093/08_2026/8i03_35093.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i03_35093/08_2026/8i03_35093.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i03_35093/08_2026/8i03_35093.map" model { file = "/net/cci-nas-00/data/ceres_data/8i03_35093/08_2026/8i03_35093.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i03_35093/08_2026/8i03_35093.cif" } resolution = 3.2 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 4 8.98 5 Zn 2 6.06 5 P 4 5.49 5 S 148 5.16 5 C 18642 2.51 5 N 5059 2.21 5 O 5571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 415 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29430 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 5072 Classifications: {'peptide': 616} Link IDs: {'PTRANS': 27, 'TRANS': 588} Chain breaks: 2 Chain: "B" Number of atoms: 5305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5305 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 21, 'TRANS': 617} Chain breaks: 4 Chain: "C" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2962 Classifications: {'peptide': 370} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 355} Chain: "D" Number of atoms: 2911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2911 Classifications: {'peptide': 363} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 348} Chain: "E" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1328 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 3, 'TRANS': 165} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 2, 'PHE:plan': 2, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "F" Number of atoms: 1831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1831 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 10, 'TRANS': 217} Chain: "G" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1306 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 1, 'TRANS': 164} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 994 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "I" Number of atoms: 1505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1505 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 11, 'TRANS': 173} Chain: "J" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3105 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 20, 'TRANS': 367} Chain breaks: 1 Chain: "K" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3105 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 20, 'TRANS': 367} Chain breaks: 1 Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.44, per 1000 atoms: 0.18 Number of scatterers: 29430 At special positions: 0 Unit cell: (113.048, 184.79, 303.273, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 K 4 19.00 S 148 16.00 P 4 15.00 O 5571 8.00 N 5059 7.00 C 18642 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: 2.59 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" ND1 HIS C 175 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" ND1 HIS D 175 " 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6944 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 25 sheets defined 50.4% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 511 through 522 removed outlier: 3.760A pdb=" N ARG A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 543 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.782A pdb=" N VAL A 552 " --> pdb=" O LYS A 548 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLU A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 573 removed outlier: 3.625A pdb=" N ASN A 567 " --> pdb=" O GLU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 593 removed outlier: 3.744A pdb=" N GLN A 592 " --> pdb=" O ASP A 589 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS A 593 " --> pdb=" O LEU A 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 589 through 593' Processing helix chain 'A' and resid 604 through 610 removed outlier: 3.840A pdb=" N LEU A 610 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 647 through 684 removed outlier: 4.106A pdb=" N ILE A 678 " --> pdb=" O GLU A 674 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS A 679 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP A 681 " --> pdb=" O GLN A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 693 Processing helix chain 'A' and resid 704 through 717 removed outlier: 4.068A pdb=" N TYR A 708 " --> pdb=" O SER A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 731 removed outlier: 3.543A pdb=" N ILE A 724 " --> pdb=" O HIS A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 770 removed outlier: 3.568A pdb=" N THR A 735 " --> pdb=" O ASN A 731 " (cutoff:3.500A) Proline residue: A 737 - end of helix removed outlier: 4.618A pdb=" N GLU A 759 " --> pdb=" O ASN A 755 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LEU A 760 " --> pdb=" O HIS A 756 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N TYR A 770 " --> pdb=" O GLU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 773 No H-bonds generated for 'chain 'A' and resid 771 through 773' Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 789 through 810 Processing helix chain 'A' and resid 827 through 842 Processing helix chain 'A' and resid 847 through 866 Processing helix chain 'A' and resid 869 through 874 Processing helix chain 'A' and resid 1007 through 1039 removed outlier: 4.770A pdb=" N GLN A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N MET A1033 " --> pdb=" O ASN A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1050 Processing helix chain 'A' and resid 1069 through 1084 removed outlier: 3.649A pdb=" N GLN A1073 " --> pdb=" O THR A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1100 Processing helix chain 'A' and resid 1103 through 1107 removed outlier: 3.530A pdb=" N LEU A1106 " --> pdb=" O ALA A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1124 Processing helix chain 'A' and resid 1126 through 1142 removed outlier: 3.719A pdb=" N ALA A1130 " --> pdb=" O ASN A1126 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN A1131 " --> pdb=" O ARG A1127 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN A1142 " --> pdb=" O LYS A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1162 Processing helix chain 'A' and resid 1196 through 1207 removed outlier: 3.698A pdb=" N SER A1207 " --> pdb=" O TYR A1203 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 422 Processing helix chain 'B' and resid 424 through 440 Processing helix chain 'B' and resid 444 through 457 Processing helix chain 'B' and resid 458 through 469 Processing helix chain 'B' and resid 484 through 493 removed outlier: 4.576A pdb=" N LEU B 489 " --> pdb=" O ARG B 486 " (cutoff:3.500A) Proline residue: B 490 - end of helix Processing helix chain 'B' and resid 504 through 508 Processing helix chain 'B' and resid 518 through 523 Processing helix chain 'B' and resid 547 through 578 removed outlier: 3.832A pdb=" N LEU B 551 " --> pdb=" O TYR B 547 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 564 " --> pdb=" O ASP B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 585 removed outlier: 7.304A pdb=" N THR B 582 " --> pdb=" O CYS B 579 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE B 583 " --> pdb=" O GLU B 580 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N HIS B 584 " --> pdb=" O PRO B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 596 removed outlier: 3.968A pdb=" N ALA B 590 " --> pdb=" O HIS B 586 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU B 595 " --> pdb=" O LEU B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 609 removed outlier: 3.547A pdb=" N ILE B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 624 removed outlier: 4.431A pdb=" N LEU B 616 " --> pdb=" O GLU B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 664 Proline residue: B 630 - end of helix removed outlier: 3.549A pdb=" N GLU B 649 " --> pdb=" O ARG B 645 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE B 653 " --> pdb=" O GLU B 649 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 655 " --> pdb=" O SER B 651 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLN B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 681 removed outlier: 3.519A pdb=" N ILE B 673 " --> pdb=" O ARG B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 699 removed outlier: 3.606A pdb=" N HIS B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 732 removed outlier: 4.048A pdb=" N LEU B 721 " --> pdb=" O SER B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 758 removed outlier: 3.765A pdb=" N LYS B 742 " --> pdb=" O SER B 738 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY B 743 " --> pdb=" O TYR B 739 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 842 Processing helix chain 'B' and resid 849 through 876 Processing helix chain 'B' and resid 884 through 898 removed outlier: 3.635A pdb=" N LYS B 898 " --> pdb=" O GLU B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 911 Processing helix chain 'B' and resid 912 through 914 No H-bonds generated for 'chain 'B' and resid 912 through 914' Processing helix chain 'B' and resid 915 through 920 Processing helix chain 'B' and resid 923 through 941 Processing helix chain 'B' and resid 943 through 954 removed outlier: 3.797A pdb=" N LEU B 947 " --> pdb=" O LYS B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 976 removed outlier: 3.859A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 1011 through 1026 Processing helix chain 'B' and resid 1107 through 1125 removed outlier: 3.520A pdb=" N GLU B1125 " --> pdb=" O ARG B1121 " (cutoff:3.500A) Processing helix chain 'B' and resid 1136 through 1145 Processing helix chain 'C' and resid 15 through 19 removed outlier: 3.992A pdb=" N TYR C 19 " --> pdb=" O VAL C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 42 removed outlier: 4.214A pdb=" N ARG C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 46 removed outlier: 3.740A pdb=" N GLU C 46 " --> pdb=" O ASN C 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 43 through 46' Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 66 through 76 Processing helix chain 'C' and resid 80 through 83 removed outlier: 3.828A pdb=" N LYS C 83 " --> pdb=" O THR C 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 80 through 83' Processing helix chain 'C' and resid 84 through 92 removed outlier: 3.562A pdb=" N LEU C 89 " --> pdb=" O GLN C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 124 Processing helix chain 'C' and resid 151 through 161 removed outlier: 3.921A pdb=" N LEU C 155 " --> pdb=" O ASN C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 184 removed outlier: 3.920A pdb=" N PHE C 184 " --> pdb=" O VAL C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 217 removed outlier: 3.806A pdb=" N LYS C 217 " --> pdb=" O GLY C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 249 Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 274 through 287 removed outlier: 4.103A pdb=" N CYS C 281 " --> pdb=" O GLY C 277 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL C 282 " --> pdb=" O HIS C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 317 Processing helix chain 'C' and resid 330 through 334 Processing helix chain 'C' and resid 352 through 369 Processing helix chain 'D' and resid 13 through 19 removed outlier: 3.515A pdb=" N VAL D 16 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY D 17 " --> pdb=" O GLU D 14 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR D 19 " --> pdb=" O VAL D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 42 removed outlier: 4.027A pdb=" N ARG D 33 " --> pdb=" O PRO D 29 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 removed outlier: 3.786A pdb=" N MET D 61 " --> pdb=" O THR D 57 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR D 62 " --> pdb=" O ARG D 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 57 through 62' Processing helix chain 'D' and resid 66 through 76 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 102 through 123 Processing helix chain 'D' and resid 151 through 161 removed outlier: 3.883A pdb=" N LEU D 155 " --> pdb=" O ASN D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'D' and resid 213 through 217 removed outlier: 3.965A pdb=" N LYS D 217 " --> pdb=" O GLY D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 249 Proline residue: D 240 - end of helix Processing helix chain 'D' and resid 274 through 287 removed outlier: 