Starting phenix.real_space_refine on Sun Jul 5 01:02:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k11_61961/07_2026/9k11_61961.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k11_61961/07_2026/9k11_61961.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k11_61961/07_2026/9k11_61961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k11_61961/07_2026/9k11_61961.map" model { file = "/net/cci-nas-00/data/ceres_data/9k11_61961/07_2026/9k11_61961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k11_61961/07_2026/9k11_61961.cif" } resolution = 2.96 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 63 5.49 5 Mg 1 5.21 5 S 141 5.16 5 C 14891 2.51 5 N 4179 2.21 5 O 4635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.02s 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: 23916 Number of models: 1 Model: "" Number of chains: 18 Chain: "T" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 534 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "N" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 534 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "P" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 239 Classifications: {'RNA': 11} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 3} Link IDs: {'rna3p': 10} Chain: "A" Number of atoms: 6608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 844, 6608 Classifications: {'peptide': 844} Link IDs: {'PTRANS': 27, 'TRANS': 816} Chain breaks: 3 Chain: "C" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2256 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain breaks: 1 Chain: "F" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 660 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 507 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "K" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 890 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "L" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 365 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "H" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1129 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "I" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 787 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 1 Chain: "E" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1706 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 205} Chain: "B" Number of atoms: 7694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7694 Classifications: {'peptide': 971} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 36, 'TRANS': 934} Chain breaks: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6518 SG CYS A1004 20.399 76.735 30.689 1.00137.58 S ATOM 8620 SG CYS C 90 79.781 42.586 135.907 1.00116.42 S ATOM 8678 SG CYS C 99 79.417 38.031 135.905 1.00117.99 S ATOM 8704 SG CYS C 102 77.292 40.488 133.723 1.00105.75 S ATOM 10886 SG CYS J 7 50.461 43.565 116.151 1.00 53.64 S ATOM 10910 SG CYS J 10 49.674 44.694 120.251 1.00 50.04 S ATOM 11176 SG CYS J 44 47.241 45.786 117.101 1.00 57.09 S ATOM 11182 SG CYS J 45 47.896 42.139 118.497 1.00 61.38 S ATOM 12274 SG CYS L 12 78.326 16.822 91.534 1.00 76.05 S ATOM 12292 SG CYS L 15 77.604 13.413 92.961 1.00 86.26 S ATOM 12394 SG CYS L 29 81.155 14.184 91.007 1.00 85.38 S ATOM 12420 SG CYS L 32 76.984 12.483 89.451 1.00 92.39 S Time building chain proxies: 4.18, per 1000 atoms: 0.17 Number of scatterers: 23916 At special positions: 0 Unit cell: (114.975, 139.065, 159.87, 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 63 15.00 Mg 1 11.99 O 4635 8.00 N 4179 7.00 C 14891 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 815.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" ND1 HIS A 938 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A 940 " pdb="ZN ZN A3001 " - pdb=" SG CYS A1004 " pdb=" ZN C 400 " 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 J 200 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 29 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 15 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 12 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 32 " Number of angles added : 12 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5356 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 36 sheets defined 34.9% alpha, 17.9% beta 16 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 359 through 369 Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.547A pdb=" N CYS A 443 " --> pdb=" O PRO A 440 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY A 444 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 473 Processing helix chain 'A' and resid 475 through 479 removed outlier: 3.802A pdb=" N LEU A 479 " --> pdb=" O ASP A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 505 removed outlier: 3.781A 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 576 through 591 removed outlier: 3.869A 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 627 through 647 removed outlier: 4.698A pdb=" N SER A 643 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Proline residue: A 644 - end of helix removed outlier: 3.978A pdb=" N SER A 647 " --> pdb=" O SER A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 675 Processing helix chain 'A' and resid 677 through 682 removed outlier: 3.672A pdb=" N ARG A 681 " --> pdb=" O SER A 677 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASN A 682 " --> pdb=" O TYR A 678 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 677 through 682' Processing helix chain 'A' and resid 689 through 700 removed outlier: 3.711A pdb=" N LYS A 694 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 695 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 729 removed outlier: 3.946A pdb=" N VAL A 718 " --> pdb=" O THR A 714 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR A 729 " --> pdb=" O TYR A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 771 removed outlier: 3.503A pdb=" N ALA A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 786 removed outlier: 3.764A pdb=" N VAL A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 847 Proline residue: A 839 - end of helix Processing helix chain 'A' and resid 848 through 863 removed outlier: 3.698A 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 891 through 904 Processing helix chain 'A' and resid 942 through 949 removed outlier: 3.527A pdb=" N TRP A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 970 removed outlier: 3.935A pdb=" N ALA A 963 " --> pdb=" O ARG A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 979 removed outlier: 3.500A pdb=" N LYS A 979 " --> pdb=" O GLU A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1027 removed outlier: 4.219A pdb=" N THR A1020 " --> pdb=" O ASP A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1034 removed outlier: 3.704A pdb=" N VAL A1031 " --> pdb=" O THR A1027 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A1032 " --> pdb=" O ILE A1028 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A1033 " --> pdb=" O TYR A1029 " (cutoff:3.500A) removed outlier: 3.678A 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: 3.586A pdb=" N ARG A1089 " --> pdb=" O GLY A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1102 removed outlier: 3.640A pdb=" N LEU A1099 " --> pdb=" O LEU A1096 " (cutoff:3.500A) removed outlier: 5.714A 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: 4.009A pdb=" N ILE A1148 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A1156 " --> pdb=" O ALA A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1172 