Starting phenix.real_space_refine on Sat Jul 4 21:48:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k15_61965/07_2026/9k15_61965.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k15_61965/07_2026/9k15_61965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k15_61965/07_2026/9k15_61965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k15_61965/07_2026/9k15_61965.map" model { file = "/net/cci-nas-00/data/ceres_data/9k15_61965/07_2026/9k15_61965.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k15_61965/07_2026/9k15_61965.cif" } resolution = 3.32 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 32 5.49 5 Mg 1 5.21 5 S 141 5.16 5 C 14470 2.51 5 N 4038 2.21 5 O 4410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23098 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 6530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6530 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 27, 'TRANS': 806} Chain breaks: 5 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: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 616 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 4, 'TRANS': 70} 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: 7645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 7645 Classifications: {'peptide': 965} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 36, 'TRANS': 928} 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: "T" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 225 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} 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: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 85 Classifications: {'RNA': 4} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna3p': 3} 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 5087 SG CYS A 989 20.440 73.220 30.809 1.00128.10 S ATOM 5194 SG CYS A1004 23.582 75.526 30.768 1.00126.98 S ATOM 7235 SG CYS C 90 79.271 43.764 139.858 1.00111.62 S ATOM 7254 SG CYS C 93 81.189 41.734 137.128 1.00121.45 S ATOM 7293 SG CYS C 99 79.184 39.969 139.691 1.00 91.69 S ATOM 7319 SG CYS C 102 77.646 42.366 136.791 1.00106.49 S ATOM 9457 SG CYS J 7 50.495 44.093 119.357 1.00 27.45 S ATOM 9481 SG CYS J 10 49.528 45.161 122.886 1.00 31.30 S ATOM 9747 SG CYS J 44 47.352 46.229 119.905 1.00 33.18 S ATOM 9753 SG CYS J 45 47.403 42.718 121.321 1.00 34.65 S ATOM 10845 SG CYS L 12 79.519 16.419 95.651 1.00 81.27 S ATOM 10863 SG CYS L 15 79.227 12.945 97.231 1.00 74.91 S ATOM 10965 SG CYS L 29 82.240 13.884 95.203 1.00 68.67 S ATOM 10991 SG CYS L 32 78.679 13.099 93.726 1.00 83.44 S ATOM 12334 SG CYS I 7 30.251 45.037 18.661 1.00 45.01 S ATOM 12519 SG CYS I 29 34.528 46.722 18.732 1.00 39.73 S ATOM 12544 SG CYS I 32 32.587 44.657 16.656 1.00 55.04 S Time building chain proxies: 4.97, per 1000 atoms: 0.22 Number of scatterers: 23098 At special positions: 0 Unit cell: (116.07, 139.065, 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 32 15.00 Mg 1 11.99 O 4410 8.00 N 4038 7.00 C 14470 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A 940 " pdb="ZN ZN A3001 " - pdb=" ND1 HIS A 938 " 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 90 " pdb="ZN ZN C 400 " - pdb=" SG CYS C 102 " pdb="ZN ZN C 400 " - pdb=" SG CYS C 99 " 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 10 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 15 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 32 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 29 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 12 " Number of angles added : 19 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5320 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 32 sheets defined 35.4% alpha, 16.8% beta 10 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 3.00 Creating SS restraints... Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 359 through 369 removed outlier: 3.559A pdb=" N ASN A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) 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 475 through 479 removed outlier: 3.596A pdb=" N LEU A 479 " --> pdb=" O ASP A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 505 removed outlier: 3.508A pdb=" N LEU A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN A 505 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 517 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: 4.246A 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 Processing helix chain 'A' and resid 620 through 624 Processing helix chain 'A' and resid 627 through 647 removed outlier: 4.760A pdb=" N SER A 643 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Proline residue: A 644 - end of helix Processing helix chain 'A' and resid 648 through 652 removed outlier: 3.949A pdb=" N LEU A 651 " --> pdb=" O ARG A 648 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER A 652 " --> pdb=" O LEU A 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 648 through 652' Processing helix chain 'A' and resid 657 through 675 removed outlier: 3.535A pdb=" N ASN A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 684 removed outlier: 3.523A pdb=" N ILE A 684 " --> pdb=" O MET A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 700 removed outlier: 3.667A pdb=" N LYS A 694 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU A 695 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 3.956A 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: 3.814A pdb=" N ALA A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 784 Processing helix chain 'A' and resid 827 through 847 removed outlier: 3.729A 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 861 removed outlier: 3.510A 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 949 removed outlier: 3.672A pdb=" N LEU A 946 " --> pdb=" O ASN A 942 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 970 removed outlier: 3.611A pdb=" N LYS A 970 " --> pdb=" O SER A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 979 removed outlier: 3.938A pdb=" N PHE A 978 " --> pdb=" O ALA A 975 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 979 " --> pdb=" O GLU A 976 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 975 through 979' Processing helix chain 'A' and resid 1016 through 1027 Processing helix chain 'A' and resid 1027 through 1034 removed outlier: 4.055A pdb=" N VAL A1031 " --> pdb=" O THR A1027 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A1032 " --> pdb=" O ILE A1028 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A1033 " --> pdb=" O TYR A1029 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU A1034 " --> pdb=" O PRO A1030 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1027 through 1034' Processing helix chain 'A' and resid 1085 through 1095 removed outlier: 3.560A pdb=" N ARG A1089 " --> pdb=" O GLY A1085 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS A1095 " --> pdb=" O VAL A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1102 removed outlier: 3.710A pdb=" N LEU A1099 " --> pdb=" O LEU A1096 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N HIS A1100 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1120 Processing helix chain 'A' and resid 1120 through 1138 Processing helix chain 'A' and resid 1144 through 1156 removed outlier: 4.057A pdb=" N ILE A1148 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR A1156 " --> pdb=" O ALA A1152 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 44 removed outlier: 3.591A pdb=" N ALA C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 73 removed outlier: 