Starting phenix.real_space_refine on Mon May 4 20:02:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k16_61966/05_2026/9k16_61966.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k16_61966/05_2026/9k16_61966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k16_61966/05_2026/9k16_61966.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k16_61966/05_2026/9k16_61966.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k16_61966/05_2026/9k16_61966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k16_61966/05_2026/9k16_61966.map" } resolution = 3.19 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 Zn 6 6.06 5 P 30 5.49 5 Mg 1 5.21 5 S 141 5.16 5 C 14535 2.51 5 N 4041 2.21 5 O 4425 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23179 Number of models: 1 Model: "" Number of chains: 18 Chain: "T" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 205 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain breaks: 1 Chain: "N" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 350 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain breaks: 1 Chain: "P" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'RNA': 3} Modifications used: {'rna3p_pyr': 3} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 6597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 843, 6597 Classifications: {'peptide': 843} Link IDs: {'PTRANS': 27, 'TRANS': 815} Chain breaks: 4 Chain: "C" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2256 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain breaks: 1 Chain: "F" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 660 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 507 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "K" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 890 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "L" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 365 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "H" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1129 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "I" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 787 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 1 Chain: "E" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1706 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 205} Chain: "B" Number of atoms: 7660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 967, 7660 Classifications: {'peptide': 967} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 36, 'TRANS': 930} Chain breaks: 6 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5708 SG CYS A 989 16.607 73.999 31.378 1.00167.89 S ATOM 5815 SG CYS A1004 19.483 76.483 30.981 1.00150.61 S ATOM 7917 SG CYS C 90 78.143 41.787 137.855 1.00132.91 S ATOM 7936 SG CYS C 93 79.666 39.677 135.083 1.00155.82 S ATOM 7975 SG CYS C 99 77.655 37.915 137.503 1.00120.13 S ATOM 8001 SG CYS C 102 76.120 40.470 134.883 1.00134.41 S ATOM 10183 SG CYS J 7 48.784 42.862 118.310 1.00 72.91 S ATOM 10207 SG CYS J 10 48.141 43.965 121.891 1.00 70.35 S ATOM 10473 SG CYS J 44 45.757 45.030 118.981 1.00 77.27 S ATOM 10479 SG CYS J 45 45.826 41.529 120.437 1.00 74.38 S ATOM 11571 SG CYS L 12 76.680 15.207 93.119 1.00100.10 S ATOM 11589 SG CYS L 15 76.262 11.931 94.922 1.00 99.41 S ATOM 11691 SG CYS L 29 79.193 12.603 92.491 1.00 94.14 S ATOM 11717 SG CYS L 32 75.550 11.818 91.384 1.00 98.52 S ATOM 13060 SG CYS I 7 25.793 46.156 18.758 1.00 83.51 S ATOM 13245 SG CYS I 29 30.062 47.723 18.492 1.00 80.83 S ATOM 13270 SG CYS I 32 28.575 45.980 16.323 1.00 67.23 S Time building chain proxies: 5.76, per 1000 atoms: 0.25 Number of scatterers: 23179 At special positions: 0 Unit cell: (113.88, 136.875, 163.155, 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 6 29.99 S 141 16.00 P 30 15.00 Mg 1 11.99 O 4425 8.00 N 4041 7.00 C 14535 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: 1.77 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" ND1 HIS A 938 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A 940 " pdb="ZN ZN A3001 " - pdb=" SG CYS A 989 " pdb="ZN ZN A3001 " - pdb=" SG CYS A1004 " pdb=" ZN C 400 " pdb="ZN ZN C 400 " - pdb=" SG CYS C 93 " pdb="ZN ZN C 400 " - pdb=" SG CYS C 99 " pdb="ZN ZN C 400 " - pdb=" SG CYS C 102 " pdb="ZN ZN C 400 " - pdb=" SG CYS C 90 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb=" ZN J 200 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 15 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 29 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 12 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 32 " Number of angles added : 20 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5348 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 34 sheets defined 35.7% alpha, 18.6% beta 10 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 2.64 Creating SS restraints... Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 359 through 369 Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 442 through 447 Processing helix chain 'A' and resid 462 through 473 Processing helix chain 'A' and resid 492 through 505 Processing helix chain 'A' and resid 509 through 518 removed outlier: 3.653A pdb=" N MET A 518 " --> pdb=" O GLN A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 547 through 549 No H-bonds generated for 'chain 'A' and resid 547 through 549' Processing helix chain 'A' and resid 576 through 591 removed outlier: 3.809A pdb=" N GLU A 591 " --> pdb=" O GLY A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 613 Proline residue: A 606 - end of helix removed outlier: 3.535A pdb=" N ASP A 613 " --> pdb=" O MET A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 624 Processing helix chain 'A' and resid 627 through 650 removed outlier: 5.109A pdb=" N SER A 643 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Proline residue: A 644 - end of helix removed outlier: 3.644A pdb=" N ARG A 648 " --> pdb=" O PRO A 644 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG A 650 " --> pdb=" O VAL A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 675 Processing helix chain 'A' and resid 679 through 683 removed outlier: 3.506A pdb=" N ASN A 682 " --> pdb=" O SER A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 700 removed outlier: 3.977A pdb=" N LYS A 694 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU A 695 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 729 Processing helix chain 'A' and resid 750 through 771 removed outlier: 3.508A pdb=" N ALA A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 787 removed outlier: 3.880A pdb=" N VAL A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 847 removed outlier: 3.530A pdb=" N LEU A 831 " --> pdb=" O PRO A 827 " (cutoff:3.500A) Proline residue: A 839 - end of helix Processing helix chain 'A' and resid 848 through 863 removed outlier: 3.578A pdb=" N VAL A 861 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 874 No H-bonds generated for 'chain 'A' and resid 872 through 874' Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 891 through 904 Processing helix chain 'A' and resid 908 through 911 No H-bonds generated for 'chain 'A' and resid 908 through 911' Processing helix chain 'A' and resid 942 through 