Processing helix chain 'C' and resid 30 through 44 removed outlier: 3.622A pdb=" N ALA C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 73 removed outlier: 3.613A pdb=" N LEU C 73 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 125 removed outlier: 3.527A pdb=" N ASP C 124 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU C 125 " --> pdb=" O SER C 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 121 through 125' Processing helix chain 'C' and resid 176 through 180 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 204 through 214 removed outlier: 3.651A pdb=" N SER C 214 " --> pdb=" O ASP C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 250 Processing helix chain 'C' and resid 276 through 294 removed outlier: 4.063A pdb=" N VAL C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA C 294 " --> pdb=" O GLN C 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 83 removed outlier: 3.548A pdb=" N ARG F 72 " --> pdb=" O TYR F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 107 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 37 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.666A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 62 removed outlier: 3.787A pdb=" N TYR J 62 " --> pdb=" O LYS J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.768A 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: 3.658A pdb=" N GLY E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 71 removed outlier: 3.579A pdb=" N PHE E 66 " --> pdb=" O SER E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 117 removed outlier: 3.657A pdb=" N SER E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 141 removed outlier: 4.106A pdb=" N LYS E 138 " --> pdb=" O ASP E 134 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU E 141 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 183 removed outlier: 3.710A pdb=" N GLN E 182 " --> pdb=" O ALA E 178 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE E 183 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 204 Processing helix chain 'B' and resid 21 through 41 Processing helix chain 'B' and resid 43 through 56 removed outlier: 3.823A pdb=" N SER B 49 " --> pdb=" O HIS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 65 Processing helix chain 'B' and resid 111 through 118 Processing helix chain 'B' and resid 239 through 242 Processing helix chain 'B' and resid 275 through 283 Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 300 through 316 removed outlier: 3.938A pdb=" N THR B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 336 Processing helix chain 'B' and resid 345 through 353 Processing helix chain 'B' and resid 360 through 380 Processing helix chain 'B' and resid 390 through 392 No H-bonds generated for 'chain 'B' and resid 390 through 392' Processing helix chain 'B' and resid 398 through 426 removed outlier: 3.904A pdb=" N VAL B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ARG B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 438 Processing helix chain 'B' and resid 441 through 455 Processing helix chain 'B' and resid 478 through 485 removed outlier: 3.580A pdb=" N SER B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 510 removed outlier: 3.929A pdb=" N TRP B 510 " --> pdb=" O PRO B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 551 removed outlier: 3.529A pdb=" N LEU B 548 " --> pdb=" O VAL B 545 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE B 549 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP B 550 " --> pdb=" O GLU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 595 Processing helix chain 'B' and resid 631 through 636 removed outlier: 4.789A pdb=" N HIS B 634 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 636 " --> pdb=" O LEU B 633 " (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 677 removed outlier: 3.777A pdb=" N LEU B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 693 removed outlier: 3.619A pdb=" N LEU B 693 " --> pdb=" O SER B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 699 removed outlier: 4.117A pdb=" N ILE B 699 " --> pdb=" O VAL B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 706 removed outlier: 3.807A 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 729 through 733 removed outlier: 3.551A pdb=" N ARG B 733 " --> pdb=" O PRO B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 758 Processing helix chain 'B' and resid 759 through 763 removed outlier: 3.973A pdb=" N LEU B 762 " --> pdb=" O LYS B 759 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE B 763 " --> pdb=" O ASP B 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 759 through 763' Processing helix chain 'B' and resid 788 through 793 Processing helix chain 'B' and resid 925 through 929 removed outlier: 3.605A pdb=" N ASN B 928 " --> pdb=" O GLU B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 951 removed outlier: 3.717A pdb=" N GLN B 951 " --> pdb=" O PHE B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 953 through 967 removed outlier: 3.503A pdb=" N CYS B 967 " --> pdb=" O LYS B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1004 Processing sheet with id=AA1, first strand: chain 'B' and resid 1046 through 1048 removed outlier: 3.713A pdb=" N SER A 323 " --> pdb=" O ARG B1048 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N PHE A 322 " --> pdb=" O TYR A 459 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 326 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN A 424 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL A 436 " --> pdb=" O ARG A 325 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL A 327 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE A 438 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR A 329 " --> pdb=" O ILE A 438 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 350 through 354 removed outlier: 3.597A pdb=" N THR A 376 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER A 374 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ARG A 403 " --> pdb=" O CYS A 372 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N CYS A 372 " --> pdb=" O ARG A 403 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 507 through 508 Processing sheet with id=AA4, first strand: chain 'A' and resid 529 through 531 removed outlier: 5.617A pdb=" N VAL A 529 " --> pdb=" O HIS H 94 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N HIS H 94 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS A 531 " --> pdb=" O VAL H 92 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR H 113 " --> pdb=" O TYR H 98 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LEU H 120 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE H 40 " --> pdb=" O ARG H 124 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N MET H 39 " --> pdb=" O SER H 34 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL H 45 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ARG H 29 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU H 17 " --> pdb=" O ARG H 29 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU H 31 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR H 33 " --> pdb=" O VAL H 13 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL H 13 " --> pdb=" O THR H 33 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 529 through 531 removed outlier: 5.617A pdb=" N VAL A 529 " --> pdb=" O HIS H 94 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N HIS H 94 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS A 531 " --> pdb=" O VAL H 92 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU H 139 " --> pdb=" O GLY H 95 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 554 through 556 removed outlier: 6.745A pdb=" N GLY A 563 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LEU A 567 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 703 through 704 Processing sheet with id=AA8, first strand: chain 'A' and resid 789 through 791 removed outlier: 6.319A pdb=" N ASN A 799 " --> pdb=" O ILE A 805 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE A 805 " --> pdb=" O ASN A 799 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1043 through 1045 Processing sheet with id=AB1, first strand: chain 'A' and resid 1043 through 1045 Processing sheet with id=AB2, first strand: chain 'A' and resid 906 through 907 removed outlier: 7.070A pdb=" N VAL A 906 " --> pdb=" O ILE A1037 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1004 through 1007 removed outlier: 3.525A pdb=" N HIS A 940 " --> pdb=" O GLU A 914 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU A 914 " --> pdb=" O HIS A 940 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N TYR I 44 " --> pdb=" O VAL A 917 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N TYR A 919 " --> pdb=" O CYS I 42 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N CYS I 42 " --> pdb=" O TYR A 919 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1227 through 1230 Processing sheet with id=AB5, first strand: chain 'C' and resid 11 through 18 removed outlier: 5.487A pdb=" N VAL C 12 " --> pdb=" O ARG C 27 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ARG C 27 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ILE C 14 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU C 25 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR C 21 " --> pdb=" O LYS C 18 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE C 24 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU C 190 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ASP C 263 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 11.372A pdb=" N MET C 188 " --> pdb=" O ASP C 263 " (cutoff:3.500A) removed outlier: 9.819A pdb=" N PHE C 265 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 11.372A pdb=" N THR C 186 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 9.753A pdb=" N PHE C 267 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 11.220A pdb=" N THR C 184 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 9.761A pdb=" N VAL C 269 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N ALA C 182 " --> pdb=" O VAL C 269 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 126 through 127 removed outlier: 3.671A pdb=" N LEU C 108 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLU C 161 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN C 58 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LYS C 163 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ARG C 169 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ILE C 50 " --> pdb=" O ARG C 169 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLY C 171 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N VAL C 48 " --> pdb=" O GLY C 171 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 118 through 120 removed outlier: 3.566A pdb=" N VAL C 154 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 220 through 222 removed outlier: 3.560A pdb=" N ASP C 221 " --> pdb=" O VAL C 230 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C 230 " --> pdb=" O ASP C 221 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AC1, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.290A pdb=" N VAL B 882 " --> pdb=" O LYS L 39 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N SER B 897 " --> pdb=" O GLN B 880 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL B 882 " --> pdb=" O THR B 895 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR B 895 " --> pdb=" O VAL B 882 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU B 884 " --> pdb=" O TYR B 893 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TYR B 893 " --> pdb=" O LEU B 884 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.290A pdb=" N VAL B 882 " --> pdb=" O LYS L 39 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 14 through 16 Processing sheet with id=AC4, first strand: chain 'I' and resid 84 through 90 removed outlier: 3.637A pdb=" N TRP I 112 " --> pdb=" O PHE I 101 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 94 through 95 removed outlier: 7.016A pdb=" N LYS E 94 " --> pdb=" O ILE E 125 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL E 127 " --> pdb=" O LYS E 94 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 169 through 170 removed outlier: 3.533A pdb=" N ARG E 169 " --> pdb=" O LYS E 212 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR E 223 " --> pdb=" O TYR E 215 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 68 through 69 Processing sheet with id=AC8, first strand: chain 'B' and resid 91 through 96 removed outlier: 4.709A pdb=" N GLU B 93 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN B 129 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA B 124 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG B 169 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N MET B 126 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AD1, first strand: chain 'B' and resid 204 through 206 Processing sheet with id=AD2, first strand: chain 'B' and resid 394 through 397 removed outlier: 6.436A pdb=" N ALA B 215 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 224 through 226 Processing sheet with id=AD4, first strand: chain 'B' and resid 457 through 458 Processing sheet with id=AD5, first strand: chain 'B' and resid 535 through 536 Processing sheet with id=AD6, first strand: chain 'B' and resid 535 through 536 Processing sheet with id=AD7, first strand: chain 'B' and resid 553 through 554 removed outlier: 7.048A pdb=" N VAL B 570 " --> pdb=" O VAL B 577 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL B 579 " --> pdb=" O HIS B 568 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N HIS B 568 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LYS B 569 " --> pdb=" O VAL B 614 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ILE B 616 " --> pdb=" O LYS B 569 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU B 571 " --> pdb=" O ILE B 616 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1011 through 1012 removed outlier: 7.137A pdb=" N ILE B 784 " --> pdb=" O GLY B 921 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE B 923 " --> pdb=" O ILE B 784 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N MET B 786 " --> pdb=" O ILE B 923 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N PHE B1028 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 855 through 857 removed outlier: 6.911A pdb=" N VAL B 869 " --> pdb=" O VAL B 856 " (cutoff:3.500A) 843 hydrogen bonds defined for protein. 