3.694A 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 removed outlier: 3.636A pdb=" N TRP C 179 " --> pdb=" O HIS C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 214 Processing helix chain 'C' and resid 241 through 250 Processing helix chain 'C' and resid 276 through 294 removed outlier: 3.565A pdb=" N ALA C 294 " --> pdb=" O GLN C 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 83 removed outlier: 3.598A pdb=" N ARG F 72 " --> pdb=" O TYR F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 108 removed outlier: 3.672A pdb=" N ILE F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 131 No H-bonds generated for 'chain 'F' and resid 129 through 131' Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 39 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.842A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR J 51 " --> pdb=" O ARG J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 62 removed outlier: 3.616A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR J 62 " --> pdb=" O LYS J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.851A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'E' and resid 30 through 51 removed outlier: 3.805A pdb=" N HIS E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 71 Processing helix chain 'E' and resid 104 through 116 removed outlier: 3.856A pdb=" N ILE E 108 " --> pdb=" O LYS E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 136 through 141 Processing helix chain 'E' and resid 153 through 156 removed outlier: 3.905A pdb=" N LEU E 156 " --> pdb=" O THR E 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 153 through 156' Processing helix chain 'E' and resid 158 through 162 Processing helix chain 'E' and resid 172 through 183 removed outlier: 4.179A pdb=" N GLN E 182 " --> pdb=" O ALA E 178 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE E 183 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 203 Processing helix chain 'B' and resid 17 through 20 Processing helix chain 'B' and resid 21 through 40 Processing helix chain 'B' and resid 43 through 65 removed outlier: 3.713A pdb=" N LEU B 47 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LEU B 58 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N GLN B 59 " --> pdb=" O GLU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 119 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: 3.562A pdb=" N THR B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 337 removed outlier: 3.690A pdb=" N GLY B 337 " --> pdb=" O GLN B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 354 removed outlier: 3.635A pdb=" N LEU B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 380 removed outlier: 3.526A pdb=" N ALA B 380 " --> pdb=" O PHE B 376 " (cutoff:3.500A) 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: 3.872A pdb=" N VAL B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N HIS B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 439 removed outlier: 3.897A pdb=" N TYR B 438 " --> pdb=" O PRO B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 455 removed outlier: 3.948A pdb=" N THR B 445 " --> pdb=" O ALA B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 485 removed outlier: 3.556A pdb=" N SER B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 552 removed outlier: 3.760A pdb=" N ASP B 550 " --> pdb=" O GLU B 547 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY B 552 " --> pdb=" O PHE B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 595 removed outlier: 3.555A pdb=" N ALA B 588 " --> pdb=" O ASP B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 637 removed outlier: 3.903A pdb=" N LEU B 636 " --> pdb=" O LEU B 633 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS B 637 " --> pdb=" O HIS B 634 " (cutoff:3.500A) 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 679 removed outlier: 3.950A pdb=" N GLN B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 693 removed outlier: 3.670A pdb=" N LEU B 693 " --> pdb=" O SER B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 706 removed outlier: 3.872A 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 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: 3.642A pdb=" N ARG B 950 " --> pdb=" O ALA B 946 " (cutoff:3.500A) removed outlier: 3.804A 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 953 through 966 Processing helix chain 'B' and resid 993 through 1005 Processing helix chain 'B' and resid 1040 through 1044 Processing sheet with id=AA1, first strand: chain 'A' and resid 323 through 330 removed outlier: 3.849A pdb=" N GLN A 424 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS A 456 " --> pdb=" O ASN A 413 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 326 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 324 " --> pdb=" O LEU A 457 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 350 through 354 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 560 through 562 removed outlier: 3.566A pdb=" N ILE A 561 " --> pdb=" O SER A 569 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 703 through 704 Processing sheet with id=AA6, first strand: chain 'A' and resid 789 through 791 removed outlier: 6.674A pdb=" N VAL A 797 " --> pdb=" O VAL A 806 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1043 through 1049 removed outlier: 6.917A pdb=" N THR A1075 " --> pdb=" O ALA A1044 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA A1046 " --> pdb=" O ASP A1073 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ASP A1073 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE A1048 " --> pdb=" O VAL A1071 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL A1071 " --> pdb=" O ILE A1048 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 906 through 907 removed outlier: 3.983A pdb=" N LYS A1038 " --> pdb=" O VAL A 906 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1004 through 1007 removed outlier: 3.547A pdb=" N ILE A 939 " --> pdb=" O LEU A1005 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A1007 " --> pdb=" O GLY A 937 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS A 936 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS A 940 " --> pdb=" O GLU A 914 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU A 914 " --> pdb=" O HIS A 940 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR I 44 " --> pdb=" O VAL A 917 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 11 through 18 removed outlier: 5.853A pdb=" N VAL C 12 " --> pdb=" O ARG C 27 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ARG C 27 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE C 14 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLU C 25 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE C 24 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU C 190 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N ASP C 263 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 11.290A pdb=" N MET C 188 " --> pdb=" O ASP C 263 " (cutoff:3.500A) removed outlier: 9.663A pdb=" N PHE C 265 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 11.251A pdb=" N THR C 186 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 10.101A pdb=" N PHE C 267 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 11.192A pdb=" N THR C 184 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 10.203A pdb=" N VAL C 269 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 9.437A pdb=" N ALA C 182 " --> pdb=" O VAL C 269 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 126 through 127 removed outlier: 3.555A