4.342A pdb=" N CYS D 281 " --> pdb=" O GLY D 277 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL D 282 " --> pdb=" O HIS D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 318 Processing helix chain 'D' and resid 330 through 335 removed outlier: 3.503A pdb=" N TYR D 333 " --> pdb=" O TYR D 330 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY D 335 " --> pdb=" O GLN D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 367 Processing helix chain 'E' and resid 312 through 343 Processing helix chain 'E' and resid 347 through 423 removed outlier: 3.854A pdb=" N ARG E 359 " --> pdb=" O LEU E 355 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N MET E 372 " --> pdb=" O THR E 368 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS E 373 " --> pdb=" O GLU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 460 removed outlier: 3.524A pdb=" N ALA E 451 " --> pdb=" O GLU E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'F' and resid 2 through 17 Processing helix chain 'F' and resid 42 through 46 removed outlier: 3.604A pdb=" N VAL F 46 " --> pdb=" O SER F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 90 Processing helix chain 'F' and resid 96 through 101 Processing helix chain 'F' and resid 106 through 112 Processing helix chain 'F' and resid 113 through 120 Processing helix chain 'F' and resid 124 through 155 removed outlier: 3.682A pdb=" N SER F 130 " --> pdb=" O SER F 126 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA F 138 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU F 139 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N HIS F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 168 removed outlier: 3.530A pdb=" N VAL F 167 " --> pdb=" O PRO F 163 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE F 168 " --> pdb=" O PRO F 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 163 through 168' Processing helix chain 'F' and resid 173 through 217 removed outlier: 4.048A pdb=" N GLU F 177 " --> pdb=" O GLU F 173 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE F 193 " --> pdb=" O SER F 189 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN F 198 " --> pdb=" O ARG F 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 6 removed outlier: 3.519A pdb=" N SER G 5 " --> pdb=" O ASP G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 43 Processing helix chain 'G' and resid 49 through 138 removed outlier: 3.680A pdb=" N LEU G 53 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR G 73 " --> pdb=" O GLU G 69 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE G 74 " --> pdb=" O ARG G 70 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU G 86 " --> pdb=" O GLU G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 242 removed outlier: 4.259A pdb=" N LYS G 238 " --> pdb=" O ARG G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 265 Processing helix chain 'H' and resid 9 through 22 removed outlier: 3.982A pdb=" N THR H 16 " --> pdb=" O LEU H 12 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP H 17 " --> pdb=" O ASN H 13 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL H 20 " --> pdb=" O THR H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 39 removed outlier: 4.486A pdb=" N VAL H 26 " --> pdb=" O VAL H 22 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE H 36 " --> pdb=" O SER H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 57 removed outlier: 3.523A pdb=" N ASN H 57 " --> pdb=" O VAL H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 112 removed outlier: 3.653A pdb=" N CYS H 69 " --> pdb=" O GLY H 65 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU H 70 " --> pdb=" O GLU H 66 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU H 72 " --> pdb=" O ARG H 68 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU H 80 " --> pdb=" O LEU H 76 " (cutoff:3.500A) Proline residue: H 81 - end of helix removed outlier: 3.735A pdb=" N ASP H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER H 85 " --> pdb=" O PRO H 81 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR H 110 " --> pdb=" O ALA H 106 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU H 112 " --> pdb=" O PHE H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 120 Processing helix chain 'I' and resid 182 through 187 Processing helix chain 'I' and resid 212 through 216 removed outlier: 3.720A pdb=" N ILE I 216 " --> pdb=" O TYR I 213 " (cutoff:3.500A) Processing helix chain 'I' and resid 226 through 230 Processing helix chain 'I' and resid 235 through 240 removed outlier: 4.260A pdb=" N ARG I 239 " --> pdb=" O PRO I 235 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG I 240 " --> pdb=" O ARG I 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 235 through 240' Processing helix chain 'I' and resid 253 through 261 Processing helix chain 'I' and resid 323 through 328 Processing helix chain 'I' and resid 332 through 344 Processing helix chain 'J' and resid 15 through 36 removed outlier: 4.050A pdb=" N ASN J 36 " --> pdb=" O ILE J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 39 No H-bonds generated for 'chain 'J' and resid 37 through 39' Processing helix chain 'J' and resid 159 through 166 Processing helix chain 'J' and resid 215 through 217 No H-bonds generated for 'chain 'J' and resid 215 through 217' Processing helix chain 'J' and resid 267 through 271 removed outlier: 4.039A pdb=" N SER J 270 " --> pdb=" O PRO J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 356 through 358 No H-bonds generated for 'chain 'J' and resid 356 through 358' Processing helix chain 'J' and resid 364 through 368 Processing helix chain 'J' and resid 413 through 418 removed outlier: 4.334A pdb=" N TRP J 417 " --> pdb=" O SER J 413 " (cutoff:3.500A) Processing helix chain 'K' and resid 15 through 36 removed outlier: 4.050A pdb=" N ASN K 36 " --> pdb=" O ILE K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 39 No H-bonds generated for 'chain 'K' and resid 37 through 39' Processing helix chain 'K' and resid 159 through 166 Processing helix chain 'K' and resid 215 through 217 No H-bonds generated for 'chain 'K' and resid 215 through 217' Processing helix chain 'K' and resid 267 through 271 removed outlier: 4.040A pdb=" N SER K 270 " --> pdb=" O PRO K 267 " (cutoff:3.500A) Processing helix chain 'K' and resid 356 through 358 No H-bonds generated for 'chain 'K' and resid 356 through 358' Processing helix chain 'K' and resid 364 through 368 Processing helix chain 'K' and resid 413 through 418 removed outlier: 4.335A pdb=" N TRP K 417 " --> pdb=" O SER K 413 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 600 through 602 Processing sheet with id=AA2, first strand: chain 'A' and resid 819 through 822 removed outlier: 3.962A pdb=" N LEU A1167 " --> pdb=" O MET A1184 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 476 through 479 removed outlier: 6.363A pdb=" N ILE B 476 " --> pdb=" O SER I 176 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ASP I 178 " --> pdb=" O ILE B 476 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL B 478 " --> pdb=" O ASP I 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 500 through 501 Processing sheet with id=AA5, first strand: chain 'B' and resid 710 through 713 Processing sheet with id=AA6, first strand: chain 'B' and resid 1078 through 1080 Processing sheet with id=AA7, first strand: chain 'B' and resid 1094 through 1098 removed outlier: 6.627A pdb=" N THR J 411 " --> pdb=" O ASP J 42 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE J 44 " --> pdb=" O ILE J 409 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE J 409 " --> pdb=" O ILE J 44 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR J 46 " --> pdb=" O LEU J 407 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU J 407 " --> pdb=" O THR J 46 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE J 406 " --> pdb=" O ALA J 402 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 48 through 51 removed outlier: 6.448A pdb=" N VAL C 8 " --> pdb=" O ASN C 49 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ILE C 51 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR C 10 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA C 129 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU C 168 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N GLN C 257 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE C 170 " --> pdb=" O GLN C 257 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N VAL C 221 " --> pdb=" O VAL C 190 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR C 192 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N VAL C 223 " --> pdb=" O THR C 192 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N SER C 194 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LEU C 225 " --> pdb=" O SER C 194 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N HIS C 196 " --> pdb=" O LEU C 225 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 48 through 51 removed outlier: 6.079A pdb=" N VAL D 8 " --> pdb=" O ASN D 49 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE D 51 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TYR D 10 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU D 168 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N GLN D 257 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE D 170 " --> pdb=" O GLN D 257 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AB2, first strand: chain 'I' and resid 200 through 202 removed outlier: 6.726A pdb=" N VAL I 275 " --> pdb=" O VAL I 314 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL I 314 " --> pdb=" O VAL I 275 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASP I 277 " --> pdb=" O LYS I 312 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 291 through 292 Processing sheet with id=AB4, first strand: chain 'J' and resid 53 through 65 removed outlier: 10.136A pdb=" N SER J 55 " --> pdb=" O ARG J 80 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N ARG J 80 " --> pdb=" O SER J 55 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N GLN J 57 " --> pdb=" O GLY J 78 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N GLY J 78 " --> pdb=" O GLN J 57 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N TYR J 59 " --> pdb=" O PHE J 76 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N PHE J 76 " --> pdb=" O TYR J 59 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU J 61 " --> pdb=" O LYS J 74 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS J 74 " --> pdb=" O GLU J 61 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N TYR J 86 " --> pdb=" O SER J 127 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N SER J 127 " --> pdb=" O TYR J 86 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU J 88 " --> pdb=" O LEU J 125 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU J 125 " --> pdb=" O LEU J 88 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 134 through 137 Processing sheet with id=AB6, first strand: chain 'J' and resid 187 through 192 removed outlier: 7.177A pdb=" N GLY J 203 " --> pdb=" O THR J 188 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL J 190 " --> pdb=" O VAL J 201 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL J 201 " --> pdb=" O VAL J 190 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TRP J 192 " --> pdb=" O THR J 199 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR J 199 " --> pdb=" O TRP J 192 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASP J 213 " --> pdb=" O LEU J 226 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LEU J 226 " --> pdb=" O ASP J 213 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 237 through 242 removed outlier: 3.509A pdb=" N ASP J 239 " --> pdb=" O VAL J 253 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR J 258 " --> pdb=" O SER J 254 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 284 through 289 removed outlier: 3.680A pdb=" N SER J 286 " --> pdb=" O CYS J 300 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 328 through 333 removed outlier: 5.656A pdb=" N ASP J 354 " --> pdb=" O LEU J 374 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LEU J 374 " --> pdb=" O ASP J 354 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 41 through 48 removed outlier: 6.628A pdb=" N THR K 411 " --> pdb=" O ASP K 42 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE K 44 " --> pdb=" O ILE K 409 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE K 409 " --> pdb=" O ILE K 44 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR K 46 " --> pdb=" O LEU K 407 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU K 407 " --> pdb=" O THR K 46 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE K 406 " --> pdb=" O ALA K 402 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 53 through 65 removed outlier: 10.136A pdb=" N SER K 55 " --> pdb=" O ARG K 80 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N ARG K 80 " --> pdb=" O SER K 55 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N GLN K 57 " --> pdb=" O GLY K 78 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N GLY K 78 " --> pdb=" O GLN K 57 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N TYR K 59 " --> pdb=" O PHE K 76 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N PHE K 76 " --> pdb=" O TYR K 59 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU K 61 " --> pdb=" O LYS K 74 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS K 74 " --> pdb=" O GLU K 61 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N TYR K 86 " --> pdb=" O SER K 127 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N SER K 127 " --> pdb=" O TYR K 86 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU K 88 " --> pdb=" O LEU K 125 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU K 125 " --> pdb=" O LEU K 88 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 134 through 137 Processing sheet with id=AC4, first strand: chain 'K' and resid 187 through 192 removed outlier: 7.177A pdb=" N GLY K 203 " --> pdb=" O THR K 188 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL K 190 " --> pdb=" O VAL K 201 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL K 201 " --> pdb=" O VAL K 190 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TRP K 192 " --> pdb=" O THR K 199 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR K 199 " --> pdb=" O TRP K 192 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASP K 213 " --> pdb=" O LEU K 226 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LEU K 226 " --> pdb=" O ASP K 213 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 237 through 242 removed outlier: 3.509A pdb=" N ASP K 239 " --> pdb=" O VAL K 253 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR K 258 " --> pdb=" O SER K 254 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 284 through 289 removed outlier: 3.680A pdb=" N SER K 286 " --> pdb=" O CYS K 300 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 328 through 333 removed outlier: 5.657A pdb=" N ASP K 354 " --> pdb=" O LEU K 374 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LEU K 374 " --> pdb=" O ASP K 354 " (cutoff:3.500A) 1467 hydrogen bonds defined for protein. 4167 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: 5.37 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9400 1.34 - 1.46: 5610 1.46 - 1.58: 14863 1.58 - 1.70: 4 1.70 - 1.82: 216 Bond restraints: 30093 Sorted by residual: bond pdb=" O1P SEP F 22 " pdb=" P SEP F 22 " ideal model delta sigma weight residual 1.610 1.513 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" O1P SEP F 27 " pdb=" P SEP F 27 " ideal model delta sigma weight residual 1.610 1.513 0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" O2P SEP F 27 " pdb=" P SEP F 27 " ideal model delta sigma weight residual 1.610 1.514 0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" O2P SEP F 24 " pdb=" P SEP F 24 " ideal model delta sigma weight residual 1.610 1.515 0.095 2.00e-02 2.50e+03 2.28e+01 bond pdb=" O3P SEP F 22 " pdb=" P SEP F 22 " ideal model delta sigma weight residual 1.610 1.515 0.095 2.00e-02 2.50e+03 2.27e+01 ... (remaining 30088 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 39953 2.65 - 5.30: 703 5.30 - 7.95: 68 7.95 - 10.60: 25 10.60 - 13.26: 1 Bond angle restraints: 40750 Sorted by residual: angle pdb=" N LYS K 31 " pdb=" CA LYS K 31 " pdb=" CB LYS K 31 " ideal model delta sigma weight residual 110.41 119.62 -9.21 1.68e+00 3.54e-01 3.01e+01 angle pdb=" N LYS J 31 " pdb=" CA LYS J 31 " pdb=" CB LYS J 31 " ideal model delta sigma weight residual 110.41 119.61 -9.20 1.68e+00 3.54e-01 3.00e+01 angle pdb=" C TYR K 30 " pdb=" N LYS K 31 " pdb=" CA LYS K 31 " ideal model delta sigma weight residual 121.58 111.75 9.83 1.95e+00 2.63e-01 2.54e+01 angle pdb=" C TYR J 30 " pdb=" N LYS J 31 " pdb=" CA LYS J 31 " ideal model delta sigma weight residual 121.58 111.78 9.80 1.95e+00 2.63e-01 2.53e+01 angle pdb=" C VAL A 978 " pdb=" CA VAL A 978 " pdb=" CB VAL A 978 " ideal model delta sigma weight residual 111.18 102.60 8.58 1.80e+00 3.09e-01 2.27e+01 ... (remaining 40745 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 15166 17.89 - 35.78: 1906 35.78 - 53.66: 771 53.66 - 71.55: 215 71.55 - 89.44: 51 Dihedral angle restraints: 18109 sinusoidal: 7388 harmonic: 10721 Sorted by residual: dihedral pdb=" CA VAL A 978 " pdb=" C VAL A 978 " pdb=" N ASN A 979 " pdb=" CA ASN A 979 " ideal model delta harmonic sigma weight residual 180.00 125.51 54.49 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA GLY F 49 " pdb=" C GLY F 49 " pdb=" N CYS F 50 " pdb=" CA CYS F 50 " ideal model delta harmonic sigma weight residual 180.00 139.17 40.83 0 5.00e+00 4.00e-02 6.67e+01 dihedral pdb=" CA TRP A 977 " pdb=" C TRP A 977 " pdb=" N VAL A 978 " pdb=" CA VAL A 978 " ideal model delta harmonic sigma weight residual 180.00 144.90 35.10 0 5.00e+00 4.00e-02 4.93e+01 ... (remaining 18106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 4179 0.101 - 0.202: 252 0.202 - 0.303: 2 0.303 - 0.404: 0 0.404 - 0.505: 1 Chirality restraints: 4434 Sorted by residual: chirality pdb=" CB VAL A 978 " pdb=" CA VAL A 978 " pdb=" CG1 VAL A 978 " pdb=" CG2 VAL A 978 " both_signs ideal model delta sigma weight residual False -2.63 -2.12 -0.50 2.00e-01 2.50e+01 6.37e+00 chirality pdb=" CA THR B1093 " pdb=" N THR B1093 " pdb=" C THR B1093 " pdb=" CB THR B1093 " both_signs ideal model delta sigma weight residual False 2.53 2.78 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA ASN B1092 " pdb=" N ASN B1092 " pdb=" C ASN B1092 " pdb=" CB ASN B1092 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 4431 not shown) Planarity restraints: 5267 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 581 " 0.064 5.00e-02 4.00e+02 9.75e-02 1.52e+01 pdb=" N PRO A 582 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 582 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 582 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 51 " -0.017 2.00e-02 2.50e+03 1.98e-02 9.80e+00 pdb=" CG TRP J 51 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP J 51 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP J 51 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP J 51 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP J 51 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP J 51 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 51 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 51 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP J 51 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 51 " 0.017 2.00e-02 2.50e+03 1.96e-02 9.61e+00 pdb=" CG TRP K 51 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP K 51 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP K 51 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP K 51 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP K 51 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP K 51 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 51 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 51 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP K 51 " 0.000 2.00e-02 2.50e+03 ... (remaining 5264 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.50: 277 2.50 - 3.16: 25159 3.16 - 3.82: 55533 3.82 - 4.48: 77221 4.48 - 5.14: 128217 Nonbonded interactions: 286407 Sorted by model distance: nonbonded pdb=" O3P SEP F 27 " pdb=" OG SER F 57 " model vdw 1.837 3.040 nonbonded pdb=" OD2 ASP C 173 " pdb="ZN ZN C 501 " model vdw 1.870 2.230 nonbonded pdb=" OD2 ASP D 173 " pdb="ZN ZN D 501 " model vdw 1.962 2.230 nonbonded pdb=" OG SER J 345 " pdb=" OD1 ASP J 347 " model vdw 1.970 3.040 nonbonded pdb=" OG SER K 345 " pdb=" OD1 ASP K 347 " model vdw 1.971 3.040 ... (remaining 286402 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 'C' and (resid 7 through 369 or resid 501 through 503)) selection = chain 'D' } ncs_group { reference = chain 'J' selection = chain 'K' } 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: 4.060 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: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 27.840 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.227 30095 Z= 0.454 Angle : 0.900 13.255 40750 Z= 0.506 Chirality : 0.053 0.505 4434 Planarity : 0.005 0.097 5267 Dihedral : 19.655 89.439 11165 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.20 % Favored : 92.74 % Rotamer: Outliers : 15.70 % Allowed : 17.81 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.12), residues: 3583 helix: -1.15 (0.11), residues: 1689 sheet: -1.39 (0.21), residues: 542 loop : -3.17 (0.13), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 266 TYR 0.032 0.003 TYR K 86 PHE 0.025 0.002 PHE C 100 TRP 0.053 0.003 TRP J 51 HIS 0.009 0.002 HIS J 183 Details of bonding type rmsd/Z covalent geometry : bond 0.01021 / 0.45 (30093) covalent geometry : angle 0.90021 / 0.51 (40750) hydrogen bonds : bond 0.14991 / 10.04 ( 1467) hydrogen bonds : angle 6.22469 / 4.44 ( 4167) metal coordination : bond 0.17592 / 9.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 3269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 508 poor density : 326 time to evaluate : 0.878 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: A 854 MET cc_start: 0.7922 (mtm) cc_final: 0.7630 (mtt) REVERT: A 1182 ARG cc_start: 0.6905 (OUTLIER) cc_final: 0.6384 (ptp90) REVERT: B 836 GLU cc_start: 0.0149 (OUTLIER) cc_final: -0.0943 (tm-30) REVERT: B 1039 MET cc_start: 0.7424 (ptt) cc_final: 0.7194 (ptt) REVERT: B 1079 PHE cc_start: 0.6974 (t80) cc_final: 0.6709 (m-80) REVERT: B 1112 LYS cc_start: 0.7155 (mttt) cc_final: 0.6790 (ttmm) REVERT: C 3 PHE cc_start: 0.7793 (t80) cc_final: 0.7489 (t80) REVERT: C 44 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8600 (tt) REVERT: C 90 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8889 (tptm) REVERT: C 142 ARG cc_start: 0.8577 (mtp-110) cc_final: 0.8370 (mtp-110) REVERT: C 189 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7803 (mmp80) REVERT: D 132 TRP cc_start: 0.9093 (OUTLIER) cc_final: 0.8762 (m100) REVERT: D 227 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.8031 (m-30) REVERT: E 361 ASP cc_start: 0.7700 (t0) cc_final: 0.7380 (t0) REVERT: E 401 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.7828 (ttp-170) REVERT: F 66 ILE cc_start: 0.8232 (mm) cc_final: 0.7921 (mm) REVERT: F 105 THR cc_start: 0.8887 (p) cc_final: 0.8618 (p) REVERT: F 168 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.8085 (p90) REVERT: F 227 GLN cc_start: 0.7407 (tp40) cc_final: 0.7190 (tp40) REVERT: G 1 MET cc_start: 0.7540 (ptt) cc_final: 0.7023 (ptt) REVERT: H 79 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.8952 (mt) REVERT: H 114 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7340 (pm20) REVERT: H 115 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8095 (tt) REVERT: I 304 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7672 (tm-30) REVERT: J 58 TRP cc_start: 0.7353 (m100) cc_final: 0.7002 (m100) REVERT: J 98 LEU cc_start: 0.3831 (OUTLIER) cc_final: 0.3270 (mp) REVERT: J 214 LEU cc_start: 0.6159 (OUTLIER) cc_final: 0.5907 (pt) REVERT: J 265 ARG cc_start: 0.5501 (OUTLIER) cc_final: 0.4513 (tmm-80) REVERT: J 355 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7950 (mt) REVERT: J 377 MET cc_start: 0.6654 (OUTLIER) cc_final: 0.6143 (ptm) REVERT: K 18 GLU cc_start: 0.3977 (OUTLIER) cc_final: 0.3100 (tp30) REVERT: K 46 THR cc_start: 0.2883 (OUTLIER) cc_final: 0.2664 (p) REVERT: K 77 LEU cc_start: 0.3938 (OUTLIER) cc_final: 0.3149 (tp) REVERT: K 175 LYS cc_start: 0.4641 (OUTLIER) cc_final: 0.3960 (tttt) REVERT: K 215 ASN cc_start: 0.1927 (OUTLIER) cc_final: 0.1027 (t0) REVERT: K 241 ARG cc_start: 0.1838 (OUTLIER) cc_final: 0.1074 (tpt170) REVERT: K 246 HIS cc_start: 0.1511 (OUTLIER) cc_final: 0.1172 (t-90) REVERT: K 263 ASP cc_start: 0.0061 (OUTLIER) cc_final: -0.0215 (p0) REVERT: K 264 ILE cc_start: -0.0477 (OUTLIER) cc_final: -0.0741 (tt) REVERT: K 265 ARG cc_start: 0.3338 (OUTLIER) cc_final: 0.2500 (mmm160) REVERT: K 311 LEU cc_start: 0.1326 (OUTLIER) cc_final: -0.0063 (tp) REVERT: K 315 ASN cc_start: 0.1504 (OUTLIER) cc_final: 0.0992 (m-40) REVERT: K 345 SER cc_start: 0.0206 (OUTLIER) cc_final: -0.0587 (p) REVERT: K 355 LEU cc_start: -0.0174 (OUTLIER) cc_final: -0.0813 (pp) REVERT: K 388 MET cc_start: 0.2026 (OUTLIER) cc_final: -0.0186 (mmm) REVERT: K 395 ASN cc_start: -0.1052 (OUTLIER) cc_final: -0.1562 (m-40) REVERT: K 416 ILE cc_start: -0.1034 (OUTLIER) cc_final: -0.1260 (pt) outliers start: 508 outliers final: 204 residues processed: 769 average time/residue: 0.1722 time to fit residues: 212.1892 Evaluate side-chains 480 residues out of total 3269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 239 poor density : 241 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 973 THR Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1022 SER Chi-restraints excluded: chain A residue 1033 MET Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1043 SER Chi-restraints excluded: chain A residue 1055 HIS Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1085 GLU Chi-restraints excluded: chain A residue 1102 HIS Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1125 THR Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1182 ARG Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain A residue 1208 TYR Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 738 SER Chi-restraints excluded: chain B residue 741 ASP Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 876 SER Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 917 THR Chi-restraints excluded: chain B residue 937 GLU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1081 SER Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1136 ASN Chi-restraints excluded: chain B residue 1137 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 303 ARG Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 132 TRP Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain E residue 401 ARG Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 412 CYS Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 438 SER Chi-restraints excluded: chain E residue 459 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 225 ASN Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 56 LYS Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 125 ASP Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 261 CYS Chi-restraints excluded: chain I residue 265 SER Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain I residue 304 GLN Chi-restraints excluded: chain I residue 305 ASP Chi-restraints excluded: chain I residue 332 THR Chi-restraints excluded: chain I residue 346 SER Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 170 SER Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 229 HIS Chi-restraints excluded: chain J residue 238 SER Chi-restraints excluded: chain J residue 241 ARG Chi-restraints excluded: chain J residue 263 ASP Chi-restraints excluded: chain J residue 265 ARG Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 320 THR Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 344 THR Chi-restraints excluded: chain J residue 355 LEU Chi-restraints excluded: chain J residue 358 ILE Chi-restraints excluded: chain J residue 377 MET Chi-restraints excluded: chain J residue 395 ASN Chi-restraints excluded: chain J residue 409 ILE Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 175 LYS Chi-restraints excluded: chain K residue 215 ASN Chi-restraints excluded: chain K residue 238 SER Chi-restraints excluded: chain K residue 241 ARG Chi-restraints excluded: chain K residue 246 HIS Chi-restraints excluded: chain K residue 263 ASP Chi-restraints excluded: chain K residue 264 ILE Chi-restraints excluded: chain K residue 265 ARG Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain K residue 311 LEU Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 345 SER Chi-restraints excluded: chain K residue 355 LEU Chi-restraints excluded: chain K residue 368 GLN Chi-restraints excluded: chain K residue 388 MET Chi-restraints excluded: chain K residue 395 ASN Chi-restraints excluded: chain K residue 400 THR Chi-restraints excluded: chain K residue 416 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 197 optimal weight: 50.0000 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 511 ASN A 665 HIS A 720 HIS A 729 GLN A 803 GLN A 846 HIS A 882 ASN A1142 GLN B 421 HIS B 584 HIS B 663 GLN B 697 GLN B 984 ASN B 997 GLN B1036 GLN B1070 HIS B1075 ASN B1114 GLN B1115 ASN C 20 HIS C 37 ASN C 88 GLN C 164 HIS C 345 ASN C 350 HIS D 20 HIS D 125 ASN D 164 HIS D 218 ASN D 324 ASN D 369 ASN E 335 ASN E 392 GLN E 414 GLN E 417 ASN F 122 GLN ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 ASN F 225 ASN H 13 ASN H 95 ASN J 21 ASN J 100 GLN J 121 ASN J 152 HIS J 193 ASN J 260 HIS J 280 HIS J 285 HIS J 319 HIS J 324 HIS J 408 GLN K 21 ASN K 121 ASN ** K 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 152 HIS K 193 ASN K 260 HIS ** K 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 285 HIS K 319 HIS K 324 HIS K 368 GLN Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.160707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.101533 restraints weight = 49249.715| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.26 r_work: 0.3093 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30095 Z= 0.146 Angle : 0.642 12.118 40750 Z= 0.338 Chirality : 0.043 0.356 4434 Planarity : 0.005 0.071 5267 Dihedral : 10.693 75.741 4402 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 5.32 % Allowed : 22.29 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.09 (0.13), residues: 3583 helix: 0.60 (0.12), residues: 1683 sheet: -0.78 (0.22), residues: 526 loop : -2.40 (0.15), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 80 TYR 0.019 0.002 TYR F 142 PHE 0.049 0.001 PHE A 836 TRP 0.030 0.002 TRP A 977 HIS 0.006 0.001 HIS D 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 (30093) covalent geometry : angle 0.64232 / 0.34 (40750) hydrogen bonds : bond 0.06288 / 4.02 ( 1467) hydrogen bonds : angle 4.73117 / 3.38 ( 4167) metal coordination : bond 0.01138 / 0.59 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 291 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 823 TYR cc_start: 0.8141 (m-80) cc_final: 0.7850 (m-80) REVERT: A 854 MET cc_start: 0.8066 (mtm) cc_final: 0.7739 (mtt) REVERT: A 1182 ARG cc_start: 0.7609 (ttm110) cc_final: 0.7315 (ptp90) REVERT: A 1191 MET cc_start: 0.2605 (mtp) cc_final: 0.2349 (mtp) REVERT: A 1210 MET cc_start: 0.5974 (pmm) cc_final: 0.5147 (pmm) REVERT: B 440 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7968 (tp30) REVERT: B 467 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7531 (pp20) REVERT: B 688 ARG cc_start: 0.8700 (ttp-110) cc_final: 0.8448 (mtm-85) REVERT: B 742 LYS cc_start: 0.7026 (OUTLIER) cc_final: 0.6790 (mptt) REVERT: B 852 MET cc_start: 0.9017 (mpp) cc_final: 0.8555 (mpp) REVERT: B 940 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7568 (tt) REVERT: B 1039 MET cc_start: 0.8008 (ptt) cc_final: 0.7773 (ptt) REVERT: B 1075 ASN cc_start: 0.8455 (m-40) cc_final: 0.7892 (m-40) REVERT: B 1079 PHE cc_start: 0.7319 (t80) cc_final: 0.6700 (m-80) REVERT: B 1090 GLU cc_start: 0.6487 (tp30) cc_final: 0.6140 (tp30) REVERT: B 1097 TYR cc_start: 0.8581 (t80) cc_final: 0.8359 (t80) REVERT: B 1112 LYS cc_start: 0.7297 (mttt) cc_final: 0.6636 (ttmm) REVERT: C 3 PHE cc_start: 0.7629 (t80) cc_final: 0.7302 (t80) REVERT: C 44 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8621 (tt) REVERT: C 71 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8327 (tt0) REVERT: C 90 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.9070 (tptm) REVERT: C 142 ARG cc_start: 0.8878 (mtp-110) cc_final: 0.8668 (mtp-110) REVERT: C 250 ARG cc_start: 0.8749 (mtp180) cc_final: 0.8067 (mtm180) REVERT: C 345 ASN cc_start: 0.9164 (OUTLIER) cc_final: 0.8889 (p0) REVERT: D 89 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8734 (tt) REVERT: D 227 ASP cc_start: 0.8896 (OUTLIER) cc_final: 0.8646 (m-30) REVERT: E 340 MET cc_start: 0.4086 (mtp) cc_final: 0.3700 (mtp) REVERT: F 18 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7423 (m-30) REVERT: F 47 TYR cc_start: 0.9308 (p90) cc_final: 0.9104 (p90) REVERT: F 61 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8163 (mm) REVERT: F 168 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8082 (p90) REVERT: F 227 GLN cc_start: 0.8155 (tp40) cc_final: 0.7852 (tp40) REVERT: G 1 MET cc_start: 0.8067 (ptt) cc_final: 0.7758 (ptt) REVERT: G 94 TYR cc_start: 0.8252 (t80) cc_final: 0.7833 (t80) REVERT: G 234 ARG cc_start: 0.7289 (ptt90) cc_final: 0.6974 (mmm-85) REVERT: H 114 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7520 (tp30) REVERT: I 208 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7807 (mm-30) REVERT: I 267 LEU cc_start: 0.8032 (mt) cc_final: 0.7819 (mp) REVERT: I 271 ARG cc_start: 0.8099 (mtm-85) cc_final: 0.7886 (mtm180) REVERT: J 58 TRP cc_start: 0.7391 (m100) cc_final: 0.7079 (m100) REVERT: J 98 LEU cc_start: 0.3733 (OUTLIER) cc_final: 0.3486 (mp) REVERT: J 214 LEU cc_start: 0.6497 (OUTLIER) cc_final: 0.6240 (pp) REVERT: J 377 MET cc_start: 0.7250 (ttt) cc_final: 0.6801 (ttt) REVERT: J 384 CYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7348 (p) REVERT: J 394 TYR cc_start: 0.6567 (m-10) cc_final: 0.6188 (m-80) REVERT: K 18 GLU cc_start: 0.2834 (OUTLIER) cc_final: 0.2374 (mp0) REVERT: K 49 LEU cc_start: 0.1421 (pt) cc_final: 0.1052 (mp) REVERT: K 174 LEU cc_start: -0.0897 (OUTLIER) cc_final: -0.1390 (tp) REVERT: K 215 ASN cc_start: 0.4319 (OUTLIER) cc_final: 0.3287 (t0) REVERT: K 241 ARG cc_start: 0.1168 (OUTLIER) cc_final: -0.0019 (ptm160) REVERT: K 265 ARG cc_start: 0.3414 (OUTLIER) cc_final: 0.3131 (mmm160) REVERT: K 326 ASP cc_start: 0.1166 (OUTLIER) cc_final: 0.0708 (p0) REVERT: K 368 GLN cc_start: 0.3763 (OUTLIER) cc_final: 0.3559 (mm-40) outliers start: 172 outliers final: 82 residues processed: 444 average time/residue: 0.1717 time to fit residues: 125.0581 Evaluate side-chains 349 residues out of total 3269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 243 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 973 THR Chi-restraints excluded: chain A residue 1033 MET Chi-restraints excluded: chain A residue 1055 HIS Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1102 HIS Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 612 GLU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 742 LYS Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 938 ILE Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 1120 TRP Chi-restraints excluded: chain B residue 1136 ASN Chi-restraints excluded: chain B residue 1137 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 345 ASN Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 225 ASN Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 130 MET Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 263 ASP Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 316 GLN Chi-restraints excluded: chain J residue 320 THR Chi-restraints excluded: chain J residue 344 THR Chi-restraints excluded: chain J residue 358 ILE Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 384 CYS Chi-restraints excluded: chain J residue 413 SER Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 215 ASN Chi-restraints excluded: chain K residue 241 ARG Chi-restraints excluded: chain K residue 265 ARG Chi-restraints excluded: chain K residue 271 THR Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 326 ASP Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 368 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 155 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 260 optimal weight: 0.9990 chunk 201 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 309 optimal weight: 10.0000 chunk 196 optimal weight: 0.6980 chunk 119 optimal weight: 7.9990 chunk 339 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 HIS A1142 GLN ** B1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 