2361 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 5.00 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6762 1.33 - 1.45: 4716 1.45 - 1.57: 12655 1.57 - 1.70: 123 1.70 - 1.82: 217 Bond restraints: 24473 Sorted by residual: bond pdb=" C1' DA T 6 " pdb=" N9 DA T 6 " ideal model delta sigma weight residual 1.468 1.367 0.101 1.40e-02 5.10e+03 5.17e+01 bond pdb=" C1' G P 18 " pdb=" N9 G P 18 " ideal model delta sigma weight residual 1.475 1.369 0.106 1.50e-02 4.44e+03 4.96e+01 bond pdb=" C1' DA T 13 " pdb=" N9 DA T 13 " ideal model delta sigma weight residual 1.468 1.371 0.097 1.40e-02 5.10e+03 4.84e+01 bond pdb=" C1' DT N 22 " pdb=" N1 DT N 22 " ideal model delta sigma weight residual 1.468 1.550 -0.082 1.40e-02 5.10e+03 3.42e+01 bond pdb=" C1' DT N 30 " pdb=" N1 DT N 30 " ideal model delta sigma weight residual 1.468 1.543 -0.075 1.40e-02 5.10e+03 2.84e+01 ... (remaining 24468 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.85: 33207 5.85 - 11.69: 73 11.69 - 17.54: 2 17.54 - 23.39: 1 23.39 - 29.23: 2 Bond angle restraints: 33285 Sorted by residual: angle pdb=" C3' DA N 20 " pdb=" O3' DA N 20 " pdb=" P DT N 21 " ideal model delta sigma weight residual 120.20 96.10 24.10 1.50e+00 4.44e-01 2.58e+02 angle pdb=" O3' DA N 20 " pdb=" P DT N 21 " pdb=" O5' DT N 21 " ideal model delta sigma weight residual 104.00 85.12 18.88 1.50e+00 4.44e-01 1.58e+02 angle pdb=" O3' DA N 20 " pdb=" P DT N 21 " pdb=" OP1 DT N 21 " ideal model delta sigma weight residual 108.00 137.23 -29.23 3.00e+00 1.11e-01 9.50e+01 angle pdb=" C3' DA T 28 " pdb=" O3' DA T 28 " pdb=" P DC T 29 " ideal model delta sigma weight residual 120.20 110.06 10.14 1.50e+00 4.44e-01 4.57e+01 angle pdb=" C3' DT N 18 " pdb=" O3' DT N 18 " pdb=" P DG N 19 " ideal model delta sigma weight residual 120.20 111.08 9.12 1.50e+00 4.44e-01 3.70e+01 ... (remaining 33280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 13721 17.32 - 34.65: 664 34.65 - 51.97: 272 51.97 - 69.29: 83 69.29 - 86.62: 27 Dihedral angle restraints: 14767 sinusoidal: 6496 harmonic: 8271 Sorted by residual: dihedral pdb=" CA TRP A1050 " pdb=" C TRP A1050 " pdb=" N ASN A1051 " pdb=" CA ASN A1051 " ideal model delta harmonic sigma weight residual -180.00 -136.19 -43.81 0 5.00e+00 4.00e-02 7.68e+01 dihedral pdb=" CA LEU I 68 " pdb=" C LEU I 68 " pdb=" N PRO I 69 " pdb=" CA PRO I 69 " ideal model delta harmonic sigma weight residual -180.00 -147.43 -32.57 0 5.00e+00 4.00e-02 4.24e+01 dihedral pdb=" CA GLY H 105 " pdb=" C GLY H 105 " pdb=" N GLN H 106 " pdb=" CA GLN H 106 " ideal model delta harmonic sigma weight residual -180.00 -147.88 -32.12 0 5.00e+00 4.00e-02 4.13e+01 ... (remaining 14764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 3465 0.108 - 0.216: 259 0.216 - 0.324: 11 0.324 - 0.431: 4 0.431 - 0.539: 7 Chirality restraints: 3746 Sorted by residual: chirality pdb=" P DA T 11 " pdb=" OP1 DA T 11 " pdb=" OP2 DA T 11 " pdb=" O5' DA T 11 " both_signs ideal model delta sigma weight residual True 2.34 -2.87 -0.54 2.00e-01 2.50e+01 7.27e+00 chirality pdb=" P DA T 28 " pdb=" OP1 DA T 28 " pdb=" OP2 DA T 28 " pdb=" O5' DA T 28 " both_signs ideal model delta sigma weight residual True 2.34 -2.83 -0.50 2.00e-01 2.50e+01 6.22e+00 chirality pdb=" P DT T 27 " pdb=" OP1 DT T 27 " pdb=" OP2 DT T 27 " pdb=" O5' DT T 27 " both_signs ideal model delta sigma weight residual True 2.34 -2.82 -0.48 2.00e-01 2.50e+01 5.87e+00 ... (remaining 3743 not shown) Planarity restraints: 4057 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 576 " 0.023 2.00e-02 2.50e+03 2.18e-02 1.18e+01 pdb=" CG TRP B 576 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP B 576 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B 576 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 576 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 576 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 576 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 576 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 576 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 576 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1034 " -0.023 2.00e-02 2.50e+03 2.43e-02 1.18e+01 pdb=" CG TYR B1034 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR B1034 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B1034 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B1034 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR B1034 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B1034 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR B1034 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 391 " -0.018 2.00e-02 2.50e+03 2.49e-02 1.09e+01 pdb=" CG PHE B 391 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE B 391 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE B 391 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 391 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE B 391 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE B 391 " -0.003 2.00e-02 2.50e+03 ... (remaining 4054 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 13 2.31 - 2.96: 10071 2.96 - 3.60: 33341 3.60 - 4.25: 53874 4.25 - 4.90: 90408 Nonbonded interactions: 187707 Sorted by model distance: nonbonded pdb=" N4 DC T 29 " pdb=" N1 DG N 6 " model vdw 1.661 2.560 nonbonded pdb=" OD1 ASP A 449 " pdb="MG MG A3000 " model vdw 2.113 2.170 nonbonded pdb=" OD1 ASP A 453 " pdb="MG MG A3000 " model vdw 2.127 2.170 nonbonded pdb=" O TYR I 27 " pdb="ZN ZN I 202 " model vdw 2.188 2.230 nonbonded pdb=" OD1 ASP A 451 " pdb="MG MG A3000 " model vdw 2.204 2.170 ... (remaining 187702 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: 1.640 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: 0.070 Set scattering table: 0.060 Process input model: 24.600 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 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:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.610 24487 Z= 0.449 Angle : 1.077 29.233 33297 Z= 0.633 Chirality : 0.064 0.539 3746 Planarity : 0.007 0.066 4057 Dihedral : 13.646 86.618 9411 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.67 % Favored : 94.26 % Rotamer: Outliers : 0.28 % Allowed : 2.07 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.60 (0.13), residues: 2805 helix: -2.44 (0.13), residues: 877 sheet: -1.92 (0.22), residues: 492 loop : -2.50 (0.14), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 625 TYR 0.057 0.003 TYR B1034 PHE 0.054 0.004 PHE C 267 TRP 0.058 0.004 TRP B 576 HIS 0.014 0.003 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00836 / 0.41 (24473) covalent geometry : angle 1.04745 / 0.63 (33285) hydrogen bonds : bond 0.20124 / 21.86 ( 872) hydrogen bonds : angle 7.91763 / 9.47 ( 2439) metal coordination : bond 0.21457 / 20.63 ( 14) metal coordination : angle 13.16011 / 20.86 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 358 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 TYR cc_start: 0.8228 (t80) cc_final: 0.7993 (t80) REVERT: A 663 ILE cc_start: 0.8037 (pt) cc_final: 0.7731 (pp) REVERT: A 846 ASP cc_start: 0.8308 (t0) cc_final: 0.7987 (t70) REVERT: A 1010 TYR cc_start: 0.6566 (t80) cc_final: 0.5968 (t80) REVERT: F 88 MET cc_start: 0.8260 (mmt) cc_final: 0.8009 (mmm) REVERT: K 53 ASP cc_start: 0.8695 (t70) cc_final: 0.8486 (t0) REVERT: L 43 ARG cc_start: 0.7947 (tpp80) cc_final: 0.7740 (tpt-90) REVERT: H 36 ASN cc_start: 0.6995 (m-40) cc_final: 0.6489 (m110) REVERT: H 48 GLU cc_start: 0.7515 (pt0) cc_final: 0.7110 (tm-30) REVERT: E 109 ARG cc_start: 0.8181 (ttm110) cc_final: 0.7875 (tpt90) REVERT: E 173 ASP cc_start: 0.8452 (t0) cc_final: 0.8177 (t0) REVERT: B 496 THR cc_start: 0.6196 (OUTLIER) cc_final: 0.5933 (t) REVERT: B 1047 PHE cc_start: 0.8178 (p90) cc_final: 0.7781 (p90) outliers start: 7 outliers final: 2 residues processed: 365 average time/residue: 0.7536 time to fit residues: 306.7588 Evaluate side-chains 195 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 192 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1034 