Starting phenix.real_space_refine on Mon May 4 22:24:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k12_61962/05_2026/9k12_61962.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k12_61962/05_2026/9k12_61962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k12_61962/05_2026/9k12_61962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k12_61962/05_2026/9k12_61962.map" model { file = "/net/cci-nas-00/data/ceres_data/9k12_61962/05_2026/9k12_61962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k12_61962/05_2026/9k12_61962.cif" } resolution = 3.46 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= 0.002 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 60 5.49 5 Mg 1 5.21 5 S 141 5.16 5 C 14832 2.51 5 N 4162 2.21 5 O 4611 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23813 Number of models: 1 Model: "" Number of chains: 18 Chain: "T" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 465 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain breaks: 1 Chain: "N" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 537 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "P" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 237 Classifications: {'RNA': 11} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 4} Link IDs: {'rna3p': 10} Chain: "A" Number of atoms: 6615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 845, 6615 Classifications: {'peptide': 845} Link IDs: {'PTRANS': 27, 'TRANS': 817} 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: 7652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7652 Classifications: {'peptide': 966} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 36, 'TRANS': 929} Chain breaks: 6 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6343 SG CYS A 989 19.641 72.266 31.708 1.00138.43 S ATOM 6450 SG CYS A1004 22.854 74.353 31.358 1.00127.19 S ATOM 8559 SG CYS C 90 78.770 42.012 139.334 1.00148.70 S ATOM 8578 SG CYS C 93 80.508 40.065 136.592 1.00173.19 S ATOM 8617 SG CYS C 99 78.988 38.097 139.449 1.00140.63 S ATOM 8643 SG CYS C 102 76.891 39.751 136.802 1.00129.21 S ATOM 10825 SG CYS J 7 49.960 43.621 119.215 1.00 96.32 S ATOM 10849 SG CYS J 10 49.131 44.444 122.832 1.00 94.32 S ATOM 11115 SG CYS J 44 46.647 45.529 120.067 1.00 96.58 S ATOM 11121 SG CYS J 45 47.256 41.839 121.124 1.00 93.08 S ATOM 12213 SG CYS L 12 77.175 14.846 95.325 1.00112.28 S ATOM 12231 SG CYS L 15 76.949 11.542 97.110 1.00118.25 S ATOM 12333 SG CYS L 29 79.920 12.275 94.796 1.00116.83 S ATOM 12359 SG CYS L 32 76.225 11.495 93.643 1.00124.40 S ATOM 13702 SG CYS I 7 28.398 44.313 19.846 1.00 87.16 S ATOM 13887 SG CYS I 29 32.578 45.862 19.379 1.00103.65 S ATOM 13912 SG CYS I 32 30.975 44.258 17.446 1.00 84.67 S Time building chain proxies: 5.17, per 1000 atoms: 0.22 Number of scatterers: 23813 At special positions: 0 Unit cell: (116.07, 135.78, 163.155, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 141 16.00 P 60 15.00 Mg 1 11.99 O 4611 8.00 N 4162 7.00 C 14832 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: 1.98 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" ND1 HIS A 938 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A 940 " pdb="ZN ZN A3001 " - pdb=" SG CYS A 989 " pdb="ZN ZN A3001 " - pdb=" SG CYS A1004 " pdb=" ZN C 400 " pdb="ZN ZN C 400 " - pdb=" SG CYS C 93 " pdb="ZN ZN C 400 " - pdb=" SG CYS C 102 " pdb="ZN ZN C 400 " - pdb=" SG CYS C 99 " pdb="ZN ZN C 400 " - pdb=" SG CYS C 90 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb=" ZN J 200 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 15 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 32 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 12 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 29 " Number of angles added : 20 5598 Ramachandran restraints generated. 2799 Oldfield, 0 Emsley, 2799 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5350 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 36 sheets defined 34.7% alpha, 19.6% beta 18 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 3.14 Creating SS restraints... Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 359 through 369 Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 442 through 447 removed outlier: 3.595A pdb=" N LEU A 446 " --> pdb=" O MET A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 473 Processing helix chain 'A' and resid 492 through 505 Processing helix chain 'A' and resid 509 through 518 removed outlier: 3.563A pdb=" N MET A 518 " --> pdb=" O GLN A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 547 through 549 No H-bonds generated for 'chain 'A' and resid 547 through 549' Processing helix chain 'A' and resid 576 through 589 Processing helix chain 'A' and resid 595 through 613 Proline residue: A 606 - end of helix Processing helix chain 'A' and resid 620 through 624 Processing helix chain 'A' and resid 627 through 650 removed outlier: 4.878A pdb=" N SER A 643 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Proline residue: A 644 - end of helix removed outlier: 3.654A pdb=" N SER A 647 " --> pdb=" O SER A 643 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A 648 " --> pdb=" O PRO A 644 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A 650 " --> pdb=" O VAL A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 675 removed outlier: 3.788A pdb=" N ASN A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 682 removed outlier: 3.781A pdb=" N ARG A 681 " --> pdb=" O SER A 677 " (cutoff:3.500A) removed outlier: 3.926A 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: 3.703A pdb=" N LYS A 694 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU A 695 " --> pdb=" O ALA A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 729 removed outlier: 4.151A pdb=" N VAL A 718 " --> pdb=" O THR A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 771 Processing helix chain 'A' and resid 773 through 786 removed outlier: 3.578A pdb=" N VAL A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 847 removed outlier: 3.625A pdb=" N LEU A 831 " --> pdb=" O PRO A 827 " (cutoff:3.500A) Proline residue: A 839 - end of helix Processing helix chain 'A' and resid 848 through 863 removed outlier: 3.502A pdb=" N VAL A 861 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 891 through 904 Processing helix chain 'A' and resid 942 through 949 removed outlier: 4.083A pdb=" N LEU A 946 " --> pdb=" O ASN A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 970 removed outlier: 3.734A pdb=" N ALA A 963 " --> pdb=" O ARG A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 979 removed outlier: 4.101A pdb=" N PHE A 978 " --> pdb=" O ALA A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1027 removed outlier: 3.626A pdb=" N THR A1020 " --> pdb=" O ASP A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1095 removed outlier: 3.612A pdb=" N ARG A1089 " --> pdb=" O GLY A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1120 Processing helix chain 'A' and resid 1120 through 1140 removed outlier: 3.957A pdb=" N VAL A1139 " --> pdb=" O SER A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1156 removed outlier: 4.087A pdb=" N ILE A1148 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A1156 " --> pdb=" O ALA A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1173 Processing helix chain 'C' and resid 30 through 44 removed outlier: 3.712A pdb=" N ALA C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 73 removed outlier: 3.556A pdb=" N ILE C 67 " --> pdb=" O ASN C 63 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 73 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 180 Processing helix chain 'C' and resid 204 through 214 Processing helix chain 'C' and resid 241 through 250 Processing helix chain 'C' and resid 276 