335 ASN E 414 GLN F 165 HIS ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 193 ASN J 247 GLN ** J 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 215 ASN ** K 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.159033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.099258 restraints weight = 49007.461| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.07 r_work: 0.3105 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 30095 Z= 0.203 Angle : 0.632 10.495 40750 Z= 0.331 Chirality : 0.044 0.226 4434 Planarity : 0.005 0.071 5267 Dihedral : 8.377 76.114 4126 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 5.22 % Allowed : 21.95 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.14), residues: 3583 helix: 0.97 (0.13), residues: 1683 sheet: -0.62 (0.22), residues: 557 loop : -2.12 (0.16), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 241 TYR 0.026 0.002 TYR F 142 PHE 0.031 0.002 PHE A 836 TRP 0.026 0.002 TRP B1120 HIS 0.007 0.001 HIS D 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 (30093) covalent geometry : angle 0.63195 / 0.33 (40750) hydrogen bonds : bond 0.06489 / 4.14 ( 1467) hydrogen bonds : angle 4.59340 / 3.29 ( 4167) metal coordination : bond 0.00468 / 0.25 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 262 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 684 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8424 (pt) REVERT: A 823 TYR cc_start: 0.8190 (m-80) cc_final: 0.7882 (m-80) REVERT: A 854 MET cc_start: 0.8132 (mtm) cc_final: 0.7766 (mtt) REVERT: A 1019 THR cc_start: 0.7941 (OUTLIER) cc_final: 0.7683 (p) REVERT: A 1182 ARG cc_start: 0.7464 (ttm110) cc_final: 0.7115 (ptp90) REVERT: A 1191 MET cc_start: 0.2703 (mtp) cc_final: 0.2441 (mtp) REVERT: A 1210 MET cc_start: 0.5792 (pmm) cc_final: 0.5237 (pmm) REVERT: B 440 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7988 (tp30) REVERT: B 688 ARG cc_start: 0.8640 (ttp-110) cc_final: 0.8375 (mtm-85) REVERT: B 940 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7563 (tt) REVERT: B 1075 ASN cc_start: 0.8446 (m-40) cc_final: 0.8097 (m-40) REVERT: B 1079 PHE cc_start: 0.7378 (t80) cc_final: 0.6896 (m-80) REVERT: B 1090 GLU cc_start: 0.6139 (tp30) cc_final: 0.5689 (tp30) REVERT: C 44 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8582 (tt) REVERT: C 71 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8318 (tt0) REVERT: C 250 ARG cc_start: 0.8755 (mtp180) cc_final: 0.8082 (mtm180) REVERT: D 227 ASP cc_start: 0.8842 (OUTLIER) cc_final: 0.8568 (m-30) REVERT: E 355 LEU cc_start: 0.8379 (pp) cc_final: 0.8135 (tt) REVERT: E 373 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.7564 (mttm) REVERT: F 13 GLN cc_start: 0.7956 (tt0) cc_final: 0.7548 (tt0) REVERT: F 18 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7340 (m-30) REVERT: F 168 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.8211 (p90) REVERT: F 227 GLN cc_start: 0.8164 (tp40) cc_final: 0.7822 (tp40) REVERT: G 1 MET cc_start: 0.8021 (ptt) cc_final: 0.7687 (ptt) REVERT: G 94 TYR cc_start: 0.8226 (t80) cc_final: 0.7800 (t80) REVERT: H 79 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8842 (mt) REVERT: I 267 LEU cc_start: 0.8103 (mt) cc_final: 0.7897 (mp) REVERT: I 271 ARG cc_start: 0.8076 (mtm-85) cc_final: 0.7874 (mtm180) REVERT: J 42 ASP cc_start: 0.5646 (OUTLIER) cc_final: 0.5418 (m-30) REVERT: J 51 TRP cc_start: 0.7592 (OUTLIER) cc_final: 0.6846 (m100) REVERT: J 58 TRP cc_start: 0.7194 (m100) cc_final: 0.6880 (m100) REVERT: J 98 LEU cc_start: 0.3603 (OUTLIER) cc_final: 0.3362 (tt) REVERT: J 309 TRP cc_start: 0.6090 (m100) cc_final: 0.5791 (m100) REVERT: J 338 GLU cc_start: 0.5219 (OUTLIER) cc_final: 0.4810 (pt0) REVERT: J 358 ILE cc_start: 0.5310 (OUTLIER) cc_final: 0.4408 (pt) REVERT: J 377 MET cc_start: 0.7253 (ttt) cc_final: 0.6722 (ttm) REVERT: J 384 CYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7551 (p) REVERT: J 394 TYR cc_start: 0.6516 (m-10) cc_final: 0.6269 (m-80) REVERT: K 18 GLU cc_start: 0.3427 (OUTLIER) cc_final: 0.3105 (mp0) REVERT: K 49 LEU cc_start: 0.1142 (pt) cc_final: 0.0852 (mp) REVERT: K 171 GLU cc_start: 0.3256 (mm-30) cc_final: 0.2858 (tp30) REVERT: K 174 LEU cc_start: -0.1406 (OUTLIER) cc_final: -0.1707 (tp) REVERT: K 215 ASN cc_start: 0.4253 (m110) cc_final: 0.3240 (t0) REVERT: K 241 ARG cc_start: 0.0895 (OUTLIER) cc_final: -0.0218 (ptm160) REVERT: K 326 ASP cc_start: 0.0805 (OUTLIER) cc_final: 0.0209 (p0) outliers start: 169 outliers final: 95 residues processed: 417 average time/residue: 0.1798 time to fit residues: 121.8130 Evaluate side-chains 348 residues out of total 3269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 232 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 973 THR Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1033 MET Chi-restraints excluded: chain A residue 1055 HIS Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 612 GLU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1120 TRP Chi-restraints excluded: chain B residue 1137 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain E residue 373 LYS Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 225 ASN Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 258 LEU Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain I residue 332 THR Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 51 TRP Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 316 GLN Chi-restraints excluded: chain J residue 320 THR Chi-restraints excluded: chain J residue 338 GLU Chi-restraints excluded: chain J residue 358 ILE Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 384 CYS Chi-restraints excluded: chain J residue 413 SER Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 241 ARG Chi-restraints excluded: chain K residue 263 ASP Chi-restraints excluded: chain K residue 271 THR Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 326 ASP Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 341 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 251 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 156 optimal weight: 0.1980 chunk 352 optimal weight: 6.9990 chunk 279 optimal weight: 9.9990 chunk 185 optimal weight: 0.7980 chunk 253 optimal weight: 0.7980 chunk 265 optimal weight: 0.0000 chunk 274 optimal weight: 0.8980 chunk 171 optimal weight: 0.6980 chunk 223 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 60.3153 > 50:) overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1142 GLN ** B1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1095 ASN E 335 ASN E 350 ASN E 414 GLN E 423 HIS ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 338 GLN ** J 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 319 HIS ** K 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.162341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.102434 restraints weight = 48708.766| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.10 r_work: 0.3154 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30095 Z= 0.116 Angle : 0.553 9.478 40750 Z= 0.289 Chirality : 0.041 0.214 4434 Planarity : 0.004 0.060 5267 Dihedral : 7.290 59.909 4090 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.42 % Allowed : 22.75 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.14), residues: 3583 helix: 1.49 (0.13), residues: 1687 sheet: -0.47 (0.22), residues: 561 loop : -1.79 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 241 TYR 0.021 0.001 TYR G 83 PHE 0.037 0.001 PHE B 415 TRP 0.027 0.001 TRP B1120 HIS 0.005 0.001 HIS A 775 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.12 (30093) covalent geometry : angle 0.55329 / 0.29 (40750) hydrogen bonds : bond 0.05238 / 3.34 ( 1467) hydrogen bonds : angle 4.26493 / 3.06 ( 4167) metal coordination : bond 0.00076 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 279 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 579 ASN cc_start: 0.8501 (OUTLIER) cc_final: 0.8221 (p0) REVERT: A 823 TYR cc_start: 0.8097 (m-80) cc_final: 0.7812 (m-80) REVERT: A 854 MET cc_start: 0.8086 (mtm) cc_final: 0.7802 (mtt) REVERT: A 1182 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.7206 (ptp90) REVERT: A 1191 MET cc_start: 0.2562 (mtp) cc_final: 0.2332 (mtp) REVERT: A 1210 MET cc_start: 0.5411 (pmm) cc_final: 0.5014 (pmm) REVERT: B 412 LEU cc_start: 0.6830 (tp) cc_final: 0.6625 (tp) REVERT: B 440 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8098 (tp30) REVERT: B 688 ARG cc_start: 0.8607 (ttp-110) cc_final: 0.8317 (mtm-85) REVERT: B 742 LYS cc_start: 0.6907 (OUTLIER) cc_final: 0.5877 (mmtt) REVERT: B 836 GLU cc_start: -0.0328 (OUTLIER) cc_final: -0.1013 (tm-30) REVERT: B 940 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7678 (tt) REVERT: B 1079 PHE cc_start: 0.7200 (OUTLIER) cc_final: 0.6799 (m-80) REVERT: B 1090 GLU cc_start: 0.6038 (tp30) cc_final: 0.5749 (tp30) REVERT: C 44 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8496 (tt) REVERT: C 250 ARG cc_start: 0.8751 (mtp180) cc_final: 0.8122 (mtm180) REVERT: D 227 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8424 (t70) REVERT: F 18 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7288 (m-30) REVERT: F 168 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8026 (p90) REVERT: F 227 GLN cc_start: 0.8136 (tp40) cc_final: 0.7824 (tp40) REVERT: G 1 MET cc_start: 0.7933 (ptt) cc_final: 0.7625 (ptt) REVERT: G 94 TYR cc_start: 0.8242 (t80) cc_final: 0.7962 (t80) REVERT: G 251 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.8098 (t0) REVERT: G 257 GLN cc_start: 0.8401 (mt0) cc_final: 0.8107 (mm-40) REVERT: H 79 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8799 (mt) REVERT: H 102 ASP cc_start: 0.7553 (m-30) cc_final: 0.7244 (m-30) REVERT: J 51 TRP cc_start: 0.7603 (OUTLIER) cc_final: 0.6865 (m100) REVERT: J 58 TRP cc_start: 0.7154 (m100) cc_final: 0.6850 (m100) REVERT: J 98 LEU cc_start: 0.3617 (OUTLIER) cc_final: 0.3342 (tt) REVERT: J 309 TRP cc_start: 0.6184 (m100) cc_final: 0.5863 (m100) REVERT: J 338 GLU cc_start: 0.4928 (OUTLIER) cc_final: 0.4713 (mt-10) REVERT: J 377 MET cc_start: 0.7288 (ttt) cc_final: 0.6761 (ttt) REVERT: J 394 TYR cc_start: 0.6348 (m-10) cc_final: 0.6113 (m-80) REVERT: J 403 GLU cc_start: 0.7821 (tt0) cc_final: 0.6758 (mt-10) REVERT: K 18 GLU cc_start: 0.3418 (OUTLIER) cc_final: 0.2422 (tp30) REVERT: K 171 GLU cc_start: 0.3242 (mm-30) cc_final: 0.2910 (tp30) REVERT: K 174 LEU cc_start: -0.1301 (OUTLIER) cc_final: -0.1845 (tp) REVERT: K 194 PHE cc_start: -0.0794 (m-80) cc_final: -0.1432 (t80) REVERT: K 215 ASN cc_start: 0.4318 (m110) cc_final: 0.3449 (t0) REVERT: K 241 ARG cc_start: 0.1467 (OUTLIER) cc_final: 0.0416 (ptm160) REVERT: K 289 PHE cc_start: 0.1387 (m-80) cc_final: 0.0961 (m-80) outliers start: 143 outliers final: 80 residues processed: 406 average time/residue: 0.1977 time to fit residues: 130.6383 Evaluate side-chains 343 residues out of total 3269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 244 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 579 ASN Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1033 MET Chi-restraints excluded: chain A residue 1055 HIS Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1102 HIS Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1125 THR Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1182 ARG Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 612 GLU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 742 LYS Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 937 GLU Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1079 PHE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1137 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 225 ASN Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain G residue 251 ASP Chi-restraints excluded: chain G residue 262 GLU Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 125 ASP Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 130 MET Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain I residue 332 THR Chi-restraints excluded: chain J residue 51 TRP Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 316 GLN Chi-restraints excluded: chain J residue 320 THR Chi-restraints excluded: chain J residue 338 GLU Chi-restraints excluded: chain J residue 413 SER Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 241 ARG Chi-restraints excluded: chain K residue 263 ASP Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain K residue 320 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 251 optimal weight: 0.6980 chunk 311 optimal weight: 8.9990 chunk 217 optimal weight: 0.7980 chunk 294 optimal weight: 3.9990 chunk 221 optimal weight: 0.6980 chunk 194 optimal weight: 0.0070 chunk 208 optimal weight: 9.9990 chunk 308 optimal weight: 5.9990 chunk 347 optimal weight: 0.4980 chunk 127 optimal weight: 1.9990 chunk 310 optimal weight: 3.