GLU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain B residue 496 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.2980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 431 HIS A 611 HIS ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 ASN A1100 HIS A1114 GLN A1154 ASN C 98 GLN C 253 GLN F 84 ASN K 65 HIS K 76 HIS L 28 GLN H 67 ASN H 132 HIS I 105 ASN B 26 GLN B 45 HIS B 59 GLN B 216 GLN B 425 HIS B 506 HIS B 648 HIS B 684 HIS B 705 HIS B 764 ASN B 766 GLN B1000 GLN ** B1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.101373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.067954 restraints weight = 53652.569| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.67 r_work: 0.2939 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 24487 Z= 0.144 Angle : 0.673 17.560 33297 Z= 0.357 Chirality : 0.045 0.191 3746 Planarity : 0.005 0.052 4057 Dihedral : 15.636 86.821 3837 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.99 % Favored : 94.97 % Rotamer: Outliers : 1.31 % Allowed : 8.47 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.14), residues: 2805 helix: -0.72 (0.16), residues: 901 sheet: -1.39 (0.23), residues: 486 loop : -2.14 (0.15), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 802 TYR 0.021 0.002 TYR B1034 PHE 0.024 0.002 PHE A 411 TRP 0.015 0.002 TRP B 576 HIS 0.008 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (24473) covalent geometry : angle 0.65697 / 0.36 (33285) hydrogen bonds : bond 0.05265 / 5.57 ( 872) hydrogen bonds : angle 5.27678 / 6.62 ( 2439) metal coordination : bond 0.01463 / 1.36 ( 14) metal coordination : angle 7.80816 / 11.14 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 221 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 GLU cc_start: 0.7938 (pp20) cc_final: 0.7484 (tm-30) REVERT: A 362 TYR cc_start: 0.8321 (t80) cc_final: 0.8072 (t80) REVERT: A 663 ILE cc_start: 0.7640 (pt) cc_final: 0.7436 (pp) REVERT: A 668 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7381 (mm-30) REVERT: A 685 ASP cc_start: 0.8065 (p0) cc_final: 0.7376 (p0) REVERT: A 846 ASP cc_start: 0.8069 (t0) cc_final: 0.7565 (t70) REVERT: A 1010 TYR cc_start: 0.6791 (t80) cc_final: 0.6079 (t80) REVERT: F 63 LYS cc_start: 0.8248 (pttt) cc_final: 0.8031 (pptt) REVERT: F 88 MET cc_start: 0.8469 (mmt) cc_final: 0.8065 (mmm) REVERT: F 94 GLU cc_start: 0.6371 (mm-30) cc_final: 0.5914 (mm-30) REVERT: F 104 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8056 (mt-10) REVERT: F 106 ARG cc_start: 0.7957 (ttm-80) cc_final: 0.7739 (ttm-80) REVERT: F 129 ASP cc_start: 0.8888 (p0) cc_final: 0.8000 (p0) REVERT: K 53 ASP cc_start: 0.8784 (t70) cc_final: 0.8464 (t0) REVERT: K 54 GLU cc_start: 0.8856 (tp30) cc_final: 0.8645 (tp30) REVERT: L 43 ARG cc_start: 0.7782 (tpp80) cc_final: 0.7553 (tpt-90) REVERT: H 41 MET cc_start: 0.8098 (tmm) cc_final: 0.7722 (tmm) REVERT: H 48 GLU cc_start: 0.8173 (pt0) cc_final: 0.7187 (tm-30) REVERT: H 130 ILE cc_start: 0.7765 (mp) cc_final: 0.7524 (pt) REVERT: I 35 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8285 (mt0) REVERT: I 100 PHE cc_start: 0.6614 (m-80) cc_final: 0.5733 (m-80) REVERT: E 230 TRP cc_start: 0.8084 (OUTLIER) cc_final: 0.5782 (t60) outliers start: 33 outliers final: 6 residues processed: 243 average time/residue: 0.6859 time to fit residues: 188.7337 Evaluate side-chains 193 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 184 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain K residue 112 PHE Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain B residue 238 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 44 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 151 optimal weight: 0.3980 chunk 161 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 661 ASN ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.100906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.066672 restraints weight = 54086.760| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.55 r_work: 0.2938 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 24487 Z= 0.135 Angle : 0.612 15.527 33297 Z= 0.325 Chirality : 0.043 0.179 3746 Planarity : 0.004 0.049 4057 Dihedral : 15.403 89.363 3833 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.55 % Allowed : 10.02 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.15), residues: 2805 helix: 0.14 (0.17), residues: 899 sheet: -1.20 (0.23), residues: 497 loop : -1.90 (0.15), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 992 TYR 0.018 0.002 TYR B1034 PHE 0.028 0.002 PHE A 572 TRP 0.013 0.001 TRP B 576 HIS 0.009 0.001 HIS H 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (24473) covalent geometry : angle 0.60002 / 0.32 (33285) hydrogen bonds : bond 0.04423 / 4.75 ( 872) hydrogen bonds : angle 4.76863 / 6.03 ( 2439) metal coordination : bond 0.00551 / 0.48 ( 14) metal coordination : angle 6.43926 / 9.08 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 202 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 GLU cc_start: 0.7986 (pp20) cc_final: 0.7551 (tm-30) REVERT: A 362 TYR cc_start: 0.8275 (t80) cc_final: 0.8039 (t80) REVERT: A 673 PHE cc_start: 0.8223 (m-80) cc_final: 0.7753 (m-80) REVERT: A 685 ASP cc_start: 0.8266 (p0) cc_final: 0.7495 (p0) REVERT: A 846 ASP cc_start: 0.8176 (t0) cc_final: 0.7622 (t70) REVERT: A 1010 TYR cc_start: 0.6773 (t80) cc_final: 0.6044 (t80) REVERT: F 88 MET cc_start: 0.8460 (mmt) cc_final: 0.8023 (mmm) REVERT: F 94 GLU cc_start: 0.6215 (OUTLIER) cc_final: 0.5771 (mm-30) REVERT: F 99 GLU cc_start: 0.8061 (tp30) cc_final: 0.7683 (tp30) REVERT: F 129 ASP cc_start: 0.8907 (p0) cc_final: 0.8070 (p0) REVERT: L 43 ARG cc_start: 0.7856 (tpp80) cc_final: 0.7528 (tpt-90) REVERT: H 48 GLU cc_start: 0.8089 (pt0) cc_final: 0.7142 (tm-30) REVERT: H 111 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7998 (pm20) REVERT: H 130 ILE cc_start: 0.7777 (mp) cc_final: 0.7493 (pt) REVERT: H 132 HIS cc_start: 0.7069 (OUTLIER) cc_final: 0.6843 (p-80) REVERT: I 35 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8321 (mt0) REVERT: I 70 ARG cc_start: 0.6115 (OUTLIER) cc_final: 0.5874 (mtt90) REVERT: E 230 TRP cc_start: 0.8126 (OUTLIER) cc_final: 0.5855 (t60) REVERT: B 424 ARG cc_start: 0.7712 (tmm-80) cc_final: 0.7416 (tmm-80) outliers start: 39 outliers final: 11 residues processed: 229 average time/residue: 0.6623 time to fit residues: 171.3308 Evaluate side-chains 197 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain K residue 112 PHE Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 5 LYS Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 840 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 104 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 250 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 213 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 615 GLN ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1154 ASN F 84 ASN ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** I 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN B 326 ASN B 491 GLN B 714 GLN ** B 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.099218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.065611 restraints weight = 53807.426| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.68 r_work: 0.2875 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 24487 Z= 0.222 Angle : 0.657 15.336 33297 Z= 0.348 Chirality : 0.045 0.253 3746 Planarity : 0.005 0.048 4057 Dihedral : 15.407 88.442 3833 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.03 % Allowed : 10.34 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.15), residues: 2805 helix: 0.51 (0.18), residues: 882 sheet: -1.11 (0.23), residues: 495 loop : -1.71 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 113 TYR 0.030 0.002 TYR B1034 PHE 0.034 0.002 PHE A 572 TRP 0.023 0.002 TRP B 576 HIS 0.008 0.001 HIS E 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 (24473) covalent geometry : angle 0.64723 / 0.35 (33285) hydrogen bonds : bond 0.04891 / 5.23 ( 872) hydrogen bonds : angle 4.70377 / 5.90 ( 2439) metal coordination : bond 0.00807 / 0.80 ( 14) metal coordination : angle 6.12445 / 8.48 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 190 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 TYR cc_start: 0.8317 (t80) cc_final: 0.7995 (t80) REVERT: A 846 ASP cc_start: 0.8252 (t0) cc_final: 0.7752 (t70) REVERT: A 1010 TYR cc_start: 0.6766 (t80) cc_final: 0.6025 (t80) REVERT: F 88 MET cc_start: 0.8589 (mmt) cc_final: 0.8374 (mmm) REVERT: F 129 ASP cc_start: 0.8892 (p0) cc_final: 0.8122 (p0) REVERT: L 43 ARG cc_start: 0.7877 (tpp80) cc_final: 0.7553 (tpt-90) REVERT: H 7 MET cc_start: 0.8239 (ptp) cc_final: 0.7820 (ptp) REVERT: H 22 LYS cc_start: 0.7897 (mmpt) cc_final: 0.7607 (mptt) REVERT: H 48 GLU cc_start: 0.8273 (pt0) cc_final: 0.7273 (tm-30) REVERT: H 121 MET cc_start: 0.8966 (ttp) cc_final: 0.8373 (ttp) REVERT: H 144 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7724 (ptt-90) REVERT: I 35 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8308 (mt0) REVERT: I 100 PHE cc_start: 0.6186 (m-80) cc_final: 0.5196 (m-80) REVERT: I 113 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7245 (mmp80) REVERT: E 230 TRP cc_start: 0.8195 (OUTLIER) cc_final: 0.5950 (t60) REVERT: B 371 MET cc_start: 0.9452 (mtp) cc_final: 0.9113 (mtp) outliers start: 51 outliers final: 25 residues processed: 227 average time/residue: 0.6471 time to fit residues: 166.3764 Evaluate side-chains 210 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 689 ASN Chi-restraints excluded: chain A residue 1058 TRP Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 112 PHE Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 144 ARG Chi-restraints excluded: chain I residue 5 LYS Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 919 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 241 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 232 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 180 optimal weight: 0.9980 chunk 266 optimal weight: 10.0000 chunk 235 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 265 optimal weight: 0.0050 chunk 57 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** I 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN B 800 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.100469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.067008 restraints weight = 53324.851| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.73 r_work: 0.2906 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24487 Z= 0.121 Angle : 0.578 13.929 33297 Z= 0.306 Chirality : 0.042 0.201 3746 Planarity : 0.004 0.041 4057 Dihedral : 15.271 87.830 3833 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.43 % Allowed : 12.01 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.16), residues: 2805 helix: 0.80 (0.18), residues: 905 sheet: -0.83 (0.24), residues: 478 loop : -1.64 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 113 TYR 0.017 0.001 TYR A 375 PHE 0.036 0.002 PHE A 572 TRP 0.018 0.001 TRP A1058 HIS 0.008 0.001 HIS H 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (24473) covalent geometry : angle 0.56698 / 0.31 (33285) hydrogen bonds : bond 0.03949 / 4.24 ( 872) hydrogen bonds : angle 4.49801 / 5.67 ( 2439) metal coordination : bond 0.00507 / 0.51 ( 14) metal coordination : angle 5.82909 / 7.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 198 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 TYR cc_start: 0.8124 (t80) cc_final: 0.7870 (t80) REVERT: A 645 MET cc_start: 0.8009 (tmm) cc_final: 0.7712 (tmm) REVERT: A 673 PHE cc_start: 0.8097 (m-80) cc_final: 0.7677 (m-80) REVERT: A 846 ASP cc_start: 0.8049 (t0) cc_final: 0.7580 (t70) REVERT: A 1010 TYR cc_start: 0.6676 (t80) cc_final: 0.5889 (t80) REVERT: F 88 MET cc_start: 0.8533 (mmt) cc_final: 0.8230 (mmm) REVERT: F 129 ASP cc_start: 0.8805 (p0) cc_final: 0.8031 (p0) REVERT: L 43 ARG cc_start: 0.7595 (tpp80) cc_final: 0.7331 (tpt-90) REVERT: H 48 GLU cc_start: 0.8079 (pt0) cc_final: 0.7210 (tm-30) REVERT: H 111 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7890 (pm20) REVERT: I 8 ARG cc_start: 0.8514 (tpp80) cc_final: 0.8242 (ttm110) REVERT: I 35 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8232 (mt0) REVERT: I 70 ARG cc_start: 0.5730 (OUTLIER) cc_final: 0.4903 (pmm-80) REVERT: I 100 PHE cc_start: 0.6035 (m-80) cc_final: 0.5590 (m-80) REVERT: E 230 TRP cc_start: 0.8123 (OUTLIER) cc_final: 0.5831 (t60) REVERT: B 424 ARG cc_start: 0.7497 (tmm-80) cc_final: 0.6843 (tmm-80) REVERT: B 425 HIS cc_start: 0.8185 (OUTLIER) cc_final: 0.6913 (m90) outliers start: 36 outliers final: 17 residues processed: 223 average time/residue: 0.6667 time to fit residues: 168.4722 Evaluate side-chains 201 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 689 ASN Chi-restraints excluded: chain A residue 1058 TRP Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain K residue 112 PHE Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 425 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 151 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 197 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 251 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 214 optimal weight: 0.9990 chunk 224 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3762 r_free = 0.3762 target = 0.100715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.067167 restraints weight = 53621.074| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.57 r_work: 0.2924 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24487 Z= 0.118 Angle : 0.568 13.215 33297 Z= 0.301 Chirality : 0.042 0.190 3746 Planarity : 0.004 0.043 4057 Dihedral : 15.197 87.189 3833 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.59 % Allowed : 12.29 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.16), residues: 2805 helix: 1.01 (0.18), residues: 905 sheet: -0.74 (0.24), residues: 478 loop : -1.54 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 113 TYR 0.016 0.001 TYR A 375 PHE 0.038 0.001 PHE A 572 TRP 0.018 0.001 TRP A1058 HIS 0.007 0.001 HIS H 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (24473) covalent geometry : angle 0.55868 / 0.30 (33285) hydrogen bonds : bond 0.03753 / 4.03 ( 872) hydrogen bonds : angle 4.40467 / 5.54 ( 2439) metal coordination : bond 0.00466 / 0.47 ( 14) metal coordination : angle 5.45380 / 7.