948 Processing helix chain 'A' and resid 952 through 970 removed outlier: 3.853A pdb=" N ALA A 963 " --> pdb=" O ARG A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1027 removed outlier: 3.848A pdb=" N THR A1020 " --> pdb=" O ASP A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1034 removed outlier: 3.876A pdb=" N LEU A1033 " --> pdb=" O TYR A1029 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU A1034 " --> pdb=" O PRO A1030 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1029 through 1034' Processing helix chain 'A' and resid 1085 through 1095 Processing helix chain 'A' and resid 1103 through 1107 removed outlier: 3.680A pdb=" N ARG A1106 " --> pdb=" O ASP A1103 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER A1107 " --> pdb=" O THR A1104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1103 through 1107' Processing helix chain 'A' and resid 1111 through 1120 Processing helix chain 'A' and resid 1121 through 1140 removed outlier: 4.088A pdb=" N VAL A1139 " --> pdb=" O SER A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1155 removed outlier: 3.946A pdb=" N ILE A1148 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1172 removed outlier: 3.540A pdb=" N LEU A1172 " --> pdb=" O GLY A1168 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 44 removed outlier: 3.744A pdb=" N ALA C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 73 removed outlier: 3.736A pdb=" N LEU C 73 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 176 through 180 Processing helix chain 'C' and resid 204 through 214 Processing helix chain 'C' and resid 241 through 251 Processing helix chain 'C' and resid 276 through 294 removed outlier: 3.570A pdb=" N VAL C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 83 Processing helix chain 'F' and resid 96 through 107 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 37 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.706A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR J 51 " --> pdb=" O ARG J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 62 removed outlier: 3.725A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 removed outlier: 3.506A pdb=" N GLY K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG K 52 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP K 53 " --> pdb=" O GLN K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'E' and resid 31 through 51 removed outlier: 3.715A pdb=" N GLY E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 71 removed outlier: 3.724A pdb=" N PHE E 66 " --> pdb=" O SER E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 116 removed outlier: 3.527A pdb=" N ILE E 108 " --> pdb=" O LYS E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 141 removed outlier: 4.120A pdb=" N LYS E 138 " --> pdb=" O ASP E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 162 removed outlier: 3.562A pdb=" N HIS E 162 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 184 removed outlier: 3.531A pdb=" N GLN E 182 " --> pdb=" O ALA E 178 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE E 183 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 204 Processing helix chain 'B' and resid 21 through 40 Processing helix chain 'B' and resid 43 through 56 removed outlier: 3.588A pdb=" N LEU B 47 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER B 49 " --> pdb=" O HIS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 65 Processing helix chain 'B' and resid 111 through 118 Processing helix chain 'B' and resid 275 through 283 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 300 through 318 removed outlier: 3.602A pdb=" N VAL B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 337 removed outlier: 3.826A pdb=" N GLY B 337 " --> pdb=" O GLN B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 354 Processing helix chain 'B' and resid 360 through 380 Processing helix chain 'B' and resid 390 through 392 No H-bonds generated for 'chain 'B' and resid 390 through 392' Processing helix chain 'B' and resid 398 through 428 removed outlier: 3.738A pdb=" N VAL B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 421 " --> pdb=" O THR B 417 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N HIS B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 439 removed outlier: 4.025A pdb=" N TYR B 438 " --> pdb=" O PRO B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 455 removed outlier: 3.671A pdb=" N THR B 445 " --> pdb=" O ALA B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 486 removed outlier: 3.686A pdb=" N LEU B 486 " --> pdb=" O SER B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 504 removed outlier: 4.471A pdb=" N ARG B 503 " --> pdb=" O GLY B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 510 removed outlier: 3.626A pdb=" N TRP B 510 " --> pdb=" O PRO B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 552 removed outlier: 4.181A pdb=" N PHE B 549 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP B 550 " --> pdb=" O GLU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 595 removed outlier: 3.818A pdb=" N ALA B 588 " --> pdb=" O ASP B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 637 removed outlier: 3.509A pdb=" N LYS B 635 " --> pdb=" O ASN B 632 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU B 636 " --> pdb=" O LEU B 633 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS B 637 " --> pdb=" O HIS B 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 632 through 637' Processing helix chain 'B' and resid 645 through 652 Processing helix chain 'B' and resid 661 through 666 Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 688 through 693 removed outlier: 3.533A pdb=" N LEU B 693 " --> pdb=" O SER B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 706 removed outlier: 3.832A pdb=" N ASP B 706 " --> pdb=" O ALA B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 717 Processing helix chain 'B' and resid 718 through 721 Processing helix chain 'B' and resid 729 through 733 removed outlier: 3.581A pdb=" N ILE B 732 " --> pdb=" O ASN B 729 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG B 733 " --> pdb=" O PRO B 730 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 729 through 733' Processing helix chain 'B' and resid 751 through 758 Processing helix chain 'B' and resid 788 through 793 Processing helix chain 'B' and resid 925 through 929 Processing helix chain 'B' and resid 943 through 945 No H-bonds generated for 'chain 'B' and resid 943 through 945' Processing helix chain 'B' and resid 946 through 951 removed outlier: 3.542A pdb=" N ARG B 950 " --> pdb=" O ALA B 946 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN B 951 " --> pdb=" O PHE B 947 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 946 through 951' Processing helix chain 'B' and resid 952 through 967 removed outlier: 4.513A pdb=" N LEU B 956 " --> pdb=" O THR B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1004 removed outlier: 3.506A pdb=" N ILE B 997 " --> pdb=" O SER B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1045 removed outlier: 3.696A pdb=" N LYS B1044 " --> pdb=" O MET B1040 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B1045 " --> pdb=" O SER B1041 