through 295 removed outlier: 3.779A pdb=" N VAL C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 83 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 18 through 27 Processing helix chain 'J' and resid 30 through 37 Processing helix chain 'J' and resid 42 through 50 removed outlier: 3.603A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 62 Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.931A 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: 3.930A pdb=" N HIS E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 71 removed outlier: 3.570A pdb=" N PHE E 66 " --> pdb=" O SER E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 116 removed outlier: 3.690A pdb=" N ILE E 108 " --> pdb=" O LYS E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 140 removed outlier: 3.509A pdb=" N LEU E 137 " --> pdb=" O THR E 133 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS E 138 " --> pdb=" O ASP E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 156 removed outlier: 3.952A pdb=" N LEU E 156 " --> pdb=" O THR E 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 153 through 156' Processing helix chain 'E' and resid 158 through 162 removed outlier: 3.768A pdb=" N HIS E 162 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 184 removed outlier: 3.515A pdb=" N GLN E 182 " --> pdb=" O ALA E 178 " (cutoff:3.500A) removed outlier: 3.695A 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 17 through 20 Processing helix chain 'B' and resid 21 through 41 Processing helix chain 'B' and resid 43 through 56 Processing helix chain 'B' and resid 56 through 65 Processing helix chain 'B' and resid 111 through 119 Processing helix chain 'B' and resid 239 through 242 Processing helix chain 'B' and resid 275 through 283 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 300 through 318 removed outlier: 3.738A pdb=" N THR B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 336 Processing helix chain 'B' and resid 345 through 354 Processing helix chain 'B' and resid 360 through 380 Processing helix chain 'B' and resid 390 through 392 No H-bonds generated for 'chain 'B' and resid 390 through 392' Processing helix chain 'B' and resid 398 through 428 removed outlier: 3.550A pdb=" N VAL B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ARG B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N HIS B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 439 removed outlier: 3.803A pdb=" N TYR B 438 " --> pdb=" O PRO B 434 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 439 " --> pdb=" O ILE B 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 434 through 439' Processing helix chain 'B' and resid 441 through 455 removed outlier: 4.144A pdb=" N THR B 445 " --> pdb=" O ALA B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 486 removed outlier: 3.792A pdb=" N LEU B 486 " --> pdb=" O SER B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 552 removed outlier: 3.925A pdb=" N PHE B 549 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP B 550 " --> pdb=" O GLU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 595 removed outlier: 3.526A pdb=" N PHE B 586 " --> pdb=" O ASP B 582 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA B 588 " --> pdb=" O ASP B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 652 Processing helix chain 'B' and resid 660 through 664 Processing helix chain 'B' and resid 672 through 679 Processing helix chain 'B' and resid 688 through 693 Processing helix chain 'B' and resid 702 through 706 removed outlier: 3.915A 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: 3.925A 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 788 through 793 Processing helix chain 'B' and resid 943 through 945 No H-bonds generated for 'chain 'B' and resid 943 through 945' Processing helix chain 'B' and resid 946 through 951 removed outlier: 3.560A pdb=" N ARG B 950 " --> pdb=" O ALA B 946 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN B 951 " --> pdb=" O PHE B 947 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 946 through 951' Processing helix chain 'B' and resid 952 through 966 removed outlier: 4.506A pdb=" N LEU B 956 " --> pdb=" O THR B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1004 removed outlier: 3.521A pdb=" N ILE B 997 " --> pdb=" O SER B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1045 removed outlier: 3.695A pdb=" N VAL B1045 " --> pdb=" O SER B1041 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 338 through 342 removed outlier: 3.905A pdb=" N GLN A 424 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE A 411 " --> pdb=" O PHE A 458 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 458 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 342 removed outlier: 3.905A pdb=" N GLN A 424 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE A 411 " --> pdb=" O PHE A 458 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 458 " --> pdb=" O PHE A 411 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A 323 " --> pdb=" O ARG B1048 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 350 through 354 removed outlier: 6.523A pdb=" N ARG A 403 " --> pdb=" O CYS A 372 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N CYS A 372 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR A 375 " --> pdb=" O TYR A 382 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN A 377 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR A 380 " --> pdb=" O GLN A 377 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 507 through 508 Processing sheet with id=AA5, first strand: chain 'A' and resid 529 through 531 removed outlier: 6.979A pdb=" N VAL H 92 " --> pdb=" O VAL A 530 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 555 through 556 removed outlier: 3.576A pdb=" N VAL A 562 " --> pdb=" O CYS A 555 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 703 through 704 removed outlier: 3.504A pdb=" N GLY A 703 " --> pdb=" O VAL A 741 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 789 through 791 removed outlier: 6.911A pdb=" N VAL A 797 " --> pdb=" O VAL A 806 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1043 through 1049 Processing sheet with id=AB1, first strand: chain 'A' and resid 906 through 907 removed outlier: 7.094A pdb=" N VAL A 906 " --> pdb=" O ILE A1037 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 981 through 986 removed outlier: 3.501A pdb=" N ASN A 982 " --> pdb=" O SER A1008 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N SER A1009 " --> pdb=" O LEU A 935 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU A 935 " --> pdb=" O SER A1009 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLU A 914 " --> pdb=" O HIS A 940 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N VAL A 913 " --> pdb=" O GLU I 47 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N GLU I 47 " --> pdb=" O VAL A 913 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N PHE A 915 " --> pdb=" O ARG I 45 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG I 45 " --> pdb=" O PHE A 915 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL A 917 " --> pdb=" O VAL I 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1227 through 1230 removed outlier: 4.070A pdb=" N GLU A1228 " --> pdb=" O ARG F 115 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG F 115 " --> pdb=" O GLU A1228 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A1230 " --> pdb=" O THR F 113 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR F 113 " --> pdb=" O LEU A1230 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 11 through 18 removed outlier: 6.080A pdb=" N VAL C 12 " --> pdb=" O ARG C 27 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ARG C 27 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ILE