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1077 GLN C 37 ASN E 414 GLN E 423 HIS J 22 GLN J 124 ASN ** J 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN ** K 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.162840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.103477 restraints weight = 48984.830| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.25 r_work: 0.3151 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 30095 Z= 0.113 Angle : 0.534 8.939 40750 Z= 0.278 Chirality : 0.041 0.181 4434 Planarity : 0.004 0.050 5267 Dihedral : 6.648 59.734 4066 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.71 % Allowed : 23.43 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.14), residues: 3583 helix: 1.82 (0.13), residues: 1667 sheet: -0.36 (0.22), residues: 535 loop : -1.54 (0.16), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1140 TYR 0.017 0.001 TYR F 142 PHE 0.037 0.001 PHE B 415 TRP 0.034 0.001 TRP B1120 HIS 0.005 0.001 HIS F 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (30093) covalent geometry : angle 0.53389 / 0.28 (40750) hydrogen bonds : bond 0.04992 / 3.19 ( 1467) hydrogen bonds : angle 4.11999 / 2.96 ( 4167) metal coordination : bond 0.00050 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 264 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 823 TYR cc_start: 0.8010 (m-80) cc_final: 0.7781 (m-80) REVERT: A 854 MET cc_start: 0.8054 (mtm) cc_final: 0.7597 (mtp) REVERT: A 1055 HIS cc_start: 0.7077 (OUTLIER) cc_final: 0.6801 (p90) REVERT: A 1182 ARG cc_start: 0.7618 (ttm110) cc_final: 0.7295 (ptp90) REVERT: A 1191 MET cc_start: 0.2574 (mtp) cc_final: 0.2302 (mtp) REVERT: A 1210 MET cc_start: 0.5301 (pmm) cc_final: 0.5025 (pmm) REVERT: B 440 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8102 (tp30) REVERT: B 742 LYS cc_start: 0.6962 (OUTLIER) cc_final: 0.5944 (mmtt) REVERT: B 836 GLU cc_start: -0.0249 (OUTLIER) cc_final: -0.0930 (tm-30) REVERT: B 940 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7664 (tt) REVERT: B 1075 ASN cc_start: 0.8415 (m-40) cc_final: 0.8007 (m-40) REVERT: B 1079 PHE cc_start: 0.7169 (OUTLIER) cc_final: 0.6818 (m-80) REVERT: C 44 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8467 (tt) REVERT: C 90 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8540 (tmtp) REVERT: C 250 ARG cc_start: 0.8724 (mtp180) cc_final: 0.8224 (mtm110) REVERT: D 96 ASP cc_start: 0.7747 (p0) cc_final: 0.7486 (p0) REVERT: D 227 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8430 (t70) REVERT: E 335 ASN cc_start: 0.6146 (m-40) cc_final: 0.5900 (m110) REVERT: E 433 MET cc_start: 0.6383 (tpt) cc_final: 0.6179 (tpt) REVERT: F 168 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.8022 (p90) REVERT: F 227 GLN cc_start: 0.8051 (tp40) cc_final: 0.7736 (tp40) REVERT: G 1 MET cc_start: 0.7948 (ptt) cc_final: 0.7617 (ptt) REVERT: G 94 TYR cc_start: 0.8256 (t80) cc_final: 0.7976 (t80) REVERT: G 234 ARG cc_start: 0.7079 (ptt90) cc_final: 0.6388 (ttm110) REVERT: G 253 GLN cc_start: 0.8713 (tp40) cc_final: 0.8155 (tp40) REVERT: J 51 TRP cc_start: 0.7616 (OUTLIER) cc_final: 0.6840 (m100) REVERT: J 58 TRP cc_start: 0.7065 (m100) cc_final: 0.6716 (m100) REVERT: J 75 MET cc_start: 0.8107 (ttm) cc_final: 0.7898 (tpp) REVERT: J 130 GLU cc_start: 0.5294 (OUTLIER) cc_final: 0.4615 (pm20) REVERT: J 320 THR cc_start: 0.7783 (OUTLIER) cc_final: 0.7011 (t) REVERT: J 338 GLU cc_start: 0.4882 (OUTLIER) cc_final: 0.4655 (mt-10) REVERT: J 377 MET cc_start: 0.7314 (ttt) cc_final: 0.6803 (ttt) REVERT: J 394 TYR cc_start: 0.6290 (m-10) cc_final: 0.6058 (m-10) REVERT: J 398 MET cc_start: 0.7755 (tpt) cc_final: 0.7299 (tpt) REVERT: J 403 GLU cc_start: 0.7796 (tt0) cc_final: 0.6781 (mt-10) REVERT: K 18 GLU cc_start: 0.3576 (OUTLIER) cc_final: 0.2501 (tm-30) REVERT: K 39 PHE cc_start: 0.4043 (t80) cc_final: 0.3339 (m-10) REVERT: K 171 GLU cc_start: 0.3382 (mm-30) cc_final: 0.3008 (tp30) REVERT: K 241 ARG cc_start: 0.1067 (OUTLIER) cc_final: 0.0388 (ptm160) REVERT: K 289 PHE cc_start: 0.0828 (m-80) cc_final: 0.0580 (m-80) REVERT: K 326 ASP cc_start: 0.1283 (OUTLIER) cc_final: 0.0719 (p0) outliers start: 120 outliers final: 77 residues processed: 375 average time/residue: 0.1969 time to fit residues: 120.4887 Evaluate side-chains 342 residues out of total 3269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 248 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 774 ASP Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 1033 MET Chi-restraints excluded: chain A residue 1055 HIS Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1102 HIS Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1125 THR Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 612 GLU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 742 LYS Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 937 GLU Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1079 PHE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1137 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 225 ASN Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 262 GLU Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain I residue 332 THR Chi-restraints excluded: chain J residue 51 TRP Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 320 THR Chi-restraints excluded: chain J residue 338 GLU Chi-restraints excluded: chain J residue 413 SER Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain K residue 241 ARG Chi-restraints excluded: chain K residue 263 ASP Chi-restraints excluded: chain K residue 295 PHE Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain K residue 326 ASP Chi-restraints excluded: chain K residue 332 SER Chi-restraints excluded: chain K residue 361 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 332 optimal weight: 8.9990 chunk 153 optimal weight: 2.9990 chunk 198 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 214 optimal weight: 5.9990 chunk 233 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 803 GLN A1142 GLN E 414 GLN ** J 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 193 ASN ** J 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 316 GLN J 319 HIS K 193 ASN ** K 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.159967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.114227 restraints weight = 48834.971| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.95 r_work: 0.3160 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 30095 Z= 0.203 Angle : 0.602 11.988 40750 Z= 0.313 Chirality : 0.044 0.207 4434 Planarity : 0.004 0.063 5267 Dihedral : 6.545 59.132 4051 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.36 % Allowed : 22.97 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.14), residues: 3583 helix: 1.59 (0.13), residues: 1666 sheet: -0.44 (0.22), residues: 535 loop : -1.61 (0.16), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 317 TYR 0.027 0.002 TYR F 142 PHE 0.020 0.002 PHE I 264 TRP 0.038 0.002 TRP J 309 HIS 0.006 0.001 HIS D 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (30093) covalent geometry : angle 0.60195 / 0.31 (40750) hydrogen bonds : bond 0.06124 / 3.91 ( 1467) hydrogen bonds : angle 4.30138 / 3.08 ( 4167) metal coordination : bond 0.00261 / 0.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 250 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 579 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.8119 (p0) REVERT: A 1182 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6789 (ptp90) REVERT: A 1191 MET cc_start: 0.3410 (mtp) cc_final: 0.3147 (mtt) REVERT: A 1210 MET cc_start: 0.5207 (pmm) cc_final: 0.4954 (pmm) REVERT: B 440 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7802 (tp30) REVERT: B 701 ILE cc_start: 0.6589 (OUTLIER) cc_final: 0.6385 (pp) REVERT: B 742 LYS cc_start: 0.7247 (OUTLIER) cc_final: 0.5986 (mmtt) REVERT: B 836 GLU cc_start: 0.0089 (OUTLIER) cc_final: -0.0743 (tm-30) REVERT: B 940 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7839 (tt) REVERT: C 44 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8554 (tt) REVERT: C 90 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.8958 (tmtp) REVERT: C 250 ARG cc_start: 0.8728 (mtp180) cc_final: 0.8273 (mtm110) REVERT: D 171 ASP cc_start: 0.7992 (t70) cc_final: 0.7473 (t0) REVERT: E 335 ASN cc_start: 0.6434 (m-40) cc_final: 0.6091 (m110) REVERT: E 355 LEU cc_start: 0.8160 (pp) cc_final: 0.7849 (tt) REVERT: E 373 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.7556 (mttm) REVERT: F 18 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7415 (m-30) REVERT: F 168 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8312 (p90) REVERT: F 227 GLN cc_start: 0.8102 (tp40) cc_final: 0.7728 (tp40) REVERT: G 1 MET cc_start: 0.8050 (ptt) cc_final: 0.7719 (ptt) REVERT: G 94 TYR cc_start: 0.8156 (t80) cc_final: 0.7867 (t80) REVERT: G 253 GLN cc_start: 0.8760 (tp40) cc_final: 0.8286 (tp40) REVERT: H 102 ASP cc_start: 0.7424 (m-30) cc_final: 0.7187 (m-30) REVERT: J 51 TRP cc_start: 0.7625 (OUTLIER) cc_final: 0.6847 (m100) REVERT: J 58 TRP cc_start: 0.7302 (m100) cc_final: 0.7027 (m100) REVERT: J 296 ILE cc_start: 0.7838 (OUTLIER) cc_final: 0.7606 (mm) REVERT: J 377 MET cc_start: 0.7028 (ttt) cc_final: 0.6685 (ttt) REVERT: J 384 CYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8063 (p) REVERT: K 18 GLU cc_start: 0.3835 (OUTLIER) cc_final: 0.2539 (tm-30) REVERT: K 39 PHE cc_start: 0.4187 (t80) cc_final: 0.3456 (m-10) REVERT: K 171 GLU cc_start: 0.3119 (mm-30) cc_final: 0.2387 (tp30) REVERT: K 236 GLN cc_start: 0.3758 (mp10) cc_final: 0.2747 (mt0) REVERT: K 241 ARG cc_start: 0.1270 (OUTLIER) cc_final: 0.0200 (ptm160) REVERT: K 326 ASP cc_start: 0.1694 (OUTLIER) cc_final: 0.0902 (p0) outliers start: 141 outliers final: 86 residues processed: 371 average time/residue: 0.1967 time to fit residues: 119.1164 Evaluate side-chains 345 residues out of total 3269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 241 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 579 ASN Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1033 MET Chi-restraints excluded: chain A residue 1055 HIS Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1102 HIS Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1125 THR Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1182 ARG Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 612 GLU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 742 LYS Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1137 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 227 ASP Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain E residue 373 LYS Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 225 ASN Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 262 GLU Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 125 ASP Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain I residue 332 THR Chi-restraints excluded: chain J residue 51 TRP Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain J residue 296 ILE Chi-restraints excluded: chain J residue 316 GLN Chi-restraints excluded: chain J residue 384 CYS Chi-restraints excluded: chain J residue 413 SER Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain K residue 241 ARG Chi-restraints excluded: chain K residue 263 ASP Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain K residue 295 PHE Chi-restraints excluded: chain K residue 326 ASP Chi-restraints excluded: chain K residue 344 THR Chi-restraints excluded: chain K residue 361 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 123 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 320 optimal weight: 5.9990 chunk 196 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 146 optimal weight: 1.9990 chunk 310 optimal weight: 9.9990 chunk 277 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 255 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 414 GLN ** J 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 