pdb=" N LEU C 108 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLU C 161 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL C 57 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LYS C 163 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ILE C 55 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG C 165 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL C 53 " --> pdb=" O ARG C 165 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE C 167 " --> pdb=" O ASP C 51 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL L 46 " --> pdb=" O ILE C 55 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 118 through 121 removed outlier: 3.857A pdb=" N VAL C 154 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 220 through 223 Processing sheet with id=AB5, first strand: chain 'F' and resid 113 through 115 Processing sheet with id=AB6, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.614A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N HIS K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 18 through 19 removed outlier: 5.349A pdb=" N VAL B 882 " --> pdb=" O LYS L 39 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N GLY B 877 " --> pdb=" O VAL B 901 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N VAL B 901 " --> pdb=" O GLY B 877 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL B 879 " --> pdb=" O ARG B 899 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ARG B 899 " --> pdb=" O VAL B 879 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS B 881 " --> pdb=" O SER B 897 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 18 through 19 removed outlier: 5.349A pdb=" N VAL B 882 " --> pdb=" O LYS L 39 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY B 877 " --> pdb=" O MET B 850 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 138 through 140 removed outlier: 5.885A pdb=" N LEU H 97 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N SER H 115 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LEU H 120 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS H 42 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ARG H 29 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU H 17 " --> pdb=" O ARG H 29 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N GLU H 31 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP H 10 " --> pdb=" O LEU H 60 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU H 60 " --> pdb=" O ASP H 10 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR H 59 " --> pdb=" O ARG H 144 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 14 through 16 removed outlier: 3.550A pdb=" N GLU I 36 " --> pdb=" O TYR I 27 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 86 through 89 Processing sheet with id=AC3, first strand: chain 'E' and resid 95 through 97 removed outlier: 6.917A pdb=" N VAL E 96 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU E 126 " --> pdb=" O PHE E 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 192 through 193 removed outlier: 3.528A pdb=" N ILE E 193 " --> pdb=" O CYS E 228 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR E 223 " --> pdb=" O TYR E 215 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 68 through 69 removed outlier: 3.730A pdb=" N MET B 68 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N PHE B 91 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP B 131 " --> pdb=" O PHE B 91 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU B 93 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY B 168 " --> pdb=" O MET B 126 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL B 128 " --> pdb=" O PRO B 166 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL B 130 " --> pdb=" O ASP B 164 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ASP B 164 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AC7, first strand: chain 'B' and resid 204 through 206 Processing sheet with id=AC8, first strand: chain 'B' and resid 394 through 397 removed outlier: 6.304A pdb=" N ALA B 215 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 225 through 226 Processing sheet with id=AD1, first strand: chain 'B' and resid 535 through 536 Processing sheet with id=AD2, first strand: chain 'B' and resid 554 through 555 removed outlier: 5.738A pdb=" N TRP B 576 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU B 572 " --> pdb=" O TRP B 576 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY B 578 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 668 through 669 Processing sheet with id=AD4, first strand: chain 'B' and resid 1011 through 1012 removed outlier: 7.776A pdb=" N MET B 786 " --> pdb=" O GLY B 921 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE B 923 " --> pdb=" O MET B 786 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N PHE B1028 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 855 through 857 removed outlier: 4.010A pdb=" N ILE B 857 " --> pdb=" O VAL B 869 " (cutoff:3.500A) 810 hydrogen bonds defined for protein. 2262 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 5.13 Time building geometry restraints manager: 2.67 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: 7460 1.34 - 1.46: 3937 1.46 - 1.58: 11893 1.58 - 1.70: 59 1.70 - 1.82: 217 Bond restraints: 23566 Sorted by residual: bond pdb=" C1' DT N 11 " pdb=" N1 DT N 11 " ideal model delta sigma weight residual 1.468 1.516 -0.048 1.40e-02 5.10e+03 1.18e+01 bond pdb=" C1' DC N 14 " pdb=" N1 DC N 14 " ideal model delta sigma weight residual 1.468 1.515 -0.047 1.40e-02 5.10e+03 1.13e+01 bond pdb=" C3' DA T 19 " pdb=" C2' DA T 19 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.84e+00 bond pdb=" C3' DT N 11 " pdb=" C2' DT N 11 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.96e+00 bond pdb=" C3' DG T 23 " pdb=" C2' DG T 23 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.40e+00 ... (remaining 23561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 31058 1.61 - 3.22: 728 3.22 - 4.83: 91 4.83 - 6.45: 20 6.45 - 8.06: 5 Bond angle restraints: 31902 Sorted by residual: angle pdb=" O4' DT N 11 " pdb=" C1' DT N 11 " pdb=" N1 DT N 11 " ideal model delta sigma weight residual 108.00 111.29 -3.29 7.00e-01 2.04e+00 2.20e+01 angle pdb=" N VAL A 806 " pdb=" CA VAL A 806 " pdb=" C VAL A 806 " ideal model delta sigma weight residual 112.96 108.61 4.35 1.00e+00 1.00e+00 1.90e+01 angle pdb=" N3 DT T 21 " pdb=" C4 DT T 21 " pdb=" O4 DT T 21 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 angle pdb=" O4' DC N 14 " pdb=" C4' DC N 14 " pdb=" C3' DC N 14 " ideal model delta sigma weight residual 106.00 103.47 2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT N 28 " pdb=" C4 DT N 28 " pdb=" O4 DT N 28 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 ... (remaining 31897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.20: 13691 35.20 - 70.40: 550 70.40 - 105.59: 43 105.59 - 140.79: 1 140.79 - 175.99: 1 Dihedral angle restraints: 14286 sinusoidal: 6078 harmonic: 8208 Sorted by residual: dihedral pdb=" CA GLU A 591 " pdb=" C GLU A 591 " pdb=" N LYS A 592 " pdb=" CA LYS A 592 " ideal model delta harmonic sigma weight residual 180.00 155.24 24.76 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA ARG H 103 " pdb=" C ARG H 103 " pdb=" N ASP H 104 " pdb=" CA ASP H 104 " ideal model delta harmonic sigma weight residual 180.00 -157.94 -22.06 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA VAL A 590 " pdb=" C VAL A 590 " pdb=" N GLU A 591 " pdb=" CA GLU A 591 " ideal model delta harmonic sigma weight residual 