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1040 through 1045' Processing sheet with id=AA1, first strand: chain 'B' and resid 1046 through 1048 removed outlier: 3.630A pdb=" N SER A 323 " --> pdb=" O ARG B1048 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER A 326 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 455 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 350 through 354 removed outlier: 3.525A pdb=" N THR A 376 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG A 403 " --> pdb=" O CYS A 372 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N CYS A 372 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN A 377 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR A 380 " --> pdb=" O GLN A 377 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 507 through 508 Processing sheet with id=AA4, first strand: chain 'A' and resid 529 through 531 removed outlier: 6.006A pdb=" N VAL A 529 " --> pdb=" O HIS H 94 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N HIS H 94 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS A 531 " --> pdb=" O VAL H 92 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 529 through 531 removed outlier: 6.006A pdb=" N VAL A 529 " --> pdb=" O HIS H 94 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N HIS H 94 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS A 531 " --> pdb=" O VAL H 92 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N TYR H 113 " --> pdb=" O TYR H 98 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU H 119 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LEU H 120 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE H 40 " --> pdb=" O ARG H 124 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N MET H 39 " --> pdb=" O SER H 34 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N THR H 33 " --> pdb=" O VAL H 14 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N VAL H 14 " --> pdb=" O THR H 33 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG H 144 " --> pdb=" O THR H 59 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 555 through 556 removed outlier: 6.366A pdb=" N ILE A 561 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 703 through 704 Processing sheet with id=AA8, first strand: chain 'A' and resid 789 through 791 removed outlier: 3.626A pdb=" N ARG A 798 " --> pdb=" O VAL A 790 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1043 through 1049 removed outlier: 3.749A pdb=" N ASN A1047 " --> pdb=" O ASP A1073 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 906 through 907 removed outlier: 3.717A pdb=" N LYS A1038 " --> pdb=" O VAL A 906 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 982 through 986 removed outlier: 3.513A pdb=" N ILE A 939 " --> pdb=" O LEU A1005 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A1007 " --> pdb=" O GLY A 937 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU A 914 " --> pdb=" O HIS A 940 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N VAL A 913 " --> pdb=" O GLU I 47 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLU I 47 " --> pdb=" O VAL A 913 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N PHE A 915 " --> pdb=" O ARG I 45 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ARG I 45 " --> pdb=" O PHE A 915 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL A 917 " --> pdb=" O VAL I 43 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL I 43 " --> pdb=" O VAL A 917 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1227 through 1230 removed outlier: 3.567A pdb=" N GLU A1228 " --> pdb=" O ARG F 115 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A1230 " --> pdb=" O THR F 113 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR F 113 " --> pdb=" O LEU A1230 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 11 through 18 removed outlier: 6.019A pdb=" N VAL C 12 " --> pdb=" O ARG C 27 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ARG C 27 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ILE C 14 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU C 25 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR C 21 " --> pdb=" O LYS C 18 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU C 190 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ASP C 263 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 11.224A pdb=" N MET C 188 " --> pdb=" O ASP C 263 " (cutoff:3.500A) removed outlier: 9.583A pdb=" N PHE C 265 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 11.060A pdb=" N THR C 186 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 10.032A pdb=" N PHE C 267 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 11.354A pdb=" N THR C 184 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 10.083A pdb=" N VAL C 269 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N ALA C 182 " --> pdb=" O VAL C 269 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 126 through 127 removed outlier: 6.219A pdb=" N GLU C 161 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL C 57 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LYS C 163 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ILE C 55 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG C 165 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL C 53 " --> pdb=" O ARG C 165 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE C 167 " --> pdb=" O ASP C 51 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 118 through 121 removed outlier: 3.567A pdb=" N VAL C 154 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 220 through 222 removed outlier: 3.568A pdb=" N ASP C 221 " --> pdb=" O VAL C 230 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.575A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N HIS K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 18 through 19 removed outlier: 5.513A pdb=" N VAL B 882 " --> pdb=" O LYS L 39 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N GLY B 877 " --> pdb=" O VAL B 901 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N VAL B 901 " --> pdb=" O GLY B 877 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL B 879 " --> pdb=" O ARG B 899 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ARG B 899 " --> pdb=" O VAL B 879 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS B 881 " --> pdb=" O SER B 897 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS B 891 " --> pdb=" O ASN B 887 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 18 through 19 removed outlier: 5.513A pdb=" N VAL B 882 " --> pdb=" O LYS L 39 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 14 through 16 Processing sheet with id=AC3, first strand: chain 'I' and resid 84 through 89 Processing sheet with id=AC4, first strand: chain 'E' and resid 94 through 96 removed outlier: 3.519A pdb=" N PHE E 150 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 168 through 170 removed outlier: 3.672A pdb=" N ARG E 169 " --> pdb=" O LYS E 212 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS E 212 " --> pdb=" O ARG E 169 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA E 225 " --> pdb=" O VAL E 213 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 68 through 70 removed outlier: 3.809A pdb=" N MET