C 14 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLU C 25 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR C 21 " --> pdb=" O LYS C 18 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR C 184 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 11 through 18 removed outlier: 6.080A pdb=" N VAL C 12 " --> pdb=" O ARG C 27 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ARG C 27 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ILE C 14 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLU C 25 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR C 21 " --> pdb=" O LYS C 18 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU C 190 " --> pdb=" O LYS C 261 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 126 through 127 removed outlier: 6.081A pdb=" N GLU C 161 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL C 57 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LYS C 163 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ILE C 55 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ARG C 165 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL C 53 " --> pdb=" O ARG C 165 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE C 167 " --> pdb=" O ASP C 51 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL L 46 " --> pdb=" O ILE C 55 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 118 through 120 removed outlier: 3.765A 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 223 removed outlier: 3.617A pdb=" N ASP C 221 " --> pdb=" O VAL C 230 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL C 230 " --> pdb=" O ASP C 221 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP C 223 " --> pdb=" O GLN C 228 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN C 228 " --> pdb=" O ASP C 223 " (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 removed outlier: 6.476A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N HIS K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 18 through 19 removed outlier: 3.625A pdb=" N LEU B 884 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N VAL B 882 " --> pdb=" O LYS L 39 " (cutoff:3.500A) removed outlier: 9.385A pdb=" N GLY B 877 " --> pdb=" O VAL B 901 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N VAL B 901 " --> pdb=" O GLY B 877 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL B 879 " --> pdb=" O ARG B 899 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG B 899 " --> pdb=" O VAL B 879 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS B 881 " --> pdb=" O SER B 897 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 18 through 19 removed outlier: 3.625A pdb=" N LEU B 884 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N VAL B 882 " --> pdb=" O LYS L 39 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 138 through 139 removed outlier: 5.862A pdb=" N LEU H 97 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N SER H 115 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU H 119 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU H 120 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N MET H 39 " --> pdb=" O SER H 34 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER H 34 " --> pdb=" O MET H 39 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ARG H 29 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU H 17 " --> pdb=" O ARG H 29 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLU H 31 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR H 33 " --> pdb=" O VAL H 13 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG H 144 " --> pdb=" O THR H 59 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 14 through 16 Processing sheet with id=AC5, first strand: chain 'I' and resid 86 through 89 Processing sheet with id=AC6, first strand: chain 'E' and resid 94 through 96 removed outlier: 6.788A pdb=" N LYS E 94 " --> pdb=" O ILE E 125 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL E 127 " --> pdb=" O LYS E 94 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL E 96 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU E 124 " --> pdb=" O GLU E 148 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N PHE E 150 " --> pdb=" O LEU E 124 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU E 126 " --> pdb=" O PHE E 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 169 through 170 removed outlier: 4.274A pdb=" N TYR E 223 " --> pdb=" O TYR E 215 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 68 through 70 removed outlier: 3.646A pdb=" N MET B 68 " --> pdb=" O VAL B 89 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 91 through 96 removed outlier: 4.830A pdb=" N GLU B 93 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN B 129 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ALA B 124 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARG B 169 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N MET B 126 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE B 167 " --> pdb=" O MET B 126 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 163 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AD2, first strand: chain 'B' and resid 204 through 206 Processing sheet with id=AD3, first strand: chain 'B' and resid 394 through 397 removed outlier: 6.537A pdb=" N ALA B 215 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 224 through 226 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 removed outlier: 3.698A pdb=" N CYS B 685 " --> pdb=" O LEU B 628 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 554 through 555 removed outlier: 3.718A pdb=" N VAL B 577 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL B 570 " --> pdb=" O VAL B 577 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N VAL B 579 " --> pdb=" O HIS B 568 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N HIS B 568 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LYS B 569 " --> pdb=" O VAL B 614 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE B 616 " --> pdb=" O LYS B 569 " (cutoff:3.500A) removed outlier: 6.259A 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: 6.847A pdb=" N ILE B 784 " --> pdb=" O TYR B 922 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N GLU B 924 " --> pdb=" O ILE B 784 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N MET B 786 " --> pdb=" O GLU B 924 " (cutoff:3.500A) removed outlier: 4.573A 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: 3.729A pdb=" N ILE B 857 " --> pdb=" O VAL B 869 " (cutoff:3.500A) 878 hydrogen bonds defined for protein. 2460 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 5.21 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7441 1.34 - 1.46: 4028 1.46 - 1.58: 12556 1.58 - 1.70: 116 1.70 - 1.82: 217 Bond restraints: 24358 Sorted by residual: bond pdb=" C1' G P 15 " pdb=" N9 G P 15 " ideal model delta sigma weight residual 1.475 1.384 0.091 1.50e-02 4.44e+03 3.69e+01 bond pdb=" C1' C P 14 " pdb=" N1 C P 14 " ideal model delta sigma weight residual 1.480 1.570 -0.090 1.50e-02 4.44e+03 3.64e+01 bond pdb=" C1' C P 17 " pdb=" N1 C P 17 " ideal model delta sigma weight residual 1.480 1.565 -0.085 1.50e-02 4.44e+03 3.24e+01 bond pdb=" C1' C P 19 " pdb=" N1 C P 19 " ideal model delta sigma weight residual 1.480 1.560 -0.080 1.50e-02 4.44e+03 2.84e+01 bond pdb=" C1' A P 16 " pdb=" N9 A P 16 " ideal model delta sigma weight residual 1.475 1.403 0.072 1.50e-02 4.44e+03 2.32e+01 ... (remaining 24353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 32879 2.92 - 5.84: 194 5.84 - 8.76: 26 8.76 - 11.68: 9 11.68 - 14.60: 1 Bond angle restraints: 33109 Sorted by residual: angle pdb=" C MET A1002 " pdb=" CA MET A1002 " pdb=" CB MET A1002 " ideal model delta sigma weight residual 109.85 115.81 -5.96 