316 GLN J 319 HIS ** K 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.160869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.113649 restraints weight = 49008.557| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.74 r_work: 0.3204 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30095 Z= 0.151 Angle : 0.566 12.782 40750 Z= 0.295 Chirality : 0.042 0.155 4434 Planarity : 0.004 0.062 5267 Dihedral : 6.318 58.210 4046 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.96 % Allowed : 23.43 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.26 (0.14), residues: 3583 helix: 1.73 (0.13), residues: 1661 sheet: -0.40 (0.22), residues: 535 loop : -1.55 (0.16), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 317 TYR 0.021 0.001 TYR F 142 PHE 0.021 0.001 PHE I 264 TRP 0.025 0.002 TRP J 417 HIS 0.005 0.001 HIS D 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (30093) covalent geometry : angle 0.56618 / 0.29 (40750) hydrogen bonds : bond 0.05640 / 3.60 ( 1467) hydrogen bonds : angle 4.22473 / 3.03 ( 4167) metal coordination : bond 0.00090 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 251 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 579 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.8069 (p0) REVERT: A 836 PHE cc_start: 0.8373 (m-80) cc_final: 0.8082 (m-80) REVERT: A 1089 ASN cc_start: 0.8570 (p0) cc_final: 0.8237 (m-40) REVERT: A 1182 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.6773 (ptp90) REVERT: A 1191 MET cc_start: 0.3224 (mtp) cc_final: 0.2987 (mtt) REVERT: B 440 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7671 (tp30) REVERT: B 742 LYS cc_start: 0.7100 (OUTLIER) cc_final: 0.5939 (mmtt) REVERT: B 836 GLU cc_start: -0.0002 (OUTLIER) cc_final: -0.0793 (tm-30) REVERT: B 940 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7795 (tt) REVERT: C 44 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8553 (tt) REVERT: C 90 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8774 (tmtp) REVERT: C 250 ARG cc_start: 0.8729 (mtp180) cc_final: 0.8262 (mtm110) REVERT: D 171 ASP cc_start: 0.7878 (t70) cc_final: 0.7327 (t0) REVERT: E 335 ASN cc_start: 0.6383 (m-40) cc_final: 0.6066 (m110) REVERT: E 355 LEU cc_start: 0.8162 (pp) cc_final: 0.7868 (tt) REVERT: F 13 GLN cc_start: 0.8292 (tt0) cc_final: 0.7865 (tt0) REVERT: F 18 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.7165 (m-30) REVERT: F 168 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.8318 (p90) REVERT: F 227 GLN cc_start: 0.7942 (tp40) cc_final: 0.7615 (tp40) REVERT: G 1 MET cc_start: 0.7900 (ptt) cc_final: 0.7561 (ptt) REVERT: G 94 TYR cc_start: 0.8150 (t80) cc_final: 0.7836 (t80) REVERT: G 234 ARG cc_start: 0.7378 (ptt90) cc_final: 0.6664 (ttm110) REVERT: G 253 GLN cc_start: 0.8728 (tp40) cc_final: 0.8359 (tp40) REVERT: J 51 TRP cc_start: 0.7551 (OUTLIER) cc_final: 0.6827 (m100) REVERT: J 58 TRP cc_start: 0.7170 (m100) cc_final: 0.6953 (m100) REVERT: J 296 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7448 (mm) REVERT: J 377 MET cc_start: 0.7091 (ttt) cc_final: 0.6746 (ttt) REVERT: J 398 MET cc_start: 0.7708 (tpp) cc_final: 0.7451 (tpp) REVERT: J 414 ARG cc_start: 0.5813 (OUTLIER) cc_final: 0.4548 (ptp90) REVERT: K 18 GLU cc_start: 0.3513 (OUTLIER) cc_final: 0.2287 (tm-30) REVERT: K 39 PHE cc_start: 0.3859 (t80) cc_final: 0.3109 (m-10) REVERT: K 54 MET cc_start: -0.0283 (tpp) cc_final: -0.0886 (tmm) REVERT: K 171 GLU cc_start: 0.2943 (mm-30) cc_final: 0.2176 (tp30) REVERT: K 236 GLN cc_start: 0.4028 (mp10) cc_final: 0.3201 (mt0) outliers start: 128 outliers final: 89 residues processed: 364 average time/residue: 0.1842 time to fit residues: 109.4544 Evaluate side-chains 343 residues out of total 3269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 240 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 579 ASN Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1033 MET Chi-restraints excluded: chain A residue 1055 HIS Chi-restraints excluded: chain A residue 1102 HIS Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1125 THR Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1182 ARG Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 612 GLU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 698 LYS Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 742 LYS Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 937 GLU Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1137 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 225 ASN Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain G residue 262 GLU Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 261 CYS Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain I residue 296 GLU Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain I residue 332 THR Chi-restraints excluded: chain J residue 51 TRP Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 296 ILE Chi-restraints excluded: chain J residue 316 GLN Chi-restraints excluded: chain J residue 413 SER Chi-restraints excluded: chain J residue 414 ARG Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain K residue 263 ASP Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain K residue 295 PHE Chi-restraints excluded: chain K residue 361 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 214 optimal weight: 3.9990 chunk 329 optimal weight: 30.0000 chunk 82 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 225 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 321 optimal weight: 6.9990 chunk 255 optimal weight: 4.9990 chunk 279 optimal weight: 9.9990 chunk 323 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 803 GLN B1119 ASN E 414 GLN ** J 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 285 HIS J 319 HIS ** K 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 280 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.159908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.115404 restraints weight = 49149.048| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.70 r_work: 0.3197 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30095 Z= 0.189 Angle : 0.590 16.269 40750 Z= 0.308 Chirality : 0.043 0.206 4434 Planarity : 0.004 0.066 5267 Dihedral : 6.188 59.044 4036 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.14 % Allowed : 23.62 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.21 (0.14), residues: 3583 helix: 1.65 (0.13), residues: 1661 sheet: -0.42 (0.22), residues: 534 loop : -1.54 (0.16), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 317 TYR 0.024 0.002 TYR F 142 PHE 0.021 0.002 PHE I 264 TRP 0.026 0.002 TRP J 33 HIS 0.009 0.001 HIS K 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (30093) covalent geometry : angle 0.59044 / 0.31 (40750) hydrogen bonds : bond 0.05958 / 3.80 ( 1467) hydrogen bonds : angle 4.26643 / 3.06 ( 4167) metal coordination : bond 0.00144 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 240 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 LYS cc_start: 0.5418 (OUTLIER) cc_final: 0.4407 (tppt) REVERT: A 579 ASN cc_start: 0.8453 (OUTLIER) cc_final: 0.8053 (p0) REVERT: A 836 PHE cc_start: 0.8374 (m-80) cc_final: 0.8102 (m-80) REVERT: A 1140 ARG cc_start: 0.5706 (mtp85) cc_final: 0.5490 (mtp85) REVERT: A 1182 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.6684 (ptp90) REVERT: A 1191 MET cc_start: 0.3336 (mtp) cc_final: 0.3070 (mtt) REVERT: B 440 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7702 (tp30) REVERT: B 742 LYS cc_start: 0.7240 (OUTLIER) cc_final: 0.5980 (mmtt) REVERT: B 836 GLU cc_start: -0.0020 (OUTLIER) cc_final: -0.0820 (tm-30) REVERT: B 940 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7783 (tt) REVERT: C 44 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8574 (tt) REVERT: C 90 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8915 (tmtp) REVERT: C 250 ARG cc_start: 0.8731 (mtp180) cc_final: 0.8256 (mtm110) REVERT: D 171 ASP cc_start: 0.7949 (t70) cc_final: 0.7445 (t0) REVERT: E 335 ASN cc_start: 0.6409 (m-40) cc_final: 0.6073 (m110) REVERT: E 355 LEU cc_start: 0.8215 (pp) cc_final: 0.7904 (tt) REVERT: F 13 GLN cc_start: 0.8344 (tt0) cc_final: 0.7920 (tt0) REVERT: F 168 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8371 (p90) REVERT: F 227 GLN cc_start: 0.8002 (tp40) cc_final: 0.7668 (tp40) REVERT: G 1 MET cc_start: 0.7959 (ptt) cc_final: 0.7650 (ptt) REVERT: G 94 TYR cc_start: 0.8125 (t80) cc_final: 0.7805 (t80) REVERT: G 234 ARG cc_start: 0.7393 (ptt90) cc_final: 0.6680 (ttm110) REVERT: G 253 GLN cc_start: 0.8766 (tp40) cc_final: 0.8303 (tp40) REVERT: G 257 GLN cc_start: 0.8334 (mt0) cc_final: 0.8065 (mt0) REVERT: J 51 TRP cc_start: 0.7552 (OUTLIER) cc_final: 0.6783 (m100) REVERT: J 58 TRP cc_start: 0.7083 (m100) cc_final: 0.6848 (m100) REVERT: J 296 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7349 (mm) REVERT: J 377 MET cc_start: 0.7082 (ttt) cc_final: 0.6756 (ttt) REVERT: J 384 CYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8122 (p) REVERT: J 398 MET cc_start: 0.7631 (tpp) cc_final: 0.7394 (tpp) REVERT: K 39 PHE cc_start: 0.3794 (t80) cc_final: 0.3050 (m-10) REVERT: K 54 MET cc_start: -0.0396 (tpp) cc_final: -0.1027 (tmm) REVERT: K 171 GLU cc_start: 0.2939 (mm-30) cc_final: 0.2094 (tp30) REVERT: K 236 GLN cc_start: 0.3908 (mp10) cc_final: 0.2988 (mt0) REVERT: K 265 ARG cc_start: 0.3302 (OUTLIER) cc_final: 0.2779 (mmm160) REVERT: K 326 ASP cc_start: 0.1325 (OUTLIER) cc_final: 0.0727 (p0) REVERT: K 333 PHE cc_start: 0.1039 (m-80) cc_final: 0.0196 (m-10) REVERT: K 361 ASP cc_start: 0.0443 (OUTLIER) cc_final: 0.0118 (m-30) outliers start: 134 outliers final: 97 residues processed: 359 average time/residue: 0.1960 time to fit residues: 114.3231 Evaluate side-chains 345 residues out of total 3269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 232 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 LYS Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 579 ASN Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1033 MET Chi-restraints excluded: chain A residue 1055 HIS Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1102 HIS Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1125 THR Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1182 ARG Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 612 GLU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 698 LYS Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 742 LYS Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 937 GLU Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1137 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 225 ASN Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain G residue 262 GLU Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 56 LYS Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 261 CYS Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain I residue 332 THR Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 51 TRP Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 296 ILE Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 384 CYS Chi-restraints excluded: chain J residue 413 SER Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain K residue 263 ASP Chi-restraints excluded: chain K residue 265 ARG Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain K residue 295 PHE Chi-restraints excluded: chain K residue 326 ASP Chi-restraints excluded: chain K residue 344 THR Chi-restraints excluded: chain K residue 361 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 181 optimal weight: 3.9990 chunk 334 optimal weight: 50.0000 chunk 139 optimal weight: 1.9990 chunk 267 optimal weight: 0.8980 chunk 283 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 217 optimal weight: 0.9980 chunk 318 optimal weight: 0.9990 chunk 286 optimal weight: 0.4980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1119 ASN C 37 ASN E 414 GLN E 423 HIS ** J 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 319 HIS ** K 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 316 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.161895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.117479 restraints weight = 49021.145| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.67 r_work: 0.3239 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30095 Z= 0.125 Angle : 0.547 15.598 40750 Z= 0.285 Chirality : 0.041 0.211 4434 Planarity : 0.004 