B 68 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N VAL B 89 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLU B 133 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N PHE B 91 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASP B 131 " --> pdb=" O PHE B 91 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLU B 93 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN B 129 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ALA B 124 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG B 169 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N MET B 126 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN B 163 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AC8, first strand: chain 'B' and resid 204 through 206 Processing sheet with id=AC9, first strand: chain 'B' and resid 394 through 397 removed outlier: 6.377A pdb=" N ALA B 215 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 224 through 226 Processing sheet with id=AD2, first strand: chain 'B' and resid 457 through 458 Processing sheet with id=AD3, first strand: chain 'B' and resid 535 through 536 Processing sheet with id=AD4, first strand: chain 'B' and resid 535 through 536 removed outlier: 3.535A pdb=" N CYS B 685 " --> pdb=" O LEU B 628 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 575 through 580 removed outlier: 5.765A pdb=" N TRP B 576 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU B 572 " --> pdb=" O TRP B 576 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY B 578 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LYS B 569 " --> pdb=" O VAL B 614 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE B 616 " --> pdb=" O LYS B 569 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU B 571 " --> pdb=" O ILE B 616 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1011 through 1012 removed outlier: 6.863A pdb=" N ILE B 784 " --> pdb=" O TYR B 922 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N GLU B 924 " --> pdb=" O ILE B 784 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N MET B 786 " --> pdb=" O GLU B 924 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE B1028 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 855 through 857 removed outlier: 3.919A pdb=" N ILE B 857 " --> pdb=" O VAL B 869 " (cutoff:3.500A) 859 hydrogen bonds defined for protein. 2385 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 4.70 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7519 1.34 - 1.46: 3805 1.46 - 1.58: 12049 1.58 - 1.70: 56 1.70 - 1.82: 217 Bond restraints: 23646 Sorted by residual: bond pdb=" CA HIS A 421 " pdb=" CB HIS A 421 " ideal model delta sigma weight residual 1.531 1.587 -0.056 3.28e-02 9.30e+02 2.93e+00 bond pdb=" C PRO B 505 " pdb=" N HIS B 506 " ideal model delta sigma weight residual 1.329 1.308 0.021 1.35e-02 5.49e+03 2.39e+00 bond pdb=" C3' DC N 18 " pdb=" O3' DC N 18 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.58e+00 bond pdb=" N ASP J 28 " pdb=" CA ASP J 28 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.36e+00 bond pdb=" CB GLU A 860 " pdb=" CG GLU A 860 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.24e+00 ... (remaining 23641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 31571 2.25 - 4.50: 367 4.50 - 6.75: 53 6.75 - 9.00: 7 9.00 - 11.25: 6 Bond angle restraints: 32004 Sorted by residual: angle pdb=" C MET A1002 " pdb=" CA MET A1002 " pdb=" CB MET A1002 " ideal model delta sigma weight residual 109.51 117.79 -8.28 1.60e+00 3.91e-01 2.68e+01 angle pdb=" C LEU E 56 " pdb=" N GLU E 57 " pdb=" CA GLU E 57 " ideal model delta sigma weight residual 121.54 130.66 -9.12 1.91e+00 2.74e-01 2.28e+01 angle pdb=" CA GLU E 57 " pdb=" CB GLU E 57 " pdb=" CG GLU E 57 " ideal model delta sigma weight residual 114.10 123.26 -9.16 2.00e+00 2.50e-01 2.10e+01 angle pdb=" N GLU E 57 " pdb=" CA GLU E 57 " pdb=" CB GLU E 57 " ideal model delta sigma weight residual 110.49 117.27 -6.78 1.69e+00 3.50e-01 1.61e+01 angle pdb=" N ILE I 24 " pdb=" CA ILE I 24 " pdb=" C ILE I 24 " ideal model delta sigma weight residual 112.96 109.09 3.87 1.00e+00 1.00e+00 1.50e+01 ... (remaining 31999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 13851 35.94 - 71.89: 460 71.89 - 107.83: 24 107.83 - 143.78: 0 143.78 - 179.72: 1 Dihedral angle restraints: 14336 sinusoidal: 6081 harmonic: 8255 Sorted by residual: dihedral pdb=" CA GLN A 505 " pdb=" C GLN A 505 " pdb=" N VAL A 506 " pdb=" CA VAL A 506 " ideal model delta harmonic sigma weight residual -180.00 -158.99 -21.01 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA LEU H 37 " pdb=" C LEU H 37 " pdb=" N ASP H 38 " pdb=" CA ASP H 38 " ideal model delta harmonic sigma weight residual -180.00 -160.13 -19.87 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" C4' DC N 18 " pdb=" C3' DC N 18 " pdb=" O3' DC N 18 " pdb=" P DA N 19 " ideal model delta sinusoidal sigma weight residual -140.00 39.72 -179.72 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 14333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2583 0.041 - 0.082: 724 0.082 - 0.122: 266 0.122 - 0.163: 26 0.163 - 0.204: 2 Chirality restraints: 3601 Sorted by residual: chirality pdb=" CA GLU E 57 " pdb=" N GLU E 57 " pdb=" C GLU E 57 " pdb=" CB GLU E 57 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ASP J 28 " pdb=" N ASP J 28 " pdb=" C ASP J 28 " pdb=" CB ASP J 28 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.23e-01 chirality pdb=" CA GLU F 99 " pdb=" N GLU F 99 " pdb=" C GLU F 99 " pdb=" CB GLU F 99 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.19e-01 ... (remaining 3598 not shown) Planarity restraints: 4013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 101 " 0.019 2.00e-02 2.50e+03 1.87e-02 6.14e+00 pdb=" CG PHE C 101 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE C 101 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 101 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE C 101 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 101 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE C 101 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 890 " -0.006 2.00e-02 2.50e+03 1.59e-02 5.05e+00 pdb=" CG TYR A 890 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A 890 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 890 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR A 890 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 890 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 890 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 890 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A1002 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C MET A1002 " 0.037 2.00e-02 2.50e+03 pdb=" O MET A1002 " -0.014 2.00e-02 2.50e+03 pdb=" N PRO A1003 " -0.012 2.00e-02 2.50e+03 ... (remaining 4010 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 30 2.61 - 3.18: 19145 3.18 - 3.76: 33430 3.76 - 4.33: 46350 4.33 - 4.90: 76693 Nonbonded interactions: 175648 Sorted by model distance: nonbonded pdb=" OD1 ASP A 449 " pdb="MG MG A3000 " model vdw 2.040 2.170 nonbonded pdb=" N GLY I 82 " pdb="ZN ZN I 201 " model vdw 2.156 2.310 nonbonded pdb=" O ASP F 129 " pdb=" OD1 ASP F 129 " model vdw 2.489 3.040 nonbonded pdb=" CA