1.14e+00 7.69e-01 2.73e+01 angle pdb=" CA GLU B 781 " pdb=" CB GLU B 781 " pdb=" CG GLU B 781 " ideal model delta sigma weight residual 114.10 123.94 -9.84 2.00e+00 2.50e-01 2.42e+01 angle pdb=" CB MET F 83 " pdb=" CG MET F 83 " pdb=" SD MET F 83 " ideal model delta sigma weight residual 112.70 127.30 -14.60 3.00e+00 1.11e-01 2.37e+01 angle pdb=" CB MET H 39 " pdb=" CG MET H 39 " pdb=" SD MET H 39 " ideal model delta sigma weight residual 112.70 124.20 -11.50 3.00e+00 1.11e-01 1.47e+01 angle pdb=" N GLY B 877 " pdb=" CA GLY B 877 " pdb=" C GLY B 877 " ideal model delta sigma weight residual 110.56 115.76 -5.20 1.36e+00 5.41e-01 1.46e+01 ... (remaining 33104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 14076 35.64 - 71.28: 597 71.28 - 106.92: 28 106.92 - 142.56: 2 142.56 - 178.20: 2 Dihedral angle restraints: 14705 sinusoidal: 6446 harmonic: 8259 Sorted by residual: dihedral pdb=" CA MET B 969 " pdb=" C MET B 969 " pdb=" N GLN B 970 " pdb=" CA GLN B 970 " ideal model delta harmonic sigma weight residual -180.00 -157.63 -22.37 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA MET A 405 " pdb=" C MET A 405 " pdb=" N ASP A 406 " pdb=" CA ASP A 406 " ideal model delta harmonic sigma weight residual -180.00 -158.87 -21.13 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA GLN E 118 " pdb=" C GLN E 118 " pdb=" N GLU E 119 " pdb=" CA GLU E 119 " ideal model delta harmonic sigma weight residual 180.00 159.04 20.96 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 14702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2661 0.039 - 0.078: 755 0.078 - 0.117: 274 0.117 - 0.156: 36 0.156 - 0.195: 4 Chirality restraints: 3730 Sorted by residual: chirality pdb=" C1' G P 15 " pdb=" O4' G P 15 " pdb=" C2' G P 15 " pdb=" N9 G P 15 " both_signs ideal model delta sigma weight residual False 2.46 2.26 0.20 2.00e-01 2.50e+01 9.52e-01 chirality pdb=" C1' A P 16 " pdb=" O4' A P 16 " pdb=" C2' A P 16 " pdb=" N9 A P 16 " both_signs ideal model delta sigma weight residual False 2.46 2.29 0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" C1' DG T 20 " pdb=" O4' DG T 20 " pdb=" C2' DG T 20 " pdb=" N9 DG T 20 " both_signs ideal model delta sigma weight residual False 2.42 2.26 0.16 2.00e-01 2.50e+01 6.58e-01 ... (remaining 3727 not shown) Planarity restraints: 4047 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP J 28 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.49e+00 pdb=" C ASP J 28 " -0.040 2.00e-02 2.50e+03 pdb=" O ASP J 28 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR J 29 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 613 " 0.037 5.00e-02 4.00e+02 5.65e-02 5.11e+00 pdb=" N PRO A 614 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 614 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 614 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A1108 " -0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO A1109 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A1109 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A1109 " -0.029 5.00e-02 4.00e+02 ... (remaining 4044 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 116 2.65 - 3.21: 21448 3.21 - 3.77: 35822 3.77 - 4.34: 48861 4.34 - 4.90: 78400 Nonbonded interactions: 184647 Sorted by model distance: nonbonded pdb=" OD1 ASP A 451 " pdb="MG MG A3000 " model vdw 2.087 2.170 nonbonded pdb=" OD1 ASP A 449 " pdb="MG MG A3000 " model vdw 2.242 2.170 nonbonded pdb=" N GLY I 82 " pdb="ZN ZN I 201 " model vdw 2.243 2.310 nonbonded pdb=" N1 DA T 15 " pdb=" N1 DA N 21 " model vdw 2.300 3.200 nonbonded pdb=" C2 DA T 15 " pdb=" C2 DA N 21 " model vdw 2.324 3.640 ... (remaining 184642 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 26.120 Find NCS groups from input model: 0.150 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: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6053 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 24377 Z= 0.177 Angle : 0.694 14.599 33129 Z= 0.385 Chirality : 0.042 0.195 3730 Planarity : 0.004 0.057 4047 Dihedral : 17.861 178.205 9355 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.84 % Allowed : 17.48 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.15), residues: 2799 helix: 0.44 (0.18), residues: 879 sheet: -1.09 (0.23), residues: 488 loop : -1.68 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 8 TYR 0.017 0.001 TYR F 68 PHE 0.019 0.001 PHE F 112 TRP 0.014 0.002 TRP A 855 HIS 0.004 0.001 HIS B 506 Details of bonding type rmsd covalent geometry : bond 0.00344 (24358) covalent geometry : angle 0.68721 (33109) hydrogen bonds : bond 0.20623 ( 893) hydrogen bonds : angle 7.45812 ( 2550) metal coordination : bond 0.00684 ( 19) metal coordination : angle 4.11307 ( 20) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5598 Ramachandran restraints generated. 2799 Oldfield, 0 Emsley, 2799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5598 Ramachandran restraints generated. 2799 Oldfield, 0 Emsley, 2799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 981 MET cc_start: 0.8125 (ppp) cc_final: 0.7637 (tmm) REVERT: C 200 MET cc_start: 0.7968 (mmm) cc_final: 0.7445 (tpp) REVERT: H 93 MET cc_start: 0.6296 (mmp) cc_final: 0.5957 (mmm) REVERT: E 46 MET cc_start: 0.6398 (OUTLIER) cc_final: 0.4567 (ptp) REVERT: E 49 ASP cc_start: 0.4665 (m-30) cc_final: 0.3626 (t70) REVERT: E 125 ILE cc_start: 0.7208 (OUTLIER) cc_final: 0.6875 (mt) REVERT: E 168 HIS cc_start: 0.6072 (m90) cc_final: 0.5771 (m90) REVERT: B 120 MET cc_start: 0.6491 (mmt) cc_final: 0.5711 (mmt) REVERT: B 464 MET cc_start: 0.6384 (tmm) cc_final: 0.5641 (mtt) outliers start: 21 outliers final: 17 residues processed: 165 average time/residue: 0.1626 time to fit residues: 43.4548 Evaluate side-chains 149 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain B residue 225 TRP Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 913 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.5980 chunk 111 optimal weight: 7.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 GLN A 901 ASN ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 GLN F 80 GLN K 51 HIS ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 ASN E 91 ASN ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 773 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.098614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.076679 restraints weight = 102189.433| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 4.99 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24377 Z= 0.189 Angle : 0.661 11.182 33129 Z= 0.347 Chirality : 0.044 0.181 3730 Planarity : 0.005 0.064 4047 Dihedral : 15.656 175.869 3824 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.50 % Allowed : 16.92 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.15), residues: 2799 helix: 0.46 (0.17), residues: 888 sheet: -0.98 (0.23), residues: 478 loop : -1.73 (0.15), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 6 TYR 0.023 0.002 TYR J 43 PHE 0.028 0.002 PHE B 296 TRP 0.012 0.002 TRP B 670 HIS 0.008 0.001 HIS H 42 Details of bonding type rmsd covalent geometry : bond 0.00432 (24358) covalent geometry : angle 0.65382 (33109) hydrogen bonds : bond 0.04949 ( 893) hydrogen bonds : angle 5.28982 ( 2550) metal coordination : bond 0.00747 ( 19) metal coordination : angle 4.02799 ( 20) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5598 Ramachandran restraints generated. 2799 Oldfield, 0 Emsley, 2799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5598 Ramachandran restraints generated. 