180.00 158.85 21.15 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 14283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2089 0.031 - 0.062: 984 0.062 - 0.092: 322 0.092 - 0.123: 179 0.123 - 0.154: 16 Chirality restraints: 3590 Sorted by residual: chirality pdb=" CA ASP C 20 " pdb=" N ASP C 20 " pdb=" C ASP C 20 " pdb=" CB ASP C 20 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CB ILE A1059 " pdb=" CA ILE A1059 " pdb=" CG1 ILE A1059 " pdb=" CG2 ILE A1059 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA THR H 71 " pdb=" N THR H 71 " pdb=" C THR H 71 " pdb=" CB THR H 71 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 3587 not shown) Planarity restraints: 3993 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 673 " -0.019 2.00e-02 2.50e+03 1.53e-02 4.09e+00 pdb=" CG PHE A 673 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A 673 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 673 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 673 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 673 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 673 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 433 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO B 434 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 434 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 434 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 522 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.78e+00 pdb=" CD GLU B 522 " -0.034 2.00e-02 2.50e+03 pdb=" OE1 GLU B 522 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU B 522 " 0.012 2.00e-02 2.50e+03 ... (remaining 3990 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.86: 3 1.86 - 2.62: 54 2.62 - 3.38: 28797 3.38 - 4.14: 50330 4.14 - 4.90: 92637 Nonbonded interactions: 171821 Sorted by model distance: nonbonded pdb=" OE2 GLU A 947 " pdb=" NE ARG I 92 " model vdw 1.100 3.120 nonbonded pdb=" OE2 GLU A 947 " pdb=" CD ARG I 92 " model vdw 1.554 3.440 nonbonded pdb=" CD GLU A 947 " pdb=" NE ARG I 92 " model vdw 1.580 3.350 nonbonded pdb=" CG GLU A 947 " pdb=" CD ARG I 92 " model vdw 1.861 3.840 nonbonded pdb=" CD GLU A 947 " pdb=" CD ARG I 92 " model vdw 1.877 3.670 ... (remaining 171816 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: 2.210 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 27.100 Find NCS groups from input model: 0.120 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 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 : 0.004 0.101 23586 Z= 0.223 Angle : 0.623 11.338 31921 Z= 0.362 Chirality : 0.043 0.154 3590 Planarity : 0.004 0.050 3993 Dihedral : 17.939 175.988 8966 Min Nonbonded Distance : 1.100 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.36 % Allowed : 19.70 % Favored : 77.94 % 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: -0.78 (0.16), residues: 2778 helix: 0.97 (0.19), residues: 824 sheet: -0.48 (0.24), residues: 492 loop : -1.43 (0.15), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 72 TYR 0.012 0.002 TYR J 29 PHE 0.033 0.002 PHE A 673 TRP 0.015 0.002 TRP A1058 HIS 0.007 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.21 (23566) covalent geometry : angle 0.61008 / 0.36 (31902) hydrogen bonds : bond 0.19586 / 13.46 ( 828) hydrogen bonds : angle 6.32786 / 4.40 ( 2312) metal coordination : bond 0.00556 / 0.29 ( 19) metal coordination : angle 5.14439 / 3.05 ( 19) Misc. bond : bond 0.10071 / 6.29 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 192 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 351 PHE cc_start: 0.7031 (OUTLIER) cc_final: 0.6058 (m-10) REVERT: A 419 HIS cc_start: 0.2093 (OUTLIER) cc_final: 0.1490 (m90) REVERT: A 442 MET cc_start: 0.8666 (mmm) cc_final: 0.8466 (mmt) REVERT: A 1227 PHE cc_start: 0.7752 (p90) cc_final: 0.7533 (p90) REVERT: F 66 THR cc_start: 0.8343 (m) cc_final: 0.8118 (m) REVERT: K 93 ASP cc_start: 0.8052 (t0) cc_final: 0.7489 (m-30) REVERT: I 97 MET cc_start: -0.0567 (ptm) cc_final: -0.0790 (mtm) REVERT: E 129 GLN cc_start: 0.6323 (tp-100) cc_final: 0.6003 (tp-100) REVERT: B 323 HIS cc_start: 0.7446 (m-70) cc_final: 0.6535 (m-70) REVERT: B 423 GLN cc_start: 0.7649 (tt0) cc_final: 0.7165 (tm-30) REVERT: B 670 TRP cc_start: 0.7941 (OUTLIER) cc_final: 0.7385 (m-10) outliers start: 59 outliers final: 50 residues processed: 242 average time/residue: 0.1656 time to fit residues: 63.9275 Evaluate side-chains 216 residues out of total 2501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 163 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 850 ASN Chi-restraints excluded: chain A residue 871 THR Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain A residue 1058 TRP Chi-restraints excluded: chain A residue 1070 TRP Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1158 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 1014 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 GLN ** B 163 GLN ** 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 = 0.4025 r_free = 0.4025 target = 0.131199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.095281 restraints weight = 47025.092| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.11 r_work: 0.3130 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.0612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23586 Z= 0.134 Angle : 0.559 9.988 31921 Z= 0.301 Chirality : 0.042 0.189 3590 Planarity : 0.004 0.064 3993 Dihedral : 12.167 171.565 3504 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.08 % Allowed : 19.02 % Favored : 77.90 % 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: -0.66 (0.16), residues: 2778 helix: 1.02 (0.18), residues: 838 sheet: -0.37 (0.24), residues: 512 loop : -1.38 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1067 TYR 0.015 0.001 TYR A 897 PHE 0.036 0.001 PHE A 673 TRP 0.016 0.001 TRP A1058 HIS 0.006 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (23566) covalent geometry : angle 0.54924 / 0.30 (31902) hydrogen bonds : bond 0.05421 / 3.73 ( 828) hydrogen bonds : angle 5.02074 / 3.45 ( 2312) metal coordination : bond 0.00455 / 0.26 ( 19) metal coordination : angle 4.31389 / 2.58 ( 19) Misc. bond : bond 0.01285 / 0.80 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 177 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 419 HIS cc_start: 0.2271 (OUTLIER) cc_final: 0.1553 (m90) REVERT: A 442 MET cc_start: 0.8154 (mmm) cc_final: 0.7905 (mmt) REVERT: A 558 ASP cc_start: 0.6353 (OUTLIER) cc_final: 0.5818 (p0) REVERT: A 702 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8193 (mp) REVERT: F 72 ARG cc_start: 0.7113 (mtm110) cc_final: 0.6669 (mtm180) REVERT: K 93 ASP cc_start: 0.8245 (t0) cc_final: 0.7580 (m-30) REVERT: H 122 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7361 (tp) REVERT: I 22 GLN cc_start: 0.6610 (pt0) cc_final: 0.6244 (pt0) REVERT: E 129 GLN cc_start: 0.6820 (tp-100) cc_final: 0.6101 (tp-100) REVERT: B 323 HIS cc_start: 0.7166 (m-70) cc_final: 0.6324 (m-70) REVERT: B 423 GLN cc_start: 0.7616 (tt0) cc_final: 0.7134 (tm-30) REVERT: B 670 TRP cc_start: 0.7868 (OUTLIER) cc_final: 0.7089 (m-10) outliers start: 77 outliers final: 47 residues processed: 247 average time/residue: 0.1509 time to fit residues: 61.2291 Evaluate side-chains 214 residues out of total 2501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 162 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 850 ASN Chi-restraints excluded: chain A residue 871 THR Chi-restraints excluded: chain A residue 981 MET Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain A residue 1058 