GLY I 82 " pdb="ZN ZN I 201 " model vdw 2.505 2.630 nonbonded pdb=" O5' DT N 28 " pdb=" O4' DT N 28 " model vdw 2.505 2.432 ... (remaining 175643 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 2.410 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: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.010 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 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 : 0.003 0.056 23665 Z= 0.146 Angle : 0.675 11.250 32024 Z= 0.375 Chirality : 0.043 0.204 3601 Planarity : 0.004 0.051 4013 Dihedral : 16.927 179.723 8988 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.84 % Allowed : 16.25 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.16), residues: 2796 helix: 0.67 (0.19), residues: 869 sheet: -0.65 (0.24), residues: 474 loop : -1.52 (0.15), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1067 TYR 0.036 0.001 TYR A 890 PHE 0.044 0.001 PHE C 101 TRP 0.035 0.001 TRP A 949 HIS 0.008 0.001 HIS E 85 Details of bonding type rmsd covalent geometry : bond 0.00299 (23646) covalent geometry : angle 0.66378 (32004) hydrogen bonds : bond 0.20356 ( 872) hydrogen bonds : angle 6.68858 ( 2431) metal coordination : bond 0.00741 ( 19) metal coordination : angle 4.84410 ( 20) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 664 GLN cc_start: 0.8189 (tp40) cc_final: 0.7574 (mm110) REVERT: A 1005 LEU cc_start: 0.9319 (tp) cc_final: 0.9109 (tt) REVERT: A 1132 LEU cc_start: 0.8591 (pp) cc_final: 0.8160 (tp) REVERT: C 199 MET cc_start: 0.8217 (ttm) cc_final: 0.7565 (ttt) REVERT: F 102 MET cc_start: 0.7954 (ttm) cc_final: 0.7754 (ttp) REVERT: H 52 MET cc_start: 0.8201 (tpp) cc_final: 0.7958 (mpp) REVERT: I 87 PHE cc_start: 0.7215 (t80) cc_final: 0.6772 (p90) REVERT: B 553 MET cc_start: 0.9249 (ttp) cc_final: 0.9016 (ttp) outliers start: 21 outliers final: 19 residues processed: 215 average time/residue: 0.1605 time to fit residues: 54.8527 Evaluate side-chains 186 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 203 TYR Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 670 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN E 34 HIS ** E 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN E 182 GLN B 251 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.096383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.061802 restraints weight = 67073.741| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.05 r_work: 0.2931 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23665 Z= 0.136 Angle : 0.596 10.079 32024 Z= 0.310 Chirality : 0.043 0.184 3601 Planarity : 0.004 0.053 4013 Dihedral : 11.988 179.222 3450 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.55 % Allowed : 14.70 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.16), residues: 2796 helix: 0.80 (0.18), residues: 896 sheet: -0.42 (0.23), residues: 472 loop : -1.51 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1067 TYR 0.015 0.001 TYR K 87 PHE 0.030 0.001 PHE C 101 TRP 0.024 0.001 TRP A 949 HIS 0.008 0.001 HIS E 85 Details of bonding type rmsd covalent geometry : bond 0.00312 (23646) covalent geometry : angle 0.58455 (32004) hydrogen bonds : bond 0.04943 ( 872) hydrogen bonds : angle 5.04069 ( 2431) metal coordination : bond 0.00607 ( 19) metal coordination : angle 4.59418 ( 20) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 171 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 664 GLN cc_start: 0.8028 (tp40) cc_final: 0.7460 (mm110) REVERT: A 1116 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7250 (tp40) REVERT: A 1132 LEU cc_start: 0.8370 (pp) cc_final: 0.8020 (tp) REVERT: C 199 MET cc_start: 0.8234 (ttm) cc_final: 0.7496 (ttt) REVERT: C 202 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8671 (p) REVERT: F 130 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: K 22 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7740 (tm-30) REVERT: E 58 ASP cc_start: 0.5783 (m-30) cc_final: 0.4923 (m-30) REVERT: B 120 MET cc_start: 0.8932 (mmm) cc_final: 0.8463 (mtt) REVERT: B 269 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7995 (pp) REVERT: B 418 MET cc_start: 0.8858 (tmm) cc_final: 0.8300 (tmm) outliers start: 64 outliers final: 30 residues processed: 226 average time/residue: 0.1442 time to fit residues: 52.6596 Evaluate side-chains 185 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1116 GLN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 106 GLU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 118 GLN Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 203 TYR Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 895 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 64 optimal weight: 7.9990 chunk 222 optimal weight: 5.9990 chunk 209 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 237 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 260 optimal weight: 8.9990 chunk 246 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 807 GLN ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN ** E 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.097055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.065255 restraints weight = 67054.633| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 3.33 r_work: 0.2942 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 23665 Z= 0.105 Angle : 0.543 9.335 32024 Z= 0.280 Chirality : 0.041 0.157 3601 Planarity : 0.004 0.052 4013 Dihedral : 11.718 179.177 3438 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.99 % Allowed : 15.41 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.16), residues: 2796 helix: 1.06 (0.18), residues: 887 sheet: -0.33 (0.23), residues: 486 loop : -1.42 (0.16), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1067 TYR 0.014 0.001 TYR K 87 PHE 0.028 0.001 PHE C 101 TRP 0.019 0.001 TRP A 949 HIS 0.007 0.001 HIS E 85 Details of bonding type rmsd covalent geometry : bond 0.00226 (23646) covalent geometry : angle 0.53325 (32004) hydrogen bonds : bond 0.03880 ( 872) hydrogen bonds : angle 4.54628 ( 2431) metal coordination : bond 0.00428 ( 19) metal coordination : angle 4.15980 ( 20) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 167 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: A 1110 TYR cc_start: 0.8202 (t80) cc_final: 0.7426 (t80) REVERT: A 1116 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7461 (tp40) REVERT: A 1132 LEU cc_start: 0.8401 (pp) cc_final: 0.8177 (tp) REVERT: C 199 MET cc_start: 0.8249 (ttm) cc_final: 0.7927 (ttm) REVERT: C 202 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8692 (p) REVERT: F 103 LYS cc_start: 0.8514 (tppt) cc_final: 0.8293 (tppt) REVERT: F 130 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7942 (mp0) REVERT: K 22 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7778 (tm-30) REVERT: I 101 PHE cc_start: 0.4651 (m-80) cc_final: 0.4212 (m-10) REVERT: E 142 LEU cc_start: 0.6883 (pt) cc_final: 0.6595 (tp) REVERT: B 269 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8005 (pp) REVERT: B 418 MET cc_start: 0.8927 (tmm) cc_final: 0.8301 (tmm) outliers start: 50 outliers final: 28 residues processed: 207 average time/residue: 0.1439 time to fit residues: 48.4714 Evaluate side-chains 189 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1116 