2799 Oldfield, 0 Emsley, 2799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 133 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 MET cc_start: 0.8549 (mtt) cc_final: 0.8155 (mtt) REVERT: A 405 MET cc_start: 0.8374 (ppp) cc_final: 0.8068 (ppp) REVERT: A 693 ASN cc_start: 0.8056 (m-40) cc_final: 0.7823 (m-40) REVERT: A 858 MET cc_start: 0.7158 (mmm) cc_final: 0.6929 (mmm) REVERT: A 1110 TYR cc_start: 0.7831 (t80) cc_final: 0.7560 (t80) REVERT: A 1166 TYR cc_start: 0.6821 (OUTLIER) cc_final: 0.6384 (m-10) REVERT: H 62 MET cc_start: 0.7821 (tpp) cc_final: 0.7567 (tpp) REVERT: H 93 MET cc_start: 0.7320 (mmp) cc_final: 0.6624 (mmm) REVERT: E 46 MET cc_start: 0.6600 (OUTLIER) cc_final: 0.4750 (ptp) REVERT: E 49 ASP cc_start: 0.5426 (m-30) cc_final: 0.3995 (t70) REVERT: E 171 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7209 (pp) REVERT: E 222 SER cc_start: 0.8853 (OUTLIER) cc_final: 0.8512 (p) REVERT: B 120 MET cc_start: 0.6591 (mmt) cc_final: 0.5929 (mmt) REVERT: B 259 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.7197 (ttt90) REVERT: B 792 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7144 (mt-10) outliers start: 88 outliers final: 50 residues processed: 216 average time/residue: 0.1478 time to fit residues: 51.9476 Evaluate side-chains 177 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 121 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 938 HIS Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1083 GLN Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 265 PHE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain F residue 137 TRP Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 259 ARG Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 873 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 5 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 273 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 214 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 228 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 174 optimal weight: 9.9990 chunk 248 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS ** A 757 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 GLN A1100 HIS ** K 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS E 42 ASN ** B1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.098591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.076215 restraints weight = 102174.894| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 4.33 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24377 Z= 0.144 Angle : 0.588 9.643 33129 Z= 0.309 Chirality : 0.041 0.154 3730 Planarity : 0.004 0.054 4047 Dihedral : 15.517 175.122 3801 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.38 % Allowed : 17.91 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.15), residues: 2799 helix: 0.76 (0.18), residues: 887 sheet: -0.83 (0.23), residues: 481 loop : -1.73 (0.15), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 6 TYR 0.020 0.001 TYR J 43 PHE 0.022 0.002 PHE B 296 TRP 0.015 0.002 TRP B 225 HIS 0.008 0.001 HIS H 42 Details of bonding type rmsd covalent geometry : bond 0.00321 (24358) covalent geometry : angle 0.58098 (33109) hydrogen bonds : bond 0.04492 ( 893) hydrogen bonds : angle 4.94391 ( 2550) metal coordination : bond 0.00636 ( 19) metal coordination : angle 3.80110 ( 20) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5598 Ramachandran restraints generated. 2799 Oldfield, 0 Emsley, 2799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5598 Ramachandran restraints generated. 2799 Oldfield, 0 Emsley, 2799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 131 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 MET cc_start: 0.8581 (mtt) cc_final: 0.8179 (mtt) REVERT: A 858 MET cc_start: 0.7415 (mmm) cc_final: 0.7215 (mmm) REVERT: A 981 MET cc_start: 0.8418 (ppp) cc_final: 0.8044 (ppp) REVERT: A 1110 TYR cc_start: 0.7798 (t80) cc_final: 0.7562 (t80) REVERT: F 115 ARG cc_start: 0.3789 (ptt180) cc_final: 0.3121 (ptt90) REVERT: H 39 MET cc_start: 0.5800 (mmm) cc_final: 0.5580 (mmm) REVERT: H 93 MET cc_start: 0.7457 (mmp) cc_final: 0.6789 (mmm) REVERT: I 97 MET cc_start: 0.5655 (ptm) cc_final: 0.5285 (ptm) REVERT: I 110 HIS cc_start: 0.4851 (OUTLIER) cc_final: 0.3992 (p-80) REVERT: E 49 ASP cc_start: 0.5554 (m-30) cc_final: 0.4098 (t70) REVERT: B 62 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7132 (m-80) REVERT: B 120 MET cc_start: 0.6311 (mmt) cc_final: 0.5772 (mmt) REVERT: B 259 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7224 (ttt90) REVERT: B 792 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7177 (mt-10) outliers start: 85 outliers final: 50 residues processed: 210 average time/residue: 0.1400 time to fit residues: 49.5137 Evaluate side-chains 172 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 118 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 938 HIS Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 137 TRP Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 110 HIS Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 259 ARG Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 752 MET Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 873 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 242 optimal weight: 7.9990 chunk 276 optimal weight: 5.9990 chunk 269 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 212 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 185 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 ASN ** K 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 HIS E 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.097481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.075873 restraints weight = 102645.201| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 4.45 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24377 Z= 0.145 Angle : 0.591 8.939 33129 Z= 0.307 Chirality : 0.042 0.284 3730 Planarity : 0.004 0.054 4047 Dihedral : 15.490 174.236 3797 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.10 % Allowed : 18.07 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.16), residues: 2799 helix: 0.81 (0.18), residues: 894 sheet: -0.80 (0.23), residues: 478 loop : -1.74 (0.15), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 6 TYR 0.022 0.002 TYR J 43 PHE 0.016 0.002 PHE B 296 TRP 0.010 0.001 TRP A 539 HIS 0.005 0.001 HIS A 940 Details of bonding type rmsd covalent geometry : bond 0.00325 (24358) covalent geometry : angle 0.58452 (33109) hydrogen bonds : bond 0.04130 ( 893) hydrogen bonds : angle 4.73033 ( 2550) metal coordination : bond 0.00710 ( 19) metal coordination : angle 3.60481 ( 20) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5598 Ramachandran restraints generated. 2799 Oldfield, 0 Emsley, 2799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5598 Ramachandran restraints generated. 2799 Oldfield, 0 Emsley, 2799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 131 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8149 (pt0) REVERT: A 981 MET cc_start: 0.8416 (ppp) cc_final: 0.8180 (ppp) REVERT: A 1021 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7199 (mt) REVERT: A 1025 CYS cc_start: 0.6840 (OUTLIER) cc_final: 0.6332 (p) REVERT: A 1166 TYR cc_start: 0.6718 (OUTLIER) cc_final: 0.6479 (m-10) REVERT: F 115 ARG cc_start: 0.3891 (ptt180) cc_final: 0.3615 (ptt90) REVERT: H 62 MET cc_start: 0.7508 (tpt) cc_final: 0.7248 (mmm) REVERT: H 93 MET cc_start: 0.7411 (mmp) cc_final: 0.6904 (mmm) REVERT: I 110 HIS cc_start: 0.4694 (OUTLIER) cc_final: 0.3902 (p-80) REVERT: E 49 ASP cc_start: 0.5999 (m-30) cc_final: 0.4435 (t70) REVERT: E 171 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7458 (pp) REVERT: B 225 TRP cc_start: 0.7646 (OUTLIER) cc_final: 0.7272 (m100) REVERT: B 304 THR cc_start: 0.7815 (OUTLIER) cc_final: 0.7589 (p) REVERT: B 473 ASN cc_start: 0.7478 (OUTLIER) cc_final: 0.7263 (m-40) REVERT: B 792 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7245 (mt-10) outliers start: 103 outliers final: 61 residues