0.058 5267 Dihedral : 5.950 60.888 4033 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.49 % Allowed : 24.39 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.47 (0.14), residues: 3583 helix: 1.88 (0.13), residues: 1668 sheet: -0.35 (0.22), residues: 539 loop : -1.42 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 41 TYR 0.018 0.001 TYR F 142 PHE 0.022 0.001 PHE I 264 TRP 0.028 0.001 TRP J 33 HIS 0.005 0.001 HIS F 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (30093) covalent geometry : angle 0.54731 / 0.29 (40750) hydrogen bonds : bond 0.05226 / 3.33 ( 1467) hydrogen bonds : angle 4.09555 / 2.94 ( 4167) metal coordination : bond 0.00146 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 252 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 579 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.8018 (p0) REVERT: A 1089 ASN cc_start: 0.8449 (p0) cc_final: 0.8208 (m-40) REVERT: A 1140 ARG cc_start: 0.5817 (mtp85) cc_final: 0.5326 (mtp85) REVERT: A 1182 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.6798 (ptp90) REVERT: A 1191 MET cc_start: 0.3362 (mtp) cc_final: 0.3079 (mtt) REVERT: B 440 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7643 (tp30) REVERT: B 742 LYS cc_start: 0.7087 (OUTLIER) cc_final: 0.5890 (mmtt) REVERT: B 836 GLU cc_start: -0.0120 (OUTLIER) cc_final: -0.0812 (tm-30) REVERT: B 940 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7718 (tt) REVERT: C 44 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8520 (tt) REVERT: C 250 ARG cc_start: 0.8656 (mtp180) cc_final: 0.8228 (mtm110) REVERT: E 335 ASN cc_start: 0.6406 (m-40) cc_final: 0.6067 (m110) REVERT: E 355 LEU cc_start: 0.8166 (pp) cc_final: 0.7826 (tt) REVERT: F 13 GLN cc_start: 0.8356 (tt0) cc_final: 0.7948 (tt0) REVERT: F 168 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.8335 (p90) REVERT: F 227 GLN cc_start: 0.7889 (tp40) cc_final: 0.7604 (tp40) REVERT: G 1 MET cc_start: 0.7850 (ptt) cc_final: 0.7559 (ptt) REVERT: G 94 TYR cc_start: 0.8089 (t80) cc_final: 0.7729 (t80) REVERT: G 234 ARG cc_start: 0.7323 (ptt90) cc_final: 0.6566 (ttm110) REVERT: G 253 GLN cc_start: 0.8652 (tp40) cc_final: 0.8409 (mm110) REVERT: G 257 GLN cc_start: 0.8330 (mt0) cc_final: 0.8130 (mt0) REVERT: J 51 TRP cc_start: 0.7494 (OUTLIER) cc_final: 0.6776 (m100) REVERT: J 58 TRP cc_start: 0.7122 (m100) cc_final: 0.6908 (m100) REVERT: J 296 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7419 (mm) REVERT: J 353 TRP cc_start: 0.6894 (m100) cc_final: 0.6543 (m100) REVERT: J 377 MET cc_start: 0.6990 (ttt) cc_final: 0.6724 (ttt) REVERT: J 398 MET cc_start: 0.7625 (tpp) cc_final: 0.7410 (tpp) REVERT: K 54 MET cc_start: -0.0407 (tpp) cc_final: -0.1068 (tmm) REVERT: K 171 GLU cc_start: 0.2961 (mm-30) cc_final: 0.2153 (tp30) REVERT: K 236 GLN cc_start: 0.3872 (mp10) cc_final: 0.2917 (mt0) REVERT: K 265 ARG cc_start: 0.3255 (OUTLIER) cc_final: 0.2795 (mmm160) REVERT: K 316 GLN cc_start: 0.3354 (OUTLIER) cc_final: 0.1398 (tp40) REVERT: K 326 ASP cc_start: 0.1249 (OUTLIER) cc_final: 0.0751 (p0) REVERT: K 333 PHE cc_start: 0.1009 (m-80) cc_final: 0.0543 (m-10) REVERT: K 361 ASP cc_start: 0.0348 (OUTLIER) cc_final: 0.0036 (m-30) outliers start: 113 outliers final: 79 residues processed: 350 average time/residue: 0.1947 time to fit residues: 111.8671 Evaluate side-chains 338 residues out of total 3269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 245 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 579 ASN Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1033 MET Chi-restraints excluded: chain A residue 1055 HIS Chi-restraints excluded: chain A residue 1102 HIS Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1125 THR Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1182 ARG Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 698 LYS Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 742 LYS Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 937 GLU Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1137 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 225 ASN Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain G residue 262 GLU Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain I residue 332 THR Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 51 TRP Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 296 ILE Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain K residue 263 ASP Chi-restraints excluded: chain K residue 265 ARG Chi-restraints excluded: chain K residue 295 PHE Chi-restraints excluded: chain K residue 316 GLN Chi-restraints excluded: chain K residue 326 ASP Chi-restraints excluded: chain K residue 344 THR Chi-restraints excluded: chain K residue 361 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 197 optimal weight: 50.0000 chunk 54 optimal weight: 2.9990 chunk 284 optimal weight: 8.9990 chunk 149 optimal weight: 3.9990 chunk 154 optimal weight: 0.6980 chunk 347 optimal weight: 0.5980 chunk 170 optimal weight: 0.6980 chunk 316 optimal weight: 20.0000 chunk 355 optimal weight: 50.0000 chunk 10 optimal weight: 0.9990 chunk 249 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN E 414 GLN E 423 HIS ** J 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 319 HIS ** K 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.161503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3427 r_free = 0.3427 target = 0.105944 restraints weight = 48799.105| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.73 r_work: 0.3186 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30095 Z= 0.139 Angle : 0.559 15.278 40750 Z= 0.293 Chirality : 0.042 0.207 4434 Planarity : 0.004 0.057 5267 Dihedral : 5.914 61.257 4028 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.31 % Allowed : 24.36 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.48 (0.14), residues: 3583 helix: 1.88 (0.13), residues: 1669 sheet: -0.34 (0.22), residues: 539 loop : -1.40 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 41 TYR 0.023 0.001 TYR A 524 PHE 0.030 0.001 PHE A 836 TRP 0.031 0.001 TRP J 33 HIS 0.004 0.001 HIS D 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (30093) covalent geometry : angle 0.55918 / 0.29 (40750) hydrogen bonds : bond 0.05331 / 3.41 ( 1467) hydrogen bonds : angle 4.10636 / 2.94 ( 4167) metal coordination : bond 0.00103 / 0.05 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 245 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 579 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.8118 (p0) REVERT: A 1079 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7723 (tm-30) REVERT: A 1089 ASN cc_start: 0.8529 (p0) cc_final: 0.8184 (m-40) REVERT: A 1140 ARG cc_start: 0.5713 (mtp85) cc_final: 0.5378 (mtp85) REVERT: A 1182 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6767 (ptp90) REVERT: A 1191 MET cc_start: 0.2956 (mtp) cc_final: 0.2744 (mtt) REVERT: B 440 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7918 (tp30) REVERT: B 742 LYS cc_start: 0.7007 (OUTLIER) cc_final: 0.5913 (mmtt) REVERT: B 836 GLU cc_start: -0.0129 (OUTLIER) cc_final: -0.0811 (tm-30) REVERT: B 940 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7704 (tt) REVERT: C 44 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8530 (tt) REVERT: C 250 ARG cc_start: 0.8684 (mtp180) cc_final: 0.8192 (mtm110) REVERT: D 171 ASP cc_start: 0.7997 (t70) cc_final: 0.7450 (t0) REVERT: E 335 ASN cc_start: 0.6284 (m-40) cc_final: 0.5999 (m110) REVERT: E 355 LEU cc_start: 0.8276 (pp) cc_final: 0.7955 (tt) REVERT: F 13 GLN cc_start: 0.8245 (tt0) cc_final: 0.7871 (tt0) REVERT: F 168 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8287 (p90) REVERT: F 227 GLN cc_start: 0.8048 (tp40) cc_final: 0.7739 (tp40) REVERT: G 1 MET cc_start: 0.7882 (ptt) cc_final: 0.7575 (ptt) REVERT: G 94 TYR cc_start: 0.8209 (t80) cc_final: 0.7832 (t80) REVERT: G 234 ARG cc_start: 0.7308 (ptt90) cc_final: 0.6598 (ttm110) REVERT: G 253 GLN cc_start: 0.8596 (tp40) cc_final: 0.8393 (mm110) REVERT: J 51 TRP cc_start: 0.7561 (OUTLIER) cc_final: 0.6754 (m100) REVERT: J 58 TRP cc_start: 0.7207 (m100) cc_final: 0.6996 (m100) REVERT: J 138 MET cc_start: 0.3951 (mmm) cc_final: 0.3543 (tmm) REVERT: J 192 TRP cc_start: 0.5010 (m100) cc_final: 0.4791 (m100) REVERT: J 296 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7509 (mm) REVERT: J 353 TRP cc_start: 0.6736 (m100) cc_final: 0.6338 (m100) REVERT: J 377 MET cc_start: 0.7307 (ttt) cc_final: 0.6728 (ttm) REVERT: J 398 MET cc_start: 0.7931 (tpp) cc_final: 0.7514 (tpp) REVERT: K 54 MET cc_start: -0.0418 (tpp) cc_final: -0.1018 (tmm) REVERT: K 171 GLU cc_start: 0.3051 (mm-30) cc_final: 0.2315 (tp30) REVERT: K 236 GLN cc_start: 0.3950 (mp10) cc_final: 0.3139 (mt0) REVERT: K 265 ARG cc_start: 0.3272 (OUTLIER) cc_final: 0.2896 (mmm160) REVERT: K 326 ASP cc_start: 0.1202 (OUTLIER) cc_final: 0.0756 (p0) REVERT: K 333 PHE cc_start: 0.1056 (m-80) cc_final: 0.0396 (m-10) REVERT: K 361 ASP cc_start: 0.0238 (OUTLIER) cc_final: -0.0036 (m-30) outliers start: 107 outliers final: 86 residues processed: 342 average time/residue: 0.1834 time to fit residues: 102.8117 Evaluate side-chains 338 residues out of total 3269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 238 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 579 ASN Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 774 ASP Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 1033 MET Chi-restraints excluded: chain A residue 1055 HIS Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1102 HIS Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1125 THR Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1182 ARG Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 698 LYS Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 742 LYS Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 937 GLU Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1137 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain F residue 225 ASN Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain G residue 262 GLU Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 56 LYS Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 261 CYS Chi-restraints excluded: chain I residue 299 SER Chi-restraints excluded: chain I residue 332 THR Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 51 TRP Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 296 ILE Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain K residue 263 ASP Chi-restraints excluded: chain K residue 265 ARG Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain K residue 326 ASP Chi-restraints excluded: chain K residue 344 THR Chi-restraints excluded: chain K residue 361 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 9 optimal weight: 0.6980 chunk 352 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 213 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 214 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 197 optimal weight: 50.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 646 ASN A 803 GLN B1119 ASN E 414 GLN E 423 HIS J 193 ASN J 247 GLN ** J 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 319 HIS ** K 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.162524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3436 r_free = 0.3436 target = 0.107175 restraints weight = 48982.215| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.80 r_work: 0.3194 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30095 Z= 0.121 Angle : 0.540 14.728 40750 Z= 0.283 Chirality : 0.041 0.202 4434 Planarity : 0.004 0.054 5267 Dihedral : 5.823 61.509 4028 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.12 % Allowed : 24.70 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.63 (0.14), residues: 3583 helix: 2.00 (0.13), residues: 1665 sheet: -0.28 (0.22), residues: 539 loop : -1.30 (0.16), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 41 TYR 0.018 0.001 TYR F 142 PHE 0.025 0.001 PHE C 3 TRP 0.032 0.001 TRP J 33 HIS 0.005 0.001 HIS F 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (30093) covalent geometry : angle 0.54041 / 0.28 (40750) hydrogen bonds : bond 0.05011 / 3.20 ( 1467) hydrogen bonds : angle 4.02000 / 2.88 ( 4167) metal coordination : bond 0.00089 / 0.04 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11287.43 seconds wall clock time: 192 minutes 58.11 seconds (11578.11 seconds total)