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 GLU cc_start: 0.7701 (mp0) cc_final: 0.7480 (pm20) REVERT: A 362 TYR cc_start: 0.8234 (t80) cc_final: 0.7946 (t80) REVERT: A 673 PHE cc_start: 0.8162 (m-80) cc_final: 0.7703 (m-80) REVERT: A 846 ASP cc_start: 0.8116 (t0) cc_final: 0.7661 (t70) REVERT: A 1010 TYR cc_start: 0.6745 (t80) cc_final: 0.5853 (t80) REVERT: C 84 MET cc_start: 0.9188 (ptm) cc_final: 0.8806 (ptm) REVERT: F 88 MET cc_start: 0.8609 (mmt) cc_final: 0.8359 (mmm) REVERT: F 103 LYS cc_start: 0.8874 (mmmt) cc_final: 0.8562 (mmmm) REVERT: F 129 ASP cc_start: 0.8835 (p0) cc_final: 0.8112 (p0) REVERT: L 43 ARG cc_start: 0.7868 (tpp80) cc_final: 0.7531 (tpt-90) REVERT: H 48 GLU cc_start: 0.8112 (pt0) cc_final: 0.7292 (tm-30) REVERT: H 111 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7963 (pm20) REVERT: I 35 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8289 (mt0) REVERT: E 230 TRP cc_start: 0.8175 (OUTLIER) cc_final: 0.5894 (t60) REVERT: B 424 ARG cc_start: 0.7552 (tmm-80) cc_final: 0.7260 (tmm-80) outliers start: 40 outliers final: 19 residues processed: 218 average time/residue: 0.6789 time to fit residues: 167.6257 Evaluate side-chains 201 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 689 ASN Chi-restraints excluded: chain A residue 1058 TRP Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain H residue 26 LYS Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 143 MET Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 560 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 46 optimal weight: 0.0570 chunk 236 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 181 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 235 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 overall best weight: 1.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 GLN F 84 ASN ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.099714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.066272 restraints weight = 53697.269| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.65 r_work: 0.2898 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24487 Z= 0.172 Angle : 0.602 13.281 33297 Z= 0.318 Chirality : 0.043 0.205 3746 Planarity : 0.004 0.043 4057 Dihedral : 15.214 87.303 3833 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.67 % Allowed : 12.72 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.16), residues: 2805 helix: 1.06 (0.18), residues: 907 sheet: -0.88 (0.24), residues: 490 loop : -1.48 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 113 TYR 0.018 0.002 TYR B 804 PHE 0.040 0.002 PHE A 572 TRP 0.016 0.002 TRP A1058 HIS 0.006 0.001 HIS H 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (24473) covalent geometry : angle 0.59324 / 0.32 (33285) hydrogen bonds : bond 0.04148 / 4.45 ( 872) hydrogen bonds : angle 4.43634 / 5.56 ( 2439) metal coordination : bond 0.00647 / 0.65 ( 14) metal coordination : angle 5.51472 / 7.47 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 185 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 GLU cc_start: 0.7720 (mp0) cc_final: 0.7507 (pm20) REVERT: A 362 TYR cc_start: 0.8224 (t80) cc_final: 0.7923 (t80) REVERT: A 375 TYR cc_start: 0.6301 (m-80) cc_final: 0.6086 (m-80) REVERT: A 673 PHE cc_start: 0.8216 (m-80) cc_final: 0.7758 (m-80) REVERT: A 846 ASP cc_start: 0.8137 (t0) cc_final: 0.7692 (t70) REVERT: A 1010 TYR cc_start: 0.6763 (t80) cc_final: 0.5885 (t80) REVERT: C 253 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7919 (tp-100) REVERT: F 88 MET cc_start: 0.8636 (mmt) cc_final: 0.8377 (mmm) REVERT: F 103 LYS cc_start: 0.8870 (mmmt) cc_final: 0.8586 (mmmm) REVERT: F 129 ASP cc_start: 0.8863 (p0) cc_final: 0.8050 (p0) REVERT: K 22 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8312 (tt0) REVERT: L 43 ARG cc_start: 0.7866 (tpp80) cc_final: 0.7541 (tpt-90) REVERT: H 48 GLU cc_start: 0.8136 (pt0) cc_final: 0.7340 (tm-30) REVERT: H 111 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7961 (pm20) REVERT: I 113 ARG cc_start: 0.7587 (mmp80) cc_final: 0.7353 (mmp80) REVERT: E 230 TRP cc_start: 0.8205 (OUTLIER) cc_final: 0.5947 (t60) REVERT: B 424 ARG cc_start: 0.7618 (tmm-80) cc_final: 0.6875 (tmm-80) REVERT: B 425 HIS cc_start: 0.8172 (OUTLIER) cc_final: 0.6885 (m90) REVERT: B 557 MET cc_start: 0.8022 (pmm) cc_final: 0.7622 (pp-130) outliers start: 42 outliers final: 25 residues processed: 212 average time/residue: 0.6894 time to fit residues: 166.0169 Evaluate side-chains 208 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 689 ASN Chi-restraints excluded: chain A residue 1058 TRP Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain H residue 26 LYS Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 143 MET Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 560 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 161 optimal weight: 0.0570 chunk 102 optimal weight: 0.0270 chunk 258 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 chunk 92 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 209 optimal weight: 3.9990 chunk 72 optimal weight: 0.1980 chunk 116 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.101509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.067462 restraints weight = 53307.927| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.50 r_work: 0.2952 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 24487 Z= 0.103 Angle : 0.553 12.443 33297 Z= 0.292 Chirality : 0.041 0.197 3746 Planarity : 0.004 0.061 4057 Dihedral : 15.087 88.950 3833 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.23 % Allowed : 13.64 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.16), residues: 2805 helix: 1.30 (0.18), residues: 902 sheet: -0.86 (0.23), residues: 511 loop : -1.39 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 8 TYR 0.015 0.001 TYR B 495 PHE 0.040 0.001 PHE A 572 TRP 0.019 0.001 TRP A1058 HIS 0.009 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (24473) covalent geometry : angle 0.54417 / 0.29 (33285) hydrogen bonds : bond 0.03347 / 3.59 ( 872) hydrogen bonds : angle 4.26299 / 5.39 ( 2439) metal coordination : bond 0.00466 / 0.45 ( 14) metal coordination : angle 5.25748 / 7.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 TYR cc_start: 0.8164 (t80) cc_final: 0.7921 (t80) REVERT: A 673 PHE cc_start: 0.8119 (m-80) cc_final: 0.7730 (m-80) REVERT: A 846 ASP cc_start: 0.8103 (t0) cc_final: 0.7670 (t70) REVERT: A 1010 TYR cc_start: 0.6802 (t80) cc_final: 0.5952 (t80) REVERT: F 88 MET cc_start: 0.8652 (mmt) cc_final: 0.8147 (mmt) REVERT: F 103 LYS cc_start: 0.8853 (mmmt) cc_final: 0.8331 (mmmm) REVERT: F 110 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.8995 (mt) REVERT: F 129 ASP cc_start: 0.8598 (p0) cc_final: 0.7946 (p0) REVERT: K 22 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8393 (tt0) REVERT: L 43 ARG cc_start: 0.7830 (tpp80) cc_final: 0.7486 (tpt-90) REVERT: H 48 GLU cc_start: 0.8085 (pt0) cc_final: 0.7368 (tm-30) REVERT: H 111 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7906 (pm20) REVERT: I 100 PHE cc_start: 0.5968 (m-80) cc_final: 0.5245 (m-80) REVERT: E 230 TRP cc_start: 0.8157 (OUTLIER) cc_final: 0.5892 (t60) REVERT: B 424 ARG cc_start: 0.7657 (tmm-80) cc_final: 0.6980 (tmm-80) REVERT: B 425 HIS cc_start: 0.8093 (OUTLIER) cc_final: 0.6769 (m90) outliers start: 31 outliers final: 15 residues processed: 220 average time/residue: 0.6717 time to fit residues: 167.6843 Evaluate side-chains 201 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 689 ASN Chi-restraints excluded: chain A residue 1058 TRP Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain F residue 72 ARG Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain H residue 26 LYS Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 560 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 7 optimal weight: 0.0770 chunk 251 optimal weight: 5.9990 chunk 250 optimal weight: 0.8980 chunk 168 optimal weight: 5.9990 chunk 237 optimal weight: 0.4980 chunk 135 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 202 optimal weight: 0.9980 chunk 85 optimal weight: 0.0050 chunk 184 