GLN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 203 TYR Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 985 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 159 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 207 optimal weight: 7.9990 chunk 278 optimal weight: 1.9990 chunk 275 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 254 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 243 optimal weight: 0.1980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 873 ASN ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN I 31 ASN I 81 HIS ** E 85 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 = 0.3835 r_free = 0.3835 target = 0.095540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.061564 restraints weight = 67642.403| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.26 r_work: 0.2908 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23665 Z= 0.125 Angle : 0.541 8.736 32024 Z= 0.281 Chirality : 0.042 0.172 3601 Planarity : 0.004 0.052 4013 Dihedral : 11.643 179.398 3435 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.63 % Allowed : 15.93 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.16), residues: 2796 helix: 1.09 (0.18), residues: 897 sheet: -0.27 (0.23), residues: 484 loop : -1.41 (0.16), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1067 TYR 0.014 0.001 TYR K 87 PHE 0.025 0.001 PHE C 101 TRP 0.014 0.001 TRP A 949 HIS 0.007 0.001 HIS E 85 Details of bonding type rmsd covalent geometry : bond 0.00293 (23646) covalent geometry : angle 0.52989 (32004) hydrogen bonds : bond 0.04168 ( 872) hydrogen bonds : angle 4.35982 ( 2431) metal coordination : bond 0.00587 ( 19) metal coordination : angle 4.37130 ( 20) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 160 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: A 1110 TYR cc_start: 0.8263 (t80) cc_final: 0.7655 (t80) REVERT: A 1116 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7536 (tp40) REVERT: A 1132 LEU cc_start: 0.8475 (pp) cc_final: 0.8265 (tp) REVERT: K 22 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7854 (tm-30) REVERT: L 21 LEU cc_start: 0.8518 (tp) cc_final: 0.8182 (tt) REVERT: I 101 PHE cc_start: 0.4618 (m-80) cc_final: 0.4210 (m-10) REVERT: E 46 MET cc_start: 0.5249 (ppp) cc_final: 0.5025 (tmm) REVERT: E 118 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.7124 (mp10) REVERT: E 142 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6833 (tp) REVERT: E 189 GLN cc_start: 0.5576 (tm-30) cc_final: 0.3949 (tm-30) REVERT: B 62 PHE cc_start: 0.9155 (OUTLIER) cc_final: 0.8240 (t80) REVERT: B 269 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8077 (pp) REVERT: B 418 MET cc_start: 0.8965 (tmm) cc_final: 0.8298 (tmm) outliers start: 66 outliers final: 33 residues processed: 215 average time/residue: 0.1437 time to fit residues: 50.8071 Evaluate side-chains 191 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 153 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1116 GLN Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 118 GLN Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 203 TYR Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 985 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 118 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 246 optimal weight: 0.0670 chunk 100 optimal weight: 0.9990 chunk 192 optimal weight: 0.5980 chunk 132 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 169 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN ** E 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1000 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.095776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.061484 restraints weight = 67585.269| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.01 r_work: 0.2934 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23665 Z= 0.103 Angle : 0.519 8.521 32024 Z= 0.269 Chirality : 0.041 0.160 3601 Planarity : 0.003 0.052 4013 Dihedral : 11.567 179.439 3434 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.31 % Allowed : 16.65 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.16), residues: 2796 helix: 1.20 (0.18), residues: 899 sheet: -0.33 (0.23), residues: 504 loop : -1.32 (0.16), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1067 TYR 0.013 0.001 TYR E 202 PHE 0.025 0.001 PHE C 101 TRP 0.014 0.001 TRP A 949 HIS 0.006 0.001 HIS H 42 Details of bonding type rmsd covalent geometry : bond 0.00232 (23646) covalent geometry : angle 0.50911 (32004) hydrogen bonds : bond 0.03686 ( 872) hydrogen bonds : angle 4.20036 ( 2431) metal coordination : bond 0.00566 ( 19) metal coordination : angle 4.04310 ( 20) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 161 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: A 1110 TYR cc_start: 0.8288 (t80) cc_final: 0.7726 (t80) REVERT: A 1116 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7486 (tp40) REVERT: F 130 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8053 (mp0) REVERT: K 22 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7848 (tm-30) REVERT: I 101 PHE cc_start: 0.4725 (m-80) cc_final: 0.4188 (m-10) REVERT: E 46 MET cc_start: 0.5519 (ppp) cc_final: 0.5262 (tmm) REVERT: E 189 GLN cc_start: 0.5385 (tm-30) cc_final: 0.4134 (tm-30) REVERT: B 62 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.8182 (t80) REVERT: B 269 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8070 (pp) REVERT: B 418 MET cc_start: 0.9059 (tmm) cc_final: 0.8348 (tmm) REVERT: B 422 MET cc_start: 0.8708 (ttt) cc_final: 0.8099 (ptm) REVERT: B 462 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7160 (mtm-85) REVERT: B 553 MET cc_start: 0.9174 (ttp) cc_final: 0.8913 (ttt) outliers start: 58 outliers final: 35 residues processed: 208 average time/residue: 0.1566 time to fit residues: 52.9634 Evaluate side-chains 184 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1116 GLN Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 69 TYR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 203 TYR Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 985 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 124 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 135 optimal weight: 0.0980 chunk 187 optimal weight: 4.9990 chunk 252 optimal weight: 0.9980 chunk 174 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN ** E 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.095745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.061769 restraints weight = 67233.869| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.99 r_work: 0.2942 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23665 Z= 0.094 Angle : 0.509 12.799 32024 Z= 0.262 Chirality : 0.041 0.211 3601 Planarity : 0.003 0.051 4013 Dihedral : 11.496 179.226 3434 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.19 % Allowed : 17.12 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.16), residues: 2796 helix: 1.39 (0.19), residues: 889 sheet: -0.20 (0.23), residues: 495 loop : -1.25 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1067 TYR 0.013 0.001 TYR K 87 PHE 0.024 0.001 PHE A 411 TRP 0.015 0.001 TRP A 949 HIS 0.005 0.001 HIS H 42 Details of bonding type rmsd covalent