TRP Chi-restraints excluded: chain A residue 1070 TRP Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1157 CYS Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 1014 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 83 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 178 optimal weight: 0.0040 chunk 94 optimal weight: 2.9990 chunk 176 optimal weight: 7.9990 chunk 239 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 GLN B 163 GLN ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.129542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.093982 restraints weight = 47134.344| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.04 r_work: 0.3099 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 23586 Z= 0.192 Angle : 0.600 9.903 31921 Z= 0.320 Chirality : 0.044 0.183 3590 Planarity : 0.005 0.060 3993 Dihedral : 12.002 170.593 3466 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.52 % Allowed : 18.65 % Favored : 76.82 % 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: -0.87 (0.16), residues: 2778 helix: 0.82 (0.18), residues: 854 sheet: -0.46 (0.24), residues: 505 loop : -1.52 (0.15), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1042 TYR 0.019 0.002 TYR L 38 PHE 0.031 0.002 PHE A 673 TRP 0.015 0.002 TRP A1058 HIS 0.008 0.001 HIS A 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (23566) covalent geometry : angle 0.58898 / 0.32 (31902) hydrogen bonds : bond 0.05801 / 4.00 ( 828) hydrogen bonds : angle 4.74152 / 3.27 ( 2312) metal coordination : bond 0.00560 / 0.31 ( 19) metal coordination : angle 4.81608 / 2.89 ( 19) Misc. bond : bond 0.00299 / 0.19 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 166 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: A 351 PHE cc_start: 0.6957 (OUTLIER) cc_final: 0.5639 (m-10) REVERT: A 419 HIS cc_start: 0.2604 (OUTLIER) cc_final: 0.1791 (m90) REVERT: A 442 MET cc_start: 0.8219 (mmm) cc_final: 0.7964 (mmt) REVERT: A 702 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8039 (mt) REVERT: K 93 ASP cc_start: 0.8264 (t0) cc_final: 0.7635 (m-30) REVERT: H 52 MET cc_start: 0.4565 (OUTLIER) cc_final: 0.4224 (tpt) REVERT: H 122 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7326 (tp) REVERT: I 25 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.6331 (tt) REVERT: E 129 GLN cc_start: 0.6824 (tp-100) cc_final: 0.6086 (tp-100) REVERT: E 209 GLN cc_start: 0.7077 (tt0) cc_final: 0.6811 (tt0) REVERT: B 323 HIS cc_start: 0.7135 (m-70) cc_final: 0.6406 (m-70) REVERT: B 423 GLN cc_start: 0.7642 (tt0) cc_final: 0.7165 (tm-30) REVERT: B 670 TRP cc_start: 0.7951 (OUTLIER) cc_final: 0.7264 (m-10) REVERT: B 1024 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7531 (mtp-110) outliers start: 113 outliers final: 72 residues processed: 266 average time/residue: 0.1501 time to fit residues: 64.8588 Evaluate side-chains 236 residues out of total 2501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 156 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 459 TYR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 850 ASN Chi-restraints excluded: chain A residue 871 THR Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain A residue 1058 TRP Chi-restraints excluded: chain A residue 1070 TRP Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1157 CYS Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 752 MET Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 983 THR Chi-restraints excluded: chain B residue 1024 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 103 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 269 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 145 optimal weight: 0.4980 chunk 219 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 220 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 HIS ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.130498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.094785 restraints weight = 47238.398| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 3.03 r_work: 0.3125 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23586 Z= 0.127 Angle : 0.538 9.730 31921 Z= 0.287 Chirality : 0.042 0.178 3590 Planarity : 0.004 0.060 3993 Dihedral : 11.901 170.394 3462 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.92 % Allowed : 19.34 % Favored : 76.74 % 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: -0.67 (0.16), residues: 2778 helix: 1.05 (0.18), residues: 850 sheet: -0.28 (0.24), residues: 491 loop : -1.45 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 149 TYR 0.013 0.001 TYR J 43 PHE 0.025 0.001 PHE A 673 TRP 0.015 0.001 TRP A1058 HIS 0.005 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (23566) covalent geometry : angle 0.52771 / 0.29 (31902) hydrogen bonds : bond 0.04765 / 3.29 ( 828) hydrogen bonds : angle 4.53639 / 3.13 ( 2312) metal coordination : bond 0.00433 / 0.24 ( 19) metal coordination : angle 4.22820 / 2.51 ( 19) Misc. bond : bond 0.00016 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 167 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 351 PHE cc_start: 0.6943 (OUTLIER) cc_final: 0.5630 (m-10) REVERT: A 419 HIS cc_start: 0.2568 (OUTLIER) cc_final: 0.1733 (m90) REVERT: A 421 HIS cc_start: 0.6491 (t-170) cc_final: 0.6137 (t70) REVERT: A 442 MET cc_start: 0.8126 (mmm) cc_final: 0.7903 (mmt) REVERT: A 446 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7487 (mt) REVERT: A 595 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.6992 (mmtm) REVERT: A 702 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8013 (mt) REVERT: A 900 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.6288 (tpt-90) REVERT: K 93 ASP cc_start: 0.8251 (t0) cc_final: 0.7583 (m-30) REVERT: H 52 MET cc_start: 0.4560 (tpt) cc_final: 0.4254 (tpt) REVERT: I 25 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.6308 (tt) REVERT: E 129 GLN cc_start: 0.6816 (tp-100) cc_final: 0.6082 (tp-100) REVERT: B 323 HIS cc_start: 0.7144 (m-70) cc_final: 0.6330 (m-70) REVERT: B 423 GLN cc_start: 0.7640 (tt0) cc_final: 0.7163 (tm-30) REVERT: B 638 GLN cc_start: 0.8117 (pp30) cc_final: 0.7755 (pt0) REVERT: B 670 TRP cc_start: 0.7868 (OUTLIER) cc_final: 0.7092 (m-10) REVERT: B 752 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8401 (tpp) REVERT: B 1024 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7501 (mtp-110) outliers start: 98 outliers final: 59 residues processed: 250 average time/residue: 0.1390 time to fit residues: 56.8445 Evaluate side-chains 231 residues out of total 2501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 162 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 459 TYR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 850 ASN Chi-restraints excluded: chain A residue 871 THR Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain A residue 1058 TRP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1157 CYS Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 752 MET Chi-restraints excluded: chain B residue 983 THR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1024 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 271 optimal weight: 0.0370 chunk 118 optimal weight: 0.9980 chunk 46 optimal weight: 0.0170 chunk 55 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 201 optimal weight: 4.9990 chunk 230 optimal weight: 6.9990 chunk 218 optimal weight: 7.9990 chunk 209 optimal weight: 3.9990 overall best weight: 1.1898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 HIS I 22 GLN ** I 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 892 