Starting phenix.real_space_refine on Sat Jul 4 23:20:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k13_61963/07_2026/9k13_61963.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k13_61963/07_2026/9k13_61963.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k13_61963/07_2026/9k13_61963.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k13_61963/07_2026/9k13_61963.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k13_61963/07_2026/9k13_61963.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k13_61963/07_2026/9k13_61963.map" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 44 5.49 5 Mg 1 5.21 5 S 141 5.16 5 C 14675 2.51 5 N 4100 2.21 5 O 4516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 122 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23483 Number of models: 1 Model: "" Number of chains: 18 Chain: "T" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 345 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain breaks: 1 Chain: "N" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 392 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain breaks: 1 Chain: "P" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 171 Classifications: {'RNA': 8} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 4} Link IDs: {'rna3p': 7} Chain: "A" Number of atoms: 6608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 844, 6608 Classifications: {'peptide': 844} Link IDs: {'PTRANS': 26, 'TRANS': 817} Chain breaks: 4 Chain: "C" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2256 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain breaks: 1 Chain: "F" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 660 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 507 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "K" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 890 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "L" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 365 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "H" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1129 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "I" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 787 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 1 Chain: "E" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1706 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 205} Chain: "B" Number of atoms: 7660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 967, 7660 Classifications: {'peptide': 967} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 36, 'TRANS': 930} Chain breaks: 6 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6005 SG CYS A 989 17.677 71.926 30.996 1.00147.34 S ATOM 6112 SG CYS A1004 19.577 75.323 30.604 1.00139.33 S ATOM 8221 SG CYS C 90 81.038 42.535 137.012 1.00115.21 S ATOM 8240 SG CYS C 93 82.546 40.415 134.209 1.00127.14 S ATOM 8279 SG CYS C 99 81.050 38.630 137.180 1.00106.31 S ATOM 8305 SG CYS C 102 78.885 40.397 134.676 1.00 99.34 S ATOM 10487 SG CYS J 7 51.366 43.472 117.908 1.00 38.21 S ATOM 10511 SG CYS J 10 50.546 44.596 121.462 1.00 44.52 S ATOM 10777 SG CYS J 44 48.215 45.552 118.523 1.00 49.70 S ATOM 10783 SG CYS J 45 48.450 42.023 119.987 1.00 47.45 S ATOM 11875 SG CYS L 12 78.640 15.372 92.815 1.00 64.50 S ATOM 11893 SG CYS L 15 78.470 12.109 94.554 1.00 71.88 S ATOM 11995 SG CYS L 29 81.342 12.876 92.052 1.00 62.13 S ATOM 12021 SG CYS L 32 77.600 11.973 91.122 1.00 69.82 S ATOM 13364 SG CYS I 7 26.545 44.441 18.718 1.00 28.57 S ATOM 13549 SG CYS I 29 28.348 47.060 17.456 1.00 26.60 S ATOM 13574 SG CYS I 32 29.267 44.133 16.457 1.00 25.74 S Time building chain proxies: 4.94, per 1000 atoms: 0.21 Number of scatterers: 23483 At special positions: 0 Unit cell: (116.07, 136.875, 162.06, 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 44 15.00 Mg 1 11.99 O 4516 8.00 N 4100 7.00 C 14675 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: 1.93 Conformation dependent library (CDL) restraints added in 1.3 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 10 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 15 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 12 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 32 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 29 " Number of angles added : 20 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 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: 90 helices and 33 sheets defined 35.4% alpha, 18.4% beta 16 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 3.07 Creating SS restraints... Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 359 through 369 removed outlier: 3.570A pdb=" N LEU A 363 " --> pdb=" O ASN A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 442 through 447 Processing helix chain 'A' and resid 462 through 473 Processing helix chain 'A' and resid 492 through 505 removed outlier: 3.523A pdb=" N GLN A 505 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 517 Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 547 through 549 No H-bonds generated for 'chain 'A' and resid 547 through 549' Processing helix chain 'A' and resid 576 through 591 removed outlier: 3.827A pdb=" N GLU A 591 " --> pdb=" O GLY A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 613 Proline residue: A 606 - end of helix removed outlier: 3.619A pdb=" N ASP A 613 " --> pdb=" O MET A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 624 Processing helix chain 'A' and resid 627 through 650 removed outlier: 5.181A pdb=" N SER A 643 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Proline residue: A 644 - end of helix removed outlier: 3.519A pdb=" N SER A 647 " --> pdb=" O SER A 643 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG A 648 " --> pdb=" O PRO A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 675 removed outlier: 3.991A pdb=" N ASN A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 683 Processing helix chain 'A' and resid 689 through 700 removed outlier: 3.809A pdb=" N LYS A 694 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU A 695 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 729 removed outlier: 4.061A 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 787 removed outlier: 3.784A pdb=" N VAL A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 847 Proline residue: A 839 - end of helix Processing helix chain 'A' and resid 848 through 863 Processing helix chain 'A' and resid 891 through 904 Processing helix chain 'A' and resid 942 through 949 removed outlier: 3.581A pdb=" N TRP A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 970 removed outlier: 3.981A pdb=" N ALA A 963 " --> pdb=" O ARG A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 979 removed outlier: 4.232A pdb=" N PHE A 978 " --> pdb=" O ALA A 975 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS A 979 " --> pdb=" O GLU A 976 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 975 through 979' Processing helix chain 'A' and resid 1016 through 1027 removed outlier: 3.637A pdb=" N THR A1020 " --> pdb=" O ASP A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1034 removed outlier: 3.585A pdb=" N VAL A1031 " --> pdb=" O THR A1027 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU A1034 " --> pdb=" O PRO A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1095 Processing helix chain 'A' and resid 1103 through 1107 removed outlier: 3.657A pdb=" N ARG A1106 " --> pdb=" O ASP A1103 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A1107 " --> pdb=" O THR A1104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1103 through 1107' Processing helix chain 'A' and resid 1111 through 1120 Processing helix chain 'A' and resid 1120 through 1138 Processing helix chain 'A' and resid 1144 through 1156 removed outlier: 3.924A pdb=" N ILE A1148 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A1156 " --> pdb=" O ALA A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1173 removed outlier: 3.586A pdb=" N ALA A1171 " --> pdb=" O GLY A1167 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 44 removed outlier: 3.765A pdb=" N ALA C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 73 removed outlier: 3.674A pdb=" N LEU C 73 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 176 through 180 removed outlier: 3.539A pdb=" N SER C 180 " --> pdb=" O ALA C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 201 removed outlier: 3.931A pdb=" N ASP C 201 " --> pdb=" O GLU C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 214 removed outlier: 3.646A pdb=" N SER C 214 " --> pdb=" O ASP C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 251 Processing helix chain 'C' and resid 276 through 295 removed outlier: 3.723A 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 108 Processing helix chain 'F' and resid 129 through 131 No H-bonds generated for 'chain 'F' and resid 129 through 131' Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 39 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.723A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR J 51 " --> pdb=" O ARG J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 62 removed outlier: 3.650A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.918A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG K 52 " --> pdb=" O MET K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'E' and resid 30 through 51 removed outlier: 4.185A pdb=" N HIS E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 71 Processing helix chain 'E' and resid 104 through 116 removed outlier: 3.993A pdb=" N ILE E 108 " --> pdb=" O LYS E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 141 removed outlier: 3.650A pdb=" N LYS E 138 " --> pdb=" O ASP E 134 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU E 141 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 162 removed outlier: 3.682A pdb=" N HIS E 162 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 184 removed outlier: 3.676A pdb=" N GLN E 182 " --> pdb=" O ALA E 178 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE E 183 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 204 Processing helix chain 'B' and resid 21 through 41 Processing helix chain 'B' and resid 43 through 56 removed outlier: 3.541A pdb=" N LEU B 47 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER B 49 " --> pdb=" O HIS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 65 Processing helix chain 'B' and resid 111 through 119 Processing helix chain 'B' and resid 239 through 242 Processing helix chain 'B' and resid 275 through 282 Processing helix chain 'B' and resid 286 through 295 removed outlier: 3.561A pdb=" N ALA B 290 " --> pdb=" O SER B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 318 removed outlier: 3.580A pdb=" N THR B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP B 315 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 3.616A 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: 3.687A pdb=" N VAL B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N HIS B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N HIS B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 455 removed outlier: 3.720A pdb=" N THR B 445 " --> pdb=" O ALA B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 486 removed outlier: 3.520A pdb=" N SER B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 486 " --> pdb=" O SER B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 510 removed outlier: 3.846A pdb=" N TRP B 510 " --> pdb=" O PRO B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 552 removed outlier: 3.780A pdb=" N PHE B 549 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER B 551 " --> pdb=" O LEU B 548 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY B 552 " --> pdb=" O PHE B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 595 removed outlier: 3.924A pdb=" N ALA B 588 " --> pdb=" O ASP B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 636 removed outlier: 4.614A pdb=" N HIS B 634 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS B 635 " --> pdb=" O ASN B 632 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU B 636 " --> pdb=" O LEU B 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 631 through 636' Processing helix chain 'B' and resid 645 through 652 Processing helix chain 'B' and resid 659 through 664 removed outlier: 3.665A pdb=" N GLU B 664 " --> pdb=" O ILE B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 679 removed outlier: 3.603A pdb=" N LEU B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 693 removed outlier: 3.512A pdb=" N PHE B 691 " --> pdb=" O ASP B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 706 removed outlier: 3.789A 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: 3.655A pdb=" N ILE B 732 " --> pdb=" O ASN B 729 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG B 733 " --> pdb=" O PRO B 730 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 729 through 733' Processing helix chain 'B' and resid 751 through 758 Processing helix chain 'B' and resid 788 through 793 Processing helix chain 'B' and resid 925 through 929 Processing helix chain 'B' and resid 946 through 951 removed outlier: 3.715A pdb=" N GLN B 951 " --> pdb=" O PHE B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 953 through 967 Processing helix chain 'B' and resid 993 through 1004 Processing helix chain 'B' and resid 1040 through 1044 Processing sheet with id=AA1, first strand: chain 'B' and resid 1046 through 1048 removed outlier: 4.157A pdb=" N SER A 323 " --> pdb=" O ARG B1048 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE A 322 " --> pdb=" O TYR A 459 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER A 326 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL A 436 " --> pdb=" O ARG A 325 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL A 327 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE A 438 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR A 329 " --> pdb=" O ILE A 438 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 350 through 354 removed outlier: 6.510A pdb=" N ARG A 403 " --> pdb=" O CYS A 372 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N CYS A 372 " --> pdb=" O ARG A 403 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 507 through 508 Processing sheet with id=AA4, first strand: chain 'A' and resid 529 through 531 removed outlier: 5.801A pdb=" N VAL A 529 " --> pdb=" O HIS H 94 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N HIS H 94 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS A 531 " --> pdb=" O VAL H 92 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 529 through 531 removed outlier: 5.801A pdb=" N VAL A 529 " --> pdb=" O HIS H 94 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N HIS H 94 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS A 531 " --> pdb=" O VAL H 92 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N TYR H 113 " --> pdb=" O TYR H 98 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU H 120 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP H 44 " --> pdb=" O LEU H 120 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N MET H 39 " --> pdb=" O SER H 34 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N THR H 33 " --> pdb=" O VAL H 14 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N VAL H 14 " --> pdb=" O THR H 33 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP H 10 " --> pdb=" O LEU H 60 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 554 through 556 removed outlier: 3.687A pdb=" N ILE A 561 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLY A 563 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU A 567 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 703 through 704 Processing sheet with id=AA8, first strand: chain 'A' and resid 789 through 791 Processing sheet with id=AA9, first strand: chain 'A' and resid 1043 through 1049 removed outlier: 4.172A pdb=" N ASN A1047 " --> pdb=" O ASP A1073 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 906 through 907 removed outlier: 6.957A pdb=" N VAL A 906 " --> pdb=" O ILE A1037 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 983 through 986 removed outlier: 3.549A pdb=" N ILE A 939 " --> pdb=" O LEU A1005 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N HIS A 936 " --> pdb=" O VAL A 917 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL A 917 " --> pdb=" O HIS A 936 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N HIS A 938 " --> pdb=" O PHE A 915 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE A 915 " --> pdb=" O HIS A 938 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N HIS A 940 " --> pdb=" O VAL A 913 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHE A 915 " --> pdb=" O ASN I 46 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN I 46 " --> pdb=" O PHE A 915 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR I 44 " --> pdb=" O VAL A 917 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N TYR A 919 " --> pdb=" O CYS I 42 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N CYS I 42 " --> pdb=" O TYR A 919 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1227 through 1230 removed outlier: 3.677A pdb=" N LEU A1230 " --> pdb=" O THR F 113 " (cutoff:3.500A) removed outlier: 3.594A 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: 6.806A pdb=" N LYS C 23 " --> pdb=" O ARG C 15 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU C 17 " --> pdb=" O TYR C 21 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N TYR C 21 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE C 24 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLU C 190 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N ASP