geometry : bond 0.00208 (23646) covalent geometry : angle 0.50083 (32004) hydrogen bonds : bond 0.03394 ( 872) hydrogen bonds : angle 4.07480 ( 2431) metal coordination : bond 0.00560 ( 19) metal coordination : angle 3.68789 ( 20) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 158 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 589 MET cc_start: 0.8998 (ttp) cc_final: 0.8766 (ttp) REVERT: A 1110 TYR cc_start: 0.8343 (t80) cc_final: 0.7832 (t80) REVERT: A 1116 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7480 (tp40) REVERT: F 96 ASP cc_start: 0.8244 (t70) cc_final: 0.7786 (t70) REVERT: F 109 LYS cc_start: 0.7392 (tttt) cc_final: 0.7161 (ttmt) REVERT: F 130 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8103 (mp0) REVERT: K 22 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7869 (tm-30) REVERT: I 101 PHE cc_start: 0.4945 (m-80) cc_final: 0.4399 (m-10) REVERT: E 46 MET cc_start: 0.5599 (ppp) cc_final: 0.5243 (tmm) REVERT: E 118 GLN cc_start: 0.7407 (OUTLIER) cc_final: 0.7181 (mp10) REVERT: E 189 GLN cc_start: 0.5545 (tm-30) cc_final: 0.4431 (tm-30) REVERT: B 62 PHE cc_start: 0.9175 (OUTLIER) cc_final: 0.8153 (t80) REVERT: B 269 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8079 (pp) REVERT: B 418 MET cc_start: 0.9044 (tmm) cc_final: 0.8413 (tmm) REVERT: B 462 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.7110 (mtm-85) outliers start: 55 outliers final: 35 residues processed: 204 average time/residue: 0.1539 time to fit residues: 50.8662 Evaluate side-chains 189 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 148 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1116 GLN Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 69 TYR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 118 GLN Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 203 TYR Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 985 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 255 optimal weight: 6.9990 chunk 170 optimal weight: 0.0970 chunk 8 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 139 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN H 67 ASN ** E 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.094053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.060116 restraints weight = 67140.336| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.98 r_work: 0.2903 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23665 Z= 0.122 Angle : 0.540 9.926 32024 Z= 0.280 Chirality : 0.042 0.189 3601 Planarity : 0.004 0.050 4013 Dihedral : 11.533 179.488 3434 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.03 % Allowed : 17.72 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.16), residues: 2796 helix: 1.33 (0.18), residues: 903 sheet: -0.20 (0.23), residues: 498 loop : -1.27 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1067 TYR 0.013 0.001 TYR J 43 PHE 0.025 0.001 PHE C 101 TRP 0.018 0.001 TRP A 949 HIS 0.005 0.001 HIS A 938 Details of bonding type rmsd covalent geometry : bond 0.00281 (23646) covalent geometry : angle 0.53021 (32004) hydrogen bonds : bond 0.03986 ( 872) hydrogen bonds : angle 4.08405 ( 2431) metal coordination : bond 0.00544 ( 19) metal coordination : angle 4.17695 ( 20) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 154 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1110 TYR cc_start: 0.8399 (t80) cc_final: 0.7939 (t80) REVERT: A 1116 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7534 (tp40) REVERT: F 130 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8247 (mp0) REVERT: H 48 GLU cc_start: 0.8295 (pm20) cc_final: 0.7741 (mp0) REVERT: I 101 PHE cc_start: 0.4780 (m-80) cc_final: 0.4263 (m-10) REVERT: E 46 MET cc_start: 0.5597 (ppp) cc_final: 0.5383 (tmm) REVERT: E 118 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.7253 (mp10) REVERT: E 189 GLN cc_start: 0.5965 (tm-30) cc_final: 0.4670 (tm-30) REVERT: B 64 SER cc_start: 0.8889 (t) cc_final: 0.8536 (p) REVERT: B 120 MET cc_start: 0.8817 (mmm) cc_final: 0.8375 (mtt) REVERT: B 269 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8178 (pp) REVERT: B 279 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.8700 (m-10) outliers start: 51 outliers final: 36 residues processed: 196 average time/residue: 0.1512 time to fit residues: 48.6230 Evaluate side-chains 187 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 661 ASN Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1116 GLN Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 69 TYR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 118 GLN Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 203 TYR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 985 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 269 optimal weight: 2.9990 chunk 257 optimal weight: 3.9990 chunk 274 optimal weight: 9.9990 chunk 170 optimal weight: 10.0000 chunk 177 optimal weight: 0.5980 chunk 148 optimal weight: 0.7980 chunk 167 optimal weight: 9.9990 chunk 160 optimal weight: 3.9990 chunk 231 optimal weight: 6.9990 chunk 52 optimal weight: 0.0970 chunk 102 optimal weight: 0.0970 overall best weight: 0.9178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.094363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.060677 restraints weight = 66472.332| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.96 r_work: 0.2916 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23665 Z= 0.102 Angle : 0.517 10.382 32024 Z= 0.266 Chirality : 0.041 0.178 3601 Planarity : 0.003 0.051 4013 Dihedral : 11.453 179.602 3432 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.99 % Allowed : 17.96 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.16), residues: 2796 helix: 1.46 (0.18), residues: 892 sheet: -0.16 (0.23), residues: 508 loop : -1.18 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1067 TYR 0.013 0.001 TYR K 87 PHE 0.024 0.001 PHE C 101 TRP 0.019 0.001 TRP A 949 HIS 0.004 0.001 HIS H 42 Details of bonding type rmsd covalent geometry : bond 0.00229 (23646) covalent geometry : angle 0.50843 (32004) hydrogen bonds : bond 0.03491 ( 872) hydrogen bonds : angle 4.01293 ( 2431) metal coordination : bond 0.00561 ( 19) metal coordination : angle 3.81683 ( 20) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 147 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 589 MET cc_start: 0.9006 (ttp) cc_final: 0.8771 (ttp) REVERT: A 1000 SER cc_start: 0.8308 (m) cc_final: 0.8055 (p) REVERT: A 1110 TYR cc_start: 0.8383 (t80) cc_final: 0.7918 (t80) REVERT: A 1116 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7468 (tp40) REVERT: F 96 ASP cc_start: 0.8278 (t70) cc_final: 0.7710 (t70) REVERT: F 130 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8219 (mp0) REVERT: H 48 GLU cc_start: 0.8232 (pm20) cc_final: 0.7754 (mp0) REVERT: I 101 PHE cc_start: 0.4781 (m-80) cc_final: 0.4272 (m-10) REVERT: E 189 GLN cc_start: 0.5754 (OUTLIER) cc_final: 0.4482 (tm-30) REVERT: B 64 SER cc_start: 0.8898 (t) cc_final: 0.8528 (p) REVERT: B 120 MET cc_start: 0.8748 (mmm) cc_final: 0.8382 (mtt) REVERT: B 269 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8164 (pp) REVERT: B 279 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.8733 (m-10) outliers start: 50 outliers final: 35 residues processed: 187 average time/residue: 0.1365 time to fit residues: 43.0737 Evaluate side-chains 184 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1116 GLN Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 69 TYR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 203 TYR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 985 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 222 optimal weight: 3.9990 chunk 272 optimal weight: 0.6980 chunk 43 optimal weight: 0.0980 chunk 204 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 chunk 107 optimal weight: 0.0470 chunk 33 optimal weight: 8.