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.130755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.094668 restraints weight = 46909.082| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.07 r_work: 0.3132 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23586 Z= 0.123 Angle : 0.528 9.039 31921 Z= 0.281 Chirality : 0.041 0.177 3590 Planarity : 0.004 0.057 3993 Dihedral : 11.801 169.976 3458 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.68 % Allowed : 19.82 % Favored : 76.50 % 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: -0.58 (0.16), residues: 2778 helix: 1.17 (0.18), residues: 849 sheet: -0.22 (0.24), residues: 493 loop : -1.43 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 72 TYR 0.013 0.001 TYR J 43 PHE 0.021 0.001 PHE A 673 TRP 0.014 0.001 TRP A1058 HIS 0.005 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (23566) covalent geometry : angle 0.51866 / 0.28 (31902) hydrogen bonds : bond 0.04488 / 3.10 ( 828) hydrogen bonds : angle 4.41484 / 3.05 ( 2312) metal coordination : bond 0.00419 / 0.23 ( 19) metal coordination : angle 4.07308 / 2.39 ( 19) Misc. bond : bond 0.00028 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 167 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: A 351 PHE cc_start: 0.6937 (OUTLIER) cc_final: 0.5729 (m-10) REVERT: A 419 HIS cc_start: 0.2547 (OUTLIER) cc_final: 0.1695 (m90) REVERT: A 421 HIS cc_start: 0.6620 (t-170) cc_final: 0.6264 (t70) REVERT: A 446 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7536 (mt) REVERT: A 595 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7009 (mmtm) REVERT: A 702 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8106 (mp) REVERT: A 900 ARG cc_start: 0.6789 (OUTLIER) cc_final: 0.6294 (tpt-90) REVERT: K 93 ASP cc_start: 0.8224 (t0) cc_final: 0.7558 (m-30) REVERT: I 25 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.6288 (tt) REVERT: E 124 LEU cc_start: 0.6380 (OUTLIER) cc_final: 0.6166 (tt) REVERT: E 129 GLN cc_start: 0.6824 (tp-100) cc_final: 0.6106 (tp-100) REVERT: B 323 HIS cc_start: 0.7125 (m-70) cc_final: 0.6329 (m-70) REVERT: B 423 GLN cc_start: 0.7626 (tt0) cc_final: 0.7154 (tm-30) REVERT: B 638 GLN cc_start: 0.8088 (pp30) cc_final: 0.7709 (pt0) REVERT: B 670 TRP cc_start: 0.7748 (OUTLIER) cc_final: 0.6907 (m-10) REVERT: B 1024 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7587 (mtp180) outliers start: 92 outliers final: 63 residues processed: 248 average time/residue: 0.1462 time to fit residues: 59.1073 Evaluate side-chains 232 residues out of total 2501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 159 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 459 TYR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 850 ASN Chi-restraints excluded: chain A residue 871 THR Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain A residue 1058 TRP Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1157 CYS Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 41 MET Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1024 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 163 optimal weight: 9.9990 chunk 187 optimal weight: 0.6980 chunk 190 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 268 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 134 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 126 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 698 GLN ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 GLN ** I 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.131217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.095986 restraints weight = 47253.781| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.90 r_work: 0.3150 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23586 Z= 0.108 Angle : 0.514 9.108 31921 Z= 0.273 Chirality : 0.041 0.176 3590 Planarity : 0.004 0.053 3993 Dihedral : 11.728 169.761 3457 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.68 % Allowed : 19.82 % Favored : 76.50 % 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: -0.43 (0.16), residues: 2778 helix: 1.30 (0.18), residues: 850 sheet: -0.17 (0.24), residues: 493 loop : -1.34 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 72 TYR 0.012 0.001 TYR J 43 PHE 0.020 0.001 PHE A 411 TRP 0.014 0.001 TRP A1058 HIS 0.017 0.001 HIS H 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (23566) covalent geometry : angle 0.50608 / 0.27 (31902) hydrogen bonds : bond 0.04108 / 2.84 ( 828) hydrogen bonds : angle 4.31105 / 2.98 ( 2312) metal coordination : bond 0.00367 / 0.21 ( 19) metal coordination : angle 3.82196 / 2.21 ( 19) Misc. bond : bond 0.00030 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 168 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 351 PHE cc_start: 0.6971 (OUTLIER) cc_final: 0.5753 (m-10) REVERT: A 419 HIS cc_start: 0.2792 (OUTLIER) cc_final: 0.1713 (m90) REVERT: A 421 HIS cc_start: 0.6575 (t-170) cc_final: 0.6208 (t70) REVERT: A 446 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7494 (mt) REVERT: A 595 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.6940 (mmtm) REVERT: A 674 MET cc_start: 0.7323 (ppp) cc_final: 0.6415 (tpp) REVERT: A 702 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8128 (mp) REVERT: A 900 ARG cc_start: 0.6819 (OUTLIER) cc_final: 0.6339 (tpt-90) REVERT: K 93 ASP cc_start: 0.8188 (t0) cc_final: 0.7522 (m-30) REVERT: I 25 LEU cc_start: 0.6550 (OUTLIER) cc_final: 0.6211 (tt) REVERT: E 124 LEU cc_start: 0.6370 (OUTLIER) cc_final: 0.6139 (tt) REVERT: E 129 GLN cc_start: 0.6850 (tp-100) cc_final: 0.6126 (tp-100) REVERT: B 323 HIS cc_start: 0.7088 (m-70) cc_final: 0.6324 (m-70) REVERT: B 339 LYS cc_start: 0.7353 (mtmt) cc_final: 0.7012 (mppt) REVERT: B 423 GLN cc_start: 0.7686 (tt0) cc_final: 0.7208 (tm-30) REVERT: B 638 GLN cc_start: 0.8082 (pp30) cc_final: 0.7716 (pt0) REVERT: B 670 TRP cc_start: 0.7695 (OUTLIER) cc_final: 0.6776 (m-10) REVERT: B 752 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8482 (tpp) outliers start: 92 outliers final: 69 residues processed: 248 average time/residue: 0.1434 time to fit residues: 58.0782 Evaluate side-chains 240 residues out of total 2501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 161 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 459 TYR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 850 ASN Chi-restraints excluded: chain A residue 871 THR Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain A residue 1058 TRP Chi-restraints excluded: chain A residue 1070 TRP Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1157 CYS Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 41 MET Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 752 MET Chi-restraints excluded: chain B residue 786 MET Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 1014 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 275 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 270 optimal weight: 0.0370 chunk 9 optimal weight: 0.1980 chunk 8 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 271 optimal weight: 1.9990 chunk 278 optimal weight: 30.0000 chunk 165 optimal weight: 0.5980 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 698 GLN ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 ASN I 22 GLN ** I 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.131141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.095524 restraints weight = 46988.159| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.75 r_work: 0.3161 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23586 Z= 0.110 Angle : 0.508 8.351 31921 Z= 0.270 Chirality : 0.041 0.200 3590 Planarity : 0.004 0.050 3993 Dihedral : 11.666 169.653 3455 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.68 % Allowed : 20.06 % Favored : 76.26 % 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: -0.40 (0.16), residues: 2778 helix: 1.36 (0.18), residues: 850 sheet: -0.25 (0.24), residues: 505 loop : -1.32 (0.16), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 72 TYR 0.012 0.001 TYR J 43 PHE 0.021 0.001 PHE A 411 TRP 0.013 0.001 TRP A1058 HIS 0.014 0.001 HIS H 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (23566) covalent geometry : angle 0.50057 / 0.27 (31902) hydrogen bonds : bond 0.04044 / 2.80 ( 828) hydrogen bonds : angle 4.23147 / 2.92 ( 2312) metal coordination : bond 0.00390 / 0.22 ( 19) metal coordination : angle 3.69540 / 2.12 ( 19) Misc. bond : bond 0.00033 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 168 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 351 PHE cc_start: 0.6964 (OUTLIER) cc_final: 0.5686 (m-10) REVERT: A 419 HIS cc_start: 0.2802 (OUTLIER) cc_final: 0.1696 (m90) REVERT: A 446 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7479 (mt) REVERT: A 595 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.6954 (mmtm) REVERT: A 674 MET cc_start: 0.7342 (ppp) cc_final: 0.6421 (tpp) REVERT: A 702 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8113 (mp) REVERT: A 900 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.6347 (tpt-90) REVERT: A 1227 PHE cc_start: 0.7592 (p90) cc_final: 0.7334 (p90) REVERT: K 93 ASP cc_start: 0.8159 (t0) cc_final: 0.7520 (m-30) REVERT: I 25 LEU cc_start: 0.6510 (OUTLIER) cc_final: 0.6173 (tt) REVERT: E 124 LEU cc_start: 0.6384 (OUTLIER) cc_final: 0.6151 (tt) REVERT: E 129 GLN cc_start: 0.6911 (tp-100) cc_final: 0.6152 (tp-100) REVERT: B 323 HIS cc_start: 0.7063 (m-70) cc_final: 0.6320 (m-70) REVERT: B 339 LYS cc_start: 0.7332 (mtmt) cc_final: 0.6972 (mppt) REVERT: B 423 GLN cc_start: 0.7700 (tt0) cc_final: 0.7233 (tm-30) REVERT: B 638 GLN cc_start: 0.8076 (pp30) cc_final: 0.7719 (pt0) REVERT: B 670 TRP cc_start: 0.7713 (OUTLIER) cc_final: 0.6794 (m-10) REVERT: B 1024 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7452 (mtp-110) outliers start: 92 outliers final: 68 residues processed: 247 average time/residue: 0.1390 time to fit residues: 55.8026 Evaluate side-chains 239 residues out of total 2501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 161 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 459 TYR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 871 THR Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain A residue 1058 TRP Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1157 CYS Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1024 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 39 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 chunk 89 optimal weight: 0.0870 chunk 144 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 GLN ** I 88 GLN ** 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 = 0.4013 r_free = 0.4013 target = 0.130567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.094695 restraints weight = 46892.904| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 3.03 r_work: 0.3136 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23586 Z= 0.129 Angle : 0.529 8.772 31921 Z= 0.279 Chirality : 0.042 0.229 3590 Planarity : 0.004 0.048 3993 Dihedral : 11.656 169.761 3453 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.80 % Allowed : 20.26 % Favored : 75.94 % 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: -0.46 (0.16), residues: 2778 helix: 1.30 (0.18), residues: 854 sheet: -0.20 (0.24), residues: 492 loop : -1.38 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 43 TYR 0.014 0.001 TYR J 43 PHE 0.020 0.001 PHE A 411 TRP 0.013 0.001 TRP A1058 HIS 0.012 0.001 HIS H 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (23566) covalent geometry : angle 0.52101 / 0.28 (31902) hydrogen bonds : bond 0.04363 / 3.01 ( 828) hydrogen bonds : angle 4.26091 / 2.95 ( 2312) metal coordination : bond 0.00430 / 0.23 ( 19) metal coordination : angle 3.89132 / 2.27 ( 19) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 167 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 351 PHE cc_start: 0.6957 (OUTLIER) cc_final: 0.5668 (m-10) REVERT: A 419 HIS cc_start: 0.2852 (OUTLIER) cc_final: 0.1764 (m90) REVERT: A 446 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7389 (mt) REVERT: A 595 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.6924 (mmtm) REVERT: A 674 MET cc_start: 0.7365 (ppp) cc_final: 0.6479 (tpp) REVERT: A 702 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8118 (mp) REVERT: A 900 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.6362 (tpt-90) REVERT: F 109 LYS cc_start: 0.8348 (mmmt) cc_final: 0.8136 (mmtp) REVERT: K 93 ASP cc_start: 0.8152 (t0) cc_final: 0.7542 (m-30) REVERT: H 41 MET cc_start: 0.6853 (tmm) cc_final: 0.6426 (tpp) REVERT: H 66 LEU cc_start: 0.6258 (OUTLIER) cc_final: 0.6017 (mp) REVERT: I 25 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6194 (tt) REVERT: E 124 LEU cc_start: 0.6362 (OUTLIER) cc_final: 0.6076 (tt) REVERT: E 129 GLN cc_start: 0.6927 (tp-100) cc_final: 0.6168 (tp-100) REVERT: B 323 HIS cc_start: 0.7118 (m-70) cc_final: 0.6347 (m-70) REVERT: B 339 LYS cc_start: 0.7429 (mtmt) cc_final: 0.7016 (mppt) REVERT: B 423 GLN cc_start: 0.7671 (tt0) cc_final: 0.7176 (tm-30) REVERT: B 638 GLN cc_start: 0.8129 (pp30) cc_final: 0.7744 (pt0) REVERT: B 670 TRP cc_start: 0.7769 (OUTLIER) cc_final: 0.6915 (m-10) REVERT: B 1024 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7477 (mtp-110) outliers start: 95 outliers final: 73 residues processed: 253 average time/residue: 0.1426 time to fit residues: 58.4286 Evaluate side-chains 244 residues out of total 2501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 160 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 459 TYR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 850 ASN Chi-restraints excluded: chain A residue 871 THR Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain A residue 1058 TRP Chi-restraints excluded: chain A residue 1070 TRP Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1157 CYS Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1024 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 236 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 169 optimal weight: 0.0980 chunk 123 optimal weight: 2.9990 chunk 200 optimal weight: 8.9990 chunk 212 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1100 HIS C 196 ASN ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 GLN ** I 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.131009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.095033 restraints weight = 47227.085| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.99 r_work: 0.3151 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23586 Z= 0.111 Angle : 0.517 8.518 31921 Z= 0.272 Chirality : 0.041 0.235 3590 Planarity : 0.003 0.050 3993 Dihedral : 11.620 169.655 3453 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.52 % Allowed : 20.46 % Favored : 76.02 % 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: -0.38 (0.16), residues: 2778 helix: 1.37 (0.18), residues: 851 sheet: -0.21 (0.24), residues: 500 loop : -1.31 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 72 TYR 0.012 0.001 TYR J 43 PHE 0.020 0.001 PHE A 411 TRP 0.013 0.001 TRP B 113 HIS 0.013 0.001 HIS H 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (23566) covalent geometry : angle 0.50895 / 0.27 (31902) hydrogen bonds : bond 0.04032 / 2.78 ( 828) hydrogen bonds : angle 4.19686 / 2.90 ( 2312) metal coordination : bond 0.00386 / 0.21 ( 19) metal coordination : angle 3.73687 / 2.14 ( 19) Misc. bond : bond 0.00020 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 161 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 351 PHE cc_start: 0.6947 (OUTLIER) cc_final: 0.5782 (m-10) REVERT: A 419 HIS cc_start: 0.3165 (OUTLIER) cc_final: 0.2027 (m90) REVERT: A 446 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7358 (mt) REVERT: A 595 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.6918 (mmtm) REVERT: A 673 PHE cc_start: 0.7403 (m-80) cc_final: 0.6961 (m-80) REVERT: A 674 MET cc_start: 0.7393 (ppp) cc_final: 0.6554 (tpp) REVERT: A 702 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8070 (mp) REVERT: A 823 GLU cc_start: 0.7480 (pt0) cc_final: 0.7119 (tp30) REVERT: A 900 ARG cc_start: 0.6743 (OUTLIER) cc_final: 0.6310 (tpt-90) REVERT: F 72 ARG cc_start: 0.7080 (ttp80) cc_final: 0.6523 (mtm110) REVERT: F 109 LYS cc_start: 0.8354 (mmmt) cc_final: 0.8144 (mmtp) REVERT: K 93 ASP cc_start: 0.8156 (t0) cc_final: 0.7527 (m-30) REVERT: H 41 MET cc_start: 0.6891 (tmm) cc_final: 0.6444 (tpp) REVERT: H 66 LEU cc_start: 0.6277 (OUTLIER) cc_final: 0.6058 (mp) REVERT: E 124 LEU cc_start: 0.6380 (OUTLIER) cc_final: 0.6021 (tt) REVERT: E 129 GLN cc_start: 0.6915 (tp-100) cc_final: 0.6150 (tp-100) REVERT: B 323 HIS cc_start: 0.7084 (m-70) cc_final: 0.6328 (m-70) REVERT: B 339 LYS cc_start: 0.7435 (mtmt) cc_final: 0.7041 (mtmm) REVERT: B 423 GLN cc_start: 0.7687 (tt0) cc_final: 0.7192 (tm-30) REVERT: B 638 GLN cc_start: 0.8087 (pp30) cc_final: 0.7728 (pt0) REVERT: B 670 TRP cc_start: 0.7689 (OUTLIER) cc_final: 0.6703 (m-10) REVERT: B 1024 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7449 (mtp-110) outliers start: 88 outliers final: 72 residues processed: 240 average time/residue: 0.1397 time to fit residues: 53.7376 Evaluate side-chains 242 residues out of total 2501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 160 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 459 TYR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 850 ASN Chi-restraints excluded: chain A residue 871 THR Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain A residue 1058 TRP Chi-restraints excluded: chain A residue 1070 TRP Chi-restraints excluded: chain A residue 1100 HIS Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1157 CYS Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1024 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 79 optimal weight: 8.9990 chunk 141 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 256 optimal weight: 9.9990 chunk 260 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 364 GLN A 982 ASN ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 GLN ** I 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.127667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.092730 restraints weight = 47399.517| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.98 r_work: 0.3073 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 23586 Z= 0.305 Angle : 0.735 10.713 31921 Z= 0.383 Chirality : 0.049 0.285 3590 Planarity : 0.006 0.071 3993 Dihedral : 11.909 171.739 3453 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.52 % Allowed : 20.30 % Favored : 76.18 % 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: -1.08 (0.16), residues: 2778 helix: 0.73 (0.18), residues: 853 sheet: -0.64 (0.24), residues: 502 loop : -1.69 (0.15), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 984 TYR 0.027 0.003 TYR A 890 PHE 0.023 0.003 PHE C 101 TRP 0.012 0.003 TRP A1058 HIS 0.033 0.003 HIS A1100 Details of bonding type rmsd/Z covalent geometry : bond 0.00749 / 0.30 (23566) covalent geometry : angle 0.72372 / 0.38 (31902) hydrogen bonds : bond 0.06592 / 4.53 ( 828) hydrogen bonds : angle 4.69012 / 3.26 ( 2312) metal coordination : bond 0.00974 / 0.50 ( 19) metal coordination : angle 5.37284 / 3.30 ( 19) Misc. bond : bond 0.00079 / 0.05 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 155 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: A 351 PHE cc_start: 0.7006 (OUTLIER) cc_final: 0.5685 (m-10) REVERT: A 419 HIS cc_start: 0.3199 (OUTLIER) cc_final: 0.2032 (m90) REVERT: A 446 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7552 (mt) REVERT: A 595 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7081 (mmtm) REVERT: A 674 MET cc_start: 0.7523 (ppp) cc_final: 0.6600 (tpp) REVERT: A 702 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8155 (mt) REVERT: A 819 GLN cc_start: 0.6135 (pt0) cc_final: 0.5853 (pp30) REVERT: A 900 ARG cc_start: 0.6816 (OUTLIER) cc_final: 0.6384 (tpt-90) REVERT: F 72 ARG cc_start: 0.7173 (ttp80) cc_final: 0.6494 (mtm110) REVERT: K 93 ASP cc_start: 0.8341 (t0) cc_final: 0.7744 (m-30) REVERT: H 41 MET cc_start: 0.6934 (tmm) cc_final: 0.6395 (tpp) REVERT: H 66 LEU cc_start: 0.6131 (OUTLIER) cc_final: 0.5840 (mp) REVERT: E 129 GLN cc_start: 0.6774 (tp-100) cc_final: 0.6028 (tp-100) REVERT: B 339 LYS cc_start: 0.7648 (mtmt) cc_final: 0.7082 (mtmm) REVERT: B 423 GLN cc_start: 0.7686 (tt0) cc_final: 0.7196 (tm-30) REVERT: B 670 TRP cc_start: 0.8034 (OUTLIER) cc_final: 0.7474 (m-10) REVERT: B 1024 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7571 (mtp-110) outliers start: 88 outliers final: 73 residues processed: 236 average time/residue: 0.1481 time to fit residues: 56.6737 Evaluate side-chains 232 residues out of total 2501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 150 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 459 TYR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 850 ASN Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain A residue 1058 TRP Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1157 CYS Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1024 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 225 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 179 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 207 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 GLN ** I 88 GLN ** 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 = 0.3996 r_free = 0.3996 target = 0.129511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.093433 restraints weight = 47129.894| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.96 r_work: 0.3121 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23586 Z= 0.138 Angle : 0.569 9.548 31921 Z= 0.299 Chirality : 0.042 0.236 3590 Planarity : 0.004 0.051 3993 Dihedral : 11.793 171.107 3451 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.28 % Allowed : 20.38 % Favored : 76.34 % 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: -0.75 (0.16), residues: 2778 helix: 1.02 (0.18), residues: 857 sheet: -0.40 (0.24), residues: 494 loop : -1.53 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 72 TYR 0.015 0.001 TYR J 43 PHE 0.019 0.001 PHE A 411 TRP 0.014 0.001 TRP B 510 HIS 0.016 0.001 HIS H 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (23566) covalent geometry : angle 0.55838 / 0.30 (31902) hydrogen bonds : bond 0.04862 / 3.36 ( 828) hydrogen bonds : angle 4.41887 / 3.07 ( 2312) metal coordination : bond 0.00510 / 0.25 ( 19) metal coordination : angle 4.48928 / 2.70 ( 19) Misc. bond : bond 0.00011 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5033.55 seconds wall clock time: 87 minutes 11.47 seconds (5231.47 seconds total)