processed: 228 average time/residue: 0.1317 time to fit residues: 50.9704 Evaluate side-chains 191 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 120 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 938 HIS Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 265 PHE Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 137 TRP Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 110 HIS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 225 TRP Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 752 MET Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 873 HIS Chi-restraints excluded: chain B residue 939 ASP Chi-restraints excluded: chain B residue 982 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 163 optimal weight: 0.6980 chunk 118 optimal weight: 0.0370 chunk 130 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 235 optimal weight: 0.6980 chunk 193 optimal weight: 0.0040 chunk 102 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 277 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.4870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 757 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 HIS ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 GLN ** B1000 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 = 0.4461 r_free = 0.4461 target = 0.099783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.077038 restraints weight = 101054.433| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 3.96 r_work: 0.3790 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 24377 Z= 0.104 Angle : 0.560 13.939 33129 Z= 0.286 Chirality : 0.040 0.145 3730 Planarity : 0.004 0.051 4047 Dihedral : 15.370 173.693 3794 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.19 % Allowed : 19.86 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.16), residues: 2799 helix: 1.18 (0.18), residues: 884 sheet: -0.57 (0.24), residues: 471 loop : -1.57 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 6 TYR 0.019 0.001 TYR A1169 PHE 0.015 0.001 PHE B 296 TRP 0.013 0.001 TRP B 113 HIS 0.006 0.001 HIS H 42 Details of bonding type rmsd covalent geometry : bond 0.00218 (24358) covalent geometry : angle 0.55501 (33109) hydrogen bonds : bond 0.03461 ( 893) hydrogen bonds : angle 4.47295 ( 2550) metal coordination : bond 0.00434 ( 19) metal coordination : angle 3.07790 ( 20) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5598 Ramachandran restraints generated. 2799 Oldfield, 0 Emsley, 2799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5598 Ramachandran restraints generated. 2799 Oldfield, 0 Emsley, 2799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 140 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: symmetry clash REVERT: A 626 MET cc_start: 0.7472 (tpp) cc_final: 0.7160 (tpp) REVERT: A 858 MET cc_start: 0.7460 (mmm) cc_final: 0.6895 (mmm) REVERT: A 981 MET cc_start: 0.8469 (ppp) cc_final: 0.8058 (ppp) REVERT: A 1166 TYR cc_start: 0.6753 (OUTLIER) cc_final: 0.6380 (m-10) REVERT: F 115 ARG cc_start: 0.4094 (ptt180) cc_final: 0.3383 (ptt90) REVERT: H 39 MET cc_start: 0.5676 (mmm) cc_final: 0.5306 (mmm) REVERT: H 57 LYS cc_start: 0.6497 (OUTLIER) cc_final: 0.5531 (mmpt) REVERT: H 62 MET cc_start: 0.7518 (tpt) cc_final: 0.7157 (mmm) REVERT: H 93 MET cc_start: 0.7766 (mmp) cc_final: 0.7282 (mmm) REVERT: I 110 HIS cc_start: 0.5423 (OUTLIER) cc_final: 0.4888 (p-80) REVERT: E 49 ASP cc_start: 0.5837 (m-30) cc_final: 0.3846 (t70) REVERT: E 171 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7614 (pp) REVERT: B 225 TRP cc_start: 0.7724 (OUTLIER) cc_final: 0.7454 (m100) REVERT: B 259 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6669 (ttt-90) REVERT: B 792 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7411 (mt-10) outliers start: 55 outliers final: 28 residues processed: 192 average time/residue: 0.1472 time to fit residues: 46.2750 Evaluate side-chains 158 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 265 PHE Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 137 TRP Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 110 HIS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 225 TRP Chi-restraints excluded: chain B residue 259 ARG Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 873 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 207 optimal weight: 8.9990 chunk 255 optimal weight: 8.9990 chunk 220 optimal weight: 5.9990 chunk 87 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 102 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 280 optimal weight: 9.9990 chunk 229 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 GLN A 546 GLN ** A 757 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 HIS ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN B 413 HIS B 481 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.097319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.075734 restraints weight = 102187.540| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 4.22 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24377 Z= 0.143 Angle : 0.586 10.782 33129 Z= 0.302 Chirality : 0.041 0.150 3730 Planarity : 0.004 0.056 4047 Dihedral : 15.388 172.516 3794 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.91 % Allowed : 19.35 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.16), residues: 2799 helix: 1.07 (0.18), residues: 889 sheet: -0.57 (0.23), residues: 478 loop : -1.65 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 6 TYR 0.023 0.001 TYR J 43 PHE 0.039 0.002 PHE F 112 TRP 0.009 0.001 TRP A 855 HIS 0.004 0.001 HIS B 45 Details of bonding type rmsd covalent geometry : bond 0.00328 (24358) covalent geometry : angle 0.58004 (33109) hydrogen bonds : bond 0.03932 ( 893) hydrogen bonds : angle 4.45363 ( 2550) metal coordination : bond 0.00731 ( 19) metal coordination : angle 3.42682 ( 20) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5598 Ramachandran restraints generated. 2799 Oldfield, 0 Emsley, 2799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5598 Ramachandran restraints generated. 2799 Oldfield, 0 Emsley, 2799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 127 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 626 MET cc_start: 0.7234 (tpp) cc_final: 0.7013 (tpp) REVERT: A 981 MET cc_start: 0.8413 (ppp) cc_final: 0.8147 (ppp) REVERT: A 1166 TYR cc_start: 0.6637 (OUTLIER) cc_final: 0.6245 (m-10) REVERT: F 115 ARG cc_start: 0.4230 (ptt180) cc_final: 0.3461 (ptt90) REVERT: H 57 LYS cc_start: 0.6407 (OUTLIER) cc_final: 0.5511 (mmpt) REVERT: H 62 MET cc_start: 0.7726 (tpt) cc_final: 0.6266 (mmm) REVERT: H 93 MET cc_start: 0.7508 (mmp) cc_final: 0.6875 (mmm) REVERT: I 112 TRP cc_start: 0.7220 (t60) cc_final: 0.6903 (p90) REVERT: E 49 ASP cc_start: 0.5339 (m-30) cc_final: 0.4096 (t70) REVERT: E 171 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7553 (pp) REVERT: B 225 TRP cc_start: 0.7789 (OUTLIER) cc_final: 0.7475 (m100) REVERT: B 259 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6734 (ttt-90) REVERT: B 473 ASN cc_start: 0.7495 (OUTLIER) cc_final: 0.7287 (m-40) REVERT: B 605 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7140 (tp) REVERT: B 792 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7187 (mt-10) outliers start: 73 outliers final: 48 residues processed: 197 average time/residue: 0.1417 time to fit residues: 46.5550 Evaluate side-chains 176 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 120 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 265 PHE Chi-restraints excluded: chain F residue 59 ARG Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 137 TRP Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 225 TRP Chi-restraints excluded: chain B residue 259 ARG Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 873 HIS Chi-restraints excluded: chain B residue 939 ASP Chi-restraints excluded: chain B residue 987 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 88 optimal weight: 6.9990 chunk 68 optimal weight: 0.0050 chunk 105 optimal weight: 0.9990 chunk 159 optimal weight: 0.0040 chunk 93 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 202 optimal weight: 0.9980 chunk 181 optimal weight: 0.5980 chunk 193 optimal weight: 0.3980 chunk 3 optimal weight: 10.0000 chunk 255 optimal weight: 0.0570 overall best weight: 0.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 757 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 HIS ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1039 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.100123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.077467 restraints weight = 102035.127| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 3.97 r_work: 0.3795 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 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 : 0.002 0.051 24377 Z= 0.103 Angle : 0.559 10.806 33129 Z= 0.285 Chirality : 0.040 0.158 3730 Planarity : 0.003 0.050 4047 Dihedral : 15.282 172.450 3794 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.07 % Allowed : 20.66 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.16), residues: 2799 helix: 1.24 (0.18), residues: 896 sheet: -0.32 (0.24), residues: 461 loop : -1.57 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 6 TYR 0.015 0.001 TYR H 91 PHE 0.024 0.001 PHE F 112 TRP 0.017 0.001 TRP A 855 HIS 0.013 0.001 HIS I 110 Details of bonding type rmsd covalent geometry : bond 0.00220 (24358) covalent geometry : angle 0.55503 (33109) hydrogen bonds : bond 0.03244 ( 893) hydrogen bonds : angle 4.28221 ( 2550) metal coordination : bond 0.00427 ( 19) metal coordination : angle 2.81553 ( 20) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5598 Ramachandran restraints generated. 2799 Oldfield, 0 Emsley, 2799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5598 Ramachandran restraints generated. 2799 Oldfield, 0 Emsley, 2799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 134 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 626 MET cc_start: 0.7392 (tpp) cc_final: 0.7142 (tpp) REVERT: A 981 MET cc_start: 0.8469 (ppp) cc_final: 0.8108 (ppp) REVERT: A 1166 TYR cc_start: 0.6708 (OUTLIER) cc_final: 0.6498 (m-10) REVERT: C 200 MET cc_start: 0.8203 (mmm) cc_final: 0.7692 (tpp) REVERT: F 115 ARG cc_start: 0.4203 (ptt180) cc_final: 0.3450 (ptt90) REVERT: H 62 MET cc_start: 0.7064 (tpt) cc_final: 0.6532 (mmm) REVERT: H 93 MET cc_start: 0.7779 (mmp) cc_final: 0.7154 (mmm) REVERT: I 97 MET cc_start: 0.5300 (ptm) cc_final: 0.4751 (ppp) REVERT: E 49 ASP cc_start: 0.5471 (m-30) cc_final: 0.4343 (t70) REVERT: E 171 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7387 (pp) REVERT: E 190 LEU cc_start: 0.1153 (OUTLIER) cc_final: 0.0878 (mp) REVERT: B 473 ASN cc_start: 0.7349 (OUTLIER) cc_final: 0.7117 (m-40) REVERT: B 792 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7474 (mt-10) outliers start: 52 outliers final: 31 residues processed: 184 average time/residue: 0.1405 time to fit residues: 42.8372 Evaluate side-chains 165 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 265 PHE Chi-restraints excluded: chain F residue 59 ARG Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 137 TRP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 259 ARG Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 873 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 255 optimal weight: 8.9990 chunk 194 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 213 optimal weight: 9.9990 chunk 112 optimal weight: 0.9990 chunk 163 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 54 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 238 optimal weight: 0.9980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 757 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 HIS ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 ASN ** B1000 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 = 0.4443 r_free = 0.4443 target = 0.098075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.075506 restraints weight = 101575.608| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 3.94 r_work: 0.3771 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 24377 Z= 0.111 Angle : 0.567 10.944 33129 Z= 0.287 Chirality : 0.040 0.220 3730 Planarity : 0.003 0.051 4047 Dihedral : 15.216 171.613 3794 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.15 % Allowed : 20.46 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.16), residues: 2799 helix: 1.24 (0.18), residues: 906 sheet: -0.30 (0.24), residues: 466 loop : -1.57 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 6 TYR 0.017 0.001 TYR J 43 PHE 0.026 0.001 PHE B 36 TRP 0.036 0.001 TRP B 225 HIS 0.006 0.001 HIS A 940 Details of bonding type rmsd covalent geometry : bond 0.00249 (24358) covalent geometry : angle 0.56194 (33109) hydrogen bonds : bond 0.03406 ( 893) hydrogen bonds : angle 4.23657 ( 2550) metal coordination : bond 0.00477 ( 19) metal coordination : angle 3.00802 ( 20) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5598 Ramachandran restraints generated. 2799 Oldfield, 0 Emsley, 2799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5598 Ramachandran restraints generated. 2799 Oldfield, 0 Emsley, 2799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 128 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 626 MET cc_start: 0.7421 (tpp) cc_final: 0.7173 (tpp) REVERT: A 858 MET cc_start: 0.7652 (mmm) cc_final: 0.7433 (mmm) REVERT: A 981 MET cc_start: 0.8496 (ppp) cc_final: 0.8126 (ppp) REVERT: A 1166 TYR cc_start: 0.6697 (OUTLIER) cc_final: 0.6363 (m-10) REVERT: C 200 MET cc_start: 0.8136 (mmm) cc_final: 0.7749 (tpp) REVERT: F 115 ARG cc_start: 0.4283 (ptt180) cc_final: 0.3508 (ptt90) REVERT: H 62 MET cc_start: 0.7084 (tpt) cc_final: 0.6572 (mmm) REVERT: H 93 MET cc_start: 0.7879 (mmp) cc_final: 0.7252 (mmm) REVERT: H 137 GLN cc_start: 0.4564 (OUTLIER) cc_final: 0.4152 (pt0) REVERT: E 49 ASP cc_start: 0.5457 (m-30) cc_final: 0.4311 (t70) REVERT: E 190 LEU cc_start: 0.1397 (OUTLIER) cc_final: 0.1151 (mp) REVERT: B 386 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.7003 (mt-10) REVERT: B 473 ASN cc_start: 0.7453 (OUTLIER) cc_final: 0.7248 (m-40) REVERT: B 605 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7181 (tp) REVERT: B 792 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7436 (mt-10) outliers start: 54 outliers final: 35 residues processed: 179 average time/residue: 0.1422 time to fit residues: 42.1725 Evaluate side-chains 166 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 124 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain F residue 59 ARG Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 137 TRP Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 225 TRP Chi-restraints excluded: chain B residue 259 ARG Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 873 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 163 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 264 optimal weight: 0.9980 chunk 230 optimal weight: 9.9990 chunk 202 optimal weight: 0.0170 chunk 113 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 236 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 224 optimal weight: 8.9990 overall best weight: 2.