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.4952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 HIS ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.101554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.068410 restraints weight = 53488.089| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.73 r_work: 0.2935 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 24487 Z= 0.107 Angle : 0.573 12.747 33297 Z= 0.300 Chirality : 0.041 0.178 3746 Planarity : 0.004 0.103 4057 Dihedral : 15.034 89.864 3833 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.27 % Allowed : 14.00 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.16), residues: 2805 helix: 1.41 (0.18), residues: 902 sheet: -0.78 (0.24), residues: 502 loop : -1.33 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 106 TYR 0.014 0.001 TYR B 495 PHE 0.063 0.001 PHE E 143 TRP 0.018 0.001 TRP A1058 HIS 0.010 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (24473) covalent geometry : angle 0.56534 / 0.30 (33285) hydrogen bonds : bond 0.03312 / 3.56 ( 872) hydrogen bonds : angle 4.22111 / 5.30 ( 2439) metal coordination : bond 0.00426 / 0.42 ( 14) metal coordination : angle 5.02376 / 6.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 TYR cc_start: 0.5821 (m-80) cc_final: 0.5209 (m-80) REVERT: A 673 PHE cc_start: 0.8050 (m-80) cc_final: 0.7706 (m-80) REVERT: A 674 MET cc_start: 0.7818 (ptt) cc_final: 0.7556 (ptt) REVERT: A 846 ASP cc_start: 0.8073 (t0) cc_final: 0.7668 (t70) REVERT: A 1010 TYR cc_start: 0.6755 (t80) cc_final: 0.5939 (t80) REVERT: F 88 MET cc_start: 0.8618 (mmt) cc_final: 0.8164 (mmt) REVERT: F 96 ASP cc_start: 0.8261 (t0) cc_final: 0.7850 (t0) REVERT: F 129 ASP cc_start: 0.8728 (p0) cc_final: 0.7954 (p0) REVERT: L 43 ARG cc_start: 0.7574 (tpp80) cc_final: 0.7303 (tpt-90) REVERT: H 48 GLU cc_start: 0.7951 (pt0) cc_final: 0.7316 (tm-30) REVERT: H 111 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7931 (pm20) REVERT: I 100 PHE cc_start: 0.5452 (m-80) cc_final: 0.5177 (m-80) REVERT: E 230 TRP cc_start: 0.8155 (OUTLIER) cc_final: 0.5900 (t60) REVERT: B 424 ARG cc_start: 0.7618 (tmm-80) cc_final: 0.6897 (tmm-80) REVERT: B 425 HIS cc_start: 0.8095 (OUTLIER) cc_final: 0.6692 (m90) outliers start: 32 outliers final: 16 residues processed: 218 average time/residue: 0.6679 time to fit residues: 165.2903 Evaluate side-chains 202 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 689 ASN Chi-restraints excluded: chain A residue 1058 TRP Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain H residue 26 LYS Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 560 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 258 optimal weight: 4.9990 chunk 153 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 170 optimal weight: 5.9990 chunk 206 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 249 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN H 35 HIS ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.099494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.065697 restraints weight = 53309.513| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.59 r_work: 0.2891 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 24487 Z= 0.223 Angle : 0.660 12.632 33297 Z= 0.346 Chirality : 0.045 0.192 3746 Planarity : 0.005 0.101 4057 Dihedral : 15.124 89.062 3833 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.23 % Allowed : 14.59 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.16), residues: 2805 helix: 1.19 (0.18), residues: 909 sheet: -0.76 (0.24), residues: 487 loop : -1.40 (0.16), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 106 TYR 0.023 0.002 TYR B 804 PHE 0.041 0.002 PHE A 572 TRP 0.019 0.002 TRP B 576 HIS 0.052 0.002 HIS A 419 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.22 (24473) covalent geometry : angle 0.65238 / 0.35 (33285) hydrogen bonds : bond 0.04370 / 4.68 ( 872) hydrogen bonds : angle 4.38974 / 5.48 ( 2439) metal coordination : bond 0.00822 / 0.82 ( 14) metal coordination : angle 5.34287 / 7.31 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5610 Ramachandran restraints generated. 2805 Oldfield, 0 Emsley, 2805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 185 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 423 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7626 (mt) REVERT: A 673 PHE cc_start: 0.8266 (m-80) cc_final: 0.7811 (m-80) REVERT: A 674 MET cc_start: 0.8210 (ptt) cc_final: 0.7963 (ptt) REVERT: A 846 ASP cc_start: 0.8152 (t0) cc_final: 0.7711 (t70) REVERT: A 1010 TYR cc_start: 0.6928 (t80) cc_final: 0.6074 (t80) REVERT: A 1141 LYS cc_start: 0.7712 (tppt) cc_final: 0.7237 (tppp) REVERT: F 88 MET cc_start: 0.8663 (mmt) cc_final: 0.8236 (mmt) REVERT: F 129 ASP cc_start: 0.8779 (p0) cc_final: 0.8023 (p0) REVERT: L 43 ARG cc_start: 0.7842 (tpp80) cc_final: 0.7516 (tpt-90) REVERT: H 48 GLU cc_start: 0.8105 (pt0) cc_final: 0.7448 (tm-30) REVERT: H 111 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7940 (pm20) REVERT: I 100 PHE cc_start: 0.5379 (m-80) cc_final: 0.5022 (m-80) REVERT: E 230 TRP cc_start: 0.8218 (OUTLIER) cc_final: 0.5977 (t60) REVERT: B 424 ARG cc_start: 0.7696 (tmm-80) cc_final: 0.7338 (tmm-80) REVERT: B 425 HIS cc_start: 0.8177 (OUTLIER) cc_final: 0.7018 (m90) outliers start: 31 outliers final: 18 residues processed: 206 average time/residue: 0.6573 time to fit residues: 153.8740 Evaluate side-chains 199 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 689 ASN Chi-restraints excluded: chain A residue 1058 TRP Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain H residue 7 MET Chi-restraints excluded: chain H residue 26 LYS Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 143 MET Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 560 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 1 optimal weight: 30.0000 chunk 213 optimal weight: 4.9990 chunk 281 optimal weight: 0.9990 chunk 250 optimal weight: 0.9990 chunk 234 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 259 optimal weight: 0.7980 chunk 255 optimal weight: 1.9990 chunk 237 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 117 optimal weight: 0.4980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 HIS ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 GLN F 84 ASN ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3763 r_free = 0.3763 target = 0.100660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.066322 restraints weight = 53122.004| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.50 r_work: 0.2924 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24487 Z= 0.121 Angle : 0.604 12.656 33297 Z= 0.315 Chirality : 0.042 0.176 3746 Planarity : 0.004 0.096 4057 Dihedral : 15.085 89.050 3833 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.11 % Allowed : 14.99 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.16), residues: 2805 helix: 1.31 (0.18), residues: 908 sheet: -0.71 (0.24), residues: 491 loop : -1.35 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 106 TYR 0.023 0.001 TYR A 890 PHE 0.043 0.002 PHE A 572 TRP 0.014 0.001 TRP A1058 HIS 0.012 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (24473) covalent geometry : angle 0.59541 / 0.31 (33285) hydrogen bonds : bond 0.03711 / 3.96 ( 872) hydrogen bonds : angle 4.31184 / 5.44 ( 2439) metal coordination : bond 0.00488 / 0.49 ( 14) metal coordination : angle 5.30374 / 7.12 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7652.14 seconds wall clock time: 130 minutes 56.24 seconds (7856.24 seconds total)