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.094477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.060672 restraints weight = 67396.911| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.01 r_work: 0.2923 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23665 Z= 0.096 Angle : 0.516 10.411 32024 Z= 0.264 Chirality : 0.040 0.163 3601 Planarity : 0.003 0.051 4013 Dihedral : 11.412 179.401 3432 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.83 % Allowed : 18.28 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.16), residues: 2796 helix: 1.49 (0.18), residues: 899 sheet: -0.13 (0.23), residues: 508 loop : -1.16 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1067 TYR 0.016 0.001 TYR E 202 PHE 0.028 0.001 PHE I 87 TRP 0.021 0.001 TRP A 949 HIS 0.005 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00215 (23646) covalent geometry : angle 0.50849 (32004) hydrogen bonds : bond 0.03306 ( 872) hydrogen bonds : angle 3.93521 ( 2431) metal coordination : bond 0.00632 ( 19) metal coordination : angle 3.62403 ( 20) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 150 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1000 SER cc_start: 0.8245 (m) cc_final: 0.8008 (p) REVERT: A 1110 TYR cc_start: 0.8374 (t80) cc_final: 0.7930 (t80) REVERT: A 1116 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7422 (tp40) REVERT: F 96 ASP cc_start: 0.8270 (t70) cc_final: 0.7687 (t70) REVERT: H 48 GLU cc_start: 0.8197 (pm20) cc_final: 0.7697 (mp0) REVERT: I 101 PHE cc_start: 0.4857 (m-80) cc_final: 0.4325 (m-10) REVERT: E 46 MET cc_start: 0.6823 (tmm) cc_final: 0.6608 (tmm) REVERT: E 189 GLN cc_start: 0.5738 (OUTLIER) cc_final: 0.4491 (tm-30) REVERT: B 64 SER cc_start: 0.8883 (t) cc_final: 0.8517 (p) REVERT: B 120 MET cc_start: 0.8720 (mmm) cc_final: 0.8366 (mtt) REVERT: B 269 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8135 (pp) REVERT: B 279 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8724 (m-10) outliers start: 46 outliers final: 35 residues processed: 185 average time/residue: 0.1435 time to fit residues: 44.3002 Evaluate side-chains 185 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1116 GLN Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 69 TYR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 203 TYR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 985 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 47 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 171 optimal weight: 0.5980 chunk 133 optimal weight: 0.1980 chunk 187 optimal weight: 4.9990 chunk 26 optimal weight: 0.3980 chunk 249 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 274 optimal weight: 10.0000 chunk 256 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.094136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.060568 restraints weight = 66597.579| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.97 r_work: 0.2919 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 23665 Z= 0.099 Angle : 0.520 10.787 32024 Z= 0.267 Chirality : 0.041 0.178 3601 Planarity : 0.003 0.051 4013 Dihedral : 11.397 179.334 3432 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.63 % Allowed : 18.52 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.16), residues: 2796 helix: 1.54 (0.18), residues: 898 sheet: -0.10 (0.24), residues: 508 loop : -1.13 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1067 TYR 0.015 0.001 TYR E 202 PHE 0.025 0.001 PHE C 101 TRP 0.021 0.001 TRP A 949 HIS 0.004 0.001 HIS H 42 Details of bonding type rmsd covalent geometry : bond 0.00224 (23646) covalent geometry : angle 0.51199 (32004) hydrogen bonds : bond 0.03361 ( 872) hydrogen bonds : angle 3.89697 ( 2431) metal coordination : bond 0.00607 ( 19) metal coordination : angle 3.71391 ( 20) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 152 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1000 SER cc_start: 0.8227 (m) cc_final: 0.8002 (p) REVERT: A 1110 TYR cc_start: 0.8433 (t80) cc_final: 0.8010 (t80) REVERT: A 1116 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7451 (tp40) REVERT: K 14 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7260 (mt-10) REVERT: L 25 ASP cc_start: 0.5407 (p0) cc_final: 0.3845 (t0) REVERT: H 48 GLU cc_start: 0.8223 (pm20) cc_final: 0.7654 (mp0) REVERT: I 101 PHE cc_start: 0.4930 (m-80) cc_final: 0.4370 (m-10) REVERT: E 189 GLN cc_start: 0.5881 (OUTLIER) cc_final: 0.4673 (tm-30) REVERT: B 64 SER cc_start: 0.8890 (t) cc_final: 0.8526 (p) REVERT: B 120 MET cc_start: 0.8740 (mmm) cc_final: 0.8383 (mtt) REVERT: B 269 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8172 (pp) REVERT: B 279 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8718 (m-10) outliers start: 41 outliers final: 34 residues processed: 182 average time/residue: 0.1410 time to fit residues: 43.6738 Evaluate side-chains 186 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1116 GLN Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 69 TYR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 203 TYR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 985 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 226 optimal weight: 3.9990 chunk 253 optimal weight: 0.0370 chunk 47 optimal weight: 7.9990 chunk 173 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 155 optimal weight: 0.4980 chunk 270 optimal weight: 0.0980 chunk 9 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.093117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.059502 restraints weight = 66900.960| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.97 r_work: 0.2892 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23665 Z= 0.117 Angle : 0.534 10.983 32024 Z= 0.275 Chirality : 0.041 0.247 3601 Planarity : 0.003 0.051 4013 Dihedral : 11.429 179.503 3432 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.59 % Allowed : 18.80 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.16), residues: 2796 helix: 1.44 (0.18), residues: 904 sheet: -0.08 (0.24), residues: 506 loop : -1.16 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1067 TYR 0.014 0.001 TYR E 202 PHE 0.027 0.001 PHE C 101 TRP 0.021 0.001 TRP A 949 HIS 0.005 0.001 HIS A 938 Details of bonding type rmsd covalent geometry : bond 0.00273 (23646) covalent geometry : angle 0.52460 (32004) hydrogen bonds : bond 0.03801 ( 872) hydrogen bonds : angle 3.94941 ( 2431) metal coordination : bond 0.00583 ( 19) metal coordination : angle 4.09546 ( 20) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5580.22 seconds wall clock time: 96 minutes 21.91 seconds (5781.91 seconds total)