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 757 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 HIS ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.096194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.074621 restraints weight = 102776.335| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 3.92 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24377 Z= 0.137 Angle : 0.602 11.978 33129 Z= 0.306 Chirality : 0.041 0.181 3730 Planarity : 0.004 0.057 4047 Dihedral : 15.216 170.557 3794 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.11 % Allowed : 20.30 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.16), residues: 2799 helix: 1.16 (0.18), residues: 899 sheet: -0.41 (0.24), residues: 465 loop : -1.55 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 414 TYR 0.023 0.001 TYR J 43 PHE 0.020 0.002 PHE F 112 TRP 0.026 0.002 TRP B 225 HIS 0.006 0.001 HIS H 42 Details of bonding type rmsd covalent geometry : bond 0.00311 (24358) covalent geometry : angle 0.59575 (33109) hydrogen bonds : bond 0.03854 ( 893) hydrogen bonds : angle 4.38199 ( 2550) metal coordination : bond 0.00762 ( 19) metal coordination : angle 3.49887 ( 20) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5598 Ramachandran restraints generated. 2799 Oldfield, 0 Emsley, 2799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5598 Ramachandran restraints generated. 2799 Oldfield, 0 Emsley, 2799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 123 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 626 MET cc_start: 0.7282 (tpp) cc_final: 0.7063 (tpp) REVERT: A 981 MET cc_start: 0.8389 (ppp) cc_final: 0.8169 (ppp) REVERT: A 1166 TYR cc_start: 0.6383 (OUTLIER) cc_final: 0.5973 (m-10) REVERT: C 41 MET cc_start: 0.7690 (mtp) cc_final: 0.7431 (mtm) REVERT: C 200 MET cc_start: 0.8191 (mmm) cc_final: 0.7869 (tpp) REVERT: F 115 ARG cc_start: 0.4522 (ptt180) cc_final: 0.3932 (ptt90) REVERT: H 62 MET cc_start: 0.7037 (tpt) cc_final: 0.6590 (mmm) REVERT: H 93 MET cc_start: 0.7438 (mmp) cc_final: 0.6806 (mmm) REVERT: H 137 GLN cc_start: 0.4638 (OUTLIER) cc_final: 0.4218 (pt0) REVERT: E 46 MET cc_start: 0.7007 (tmm) cc_final: 0.6565 (tmm) REVERT: E 49 ASP cc_start: 0.5462 (m-30) cc_final: 0.4096 (t70) REVERT: E 190 LEU cc_start: 0.1890 (OUTLIER) cc_final: 0.1607 (mp) REVERT: B 473 ASN cc_start: 0.7591 (OUTLIER) cc_final: 0.7388 (m-40) REVERT: B 605 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7202 (tp) REVERT: B 792 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7221 (mt-10) outliers start: 53 outliers final: 39 residues processed: 174 average time/residue: 0.1403 time to fit residues: 41.2862 Evaluate side-chains 166 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 121 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain F residue 59 ARG Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 225 TRP Chi-restraints excluded: chain B residue 259 ARG Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 752 MET Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 873 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 216 optimal weight: 0.2980 chunk 81 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 188 optimal weight: 0.0670 chunk 14 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 249 optimal weight: 2.9990 chunk 33 optimal weight: 0.0070 chunk 120 optimal weight: 0.0570 chunk 105 optimal weight: 0.8980 chunk 227 optimal weight: 6.9990 overall best weight: 0.2654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 757 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 HIS ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1000 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 = 0.4460 r_free = 0.4460 target = 0.098971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.076310 restraints weight = 103293.944| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 4.02 r_work: 0.3788 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 24377 Z= 0.100 Angle : 0.563 11.645 33129 Z= 0.284 Chirality : 0.040 0.166 3730 Planarity : 0.003 0.051 4047 Dihedral : 15.095 170.740 3793 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.59 % Allowed : 20.74 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.16), residues: 2799 helix: 1.36 (0.18), residues: 899 sheet: -0.19 (0.24), residues: 451 loop : -1.45 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 6 TYR 0.016 0.001 TYR H 91 PHE 0.023 0.001 PHE F 112 TRP 0.027 0.001 TRP B 225 HIS 0.005 0.001 HIS H 42 Details of bonding type rmsd covalent geometry : bond 0.00214 (24358) covalent geometry : angle 0.55985 (33109) hydrogen bonds : bond 0.03146 ( 893) hydrogen bonds : angle 4.18177 ( 2550) metal coordination : bond 0.00344 ( 19) metal coordination : angle 2.55022 ( 20) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5598 Ramachandran restraints generated. 2799 Oldfield, 0 Emsley, 2799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5598 Ramachandran restraints generated. 2799 Oldfield, 0 Emsley, 2799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 131 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 626 MET cc_start: 0.7522 (tpp) cc_final: 0.7132 (tpp) REVERT: A 836 MET cc_start: 0.7825 (mmm) cc_final: 0.7546 (mmm) REVERT: A 981 MET cc_start: 0.8488 (ppp) cc_final: 0.8112 (ppp) REVERT: A 1166 TYR cc_start: 0.6498 (OUTLIER) cc_final: 0.6113 (m-10) REVERT: C 200 MET cc_start: 0.8195 (mmm) cc_final: 0.7793 (tpp) REVERT: F 115 ARG cc_start: 0.4403 (ptt180) cc_final: 0.3883 (ptt90) REVERT: H 93 MET cc_start: 0.7901 (mmp) cc_final: 0.7269 (mmm) REVERT: H 137 GLN cc_start: 0.4540 (OUTLIER) cc_final: 0.4175 (pt0) REVERT: E 46 MET cc_start: 0.6967 (tmm) cc_final: 0.6536 (tmm) REVERT: E 49 ASP cc_start: 0.5177 (m-30) cc_final: 0.3977 (t70) REVERT: E 190 LEU cc_start: 0.1587 (OUTLIER) cc_final: 0.1211 (mp) REVERT: B 605 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7136 (tp) REVERT: B 792 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7462 (mt-10) outliers start: 40 outliers final: 31 residues processed: 170 average time/residue: 0.1397 time to fit residues: 39.8337 Evaluate side-chains 161 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain F residue 59 ARG Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 225 TRP Chi-restraints excluded: chain B residue 259 ARG Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 873 HIS Chi-restraints excluded: chain B residue 913 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 245 optimal weight: 4.9990 chunk 276 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 274 optimal weight: 7.9990 chunk 221 optimal weight: 5.9990 chunk 249 optimal weight: 6.9990 chunk 68 optimal weight: 0.3980 chunk 181 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 275 optimal weight: 2.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 757 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 ASN ** K 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.095294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.073846 restraints weight = 103916.906| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 4.03 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24377 Z= 0.171 Angle : 0.646 23.740 33129 Z= 0.324 Chirality : 0.043 0.248 3730 Planarity : 0.004 0.061 4047 Dihedral : 15.203 170.177 3793 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.83 % Allowed : 20.86 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.16), residues: 2799 helix: 1.05 (0.18), residues: 900 sheet: -0.48 (0.24), residues: 459 loop : -1.55 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 797 TYR 0.027 0.002 TYR J 43 PHE 0.016 0.002 PHE F 112 TRP 0.028 0.002 TRP B 225 HIS 0.007 0.001 HIS J 52 Details of bonding type rmsd covalent geometry : bond 0.00393 (24358) covalent geometry : angle 0.63904 (33109) hydrogen bonds : bond 0.04144 ( 893) hydrogen bonds : angle 4.44474 ( 2550) metal coordination : bond 0.01050 ( 19) metal coordination : angle 3.94700 ( 20) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5501.25 seconds wall clock time: 95 minutes 6.26 seconds (5706.26 seconds total)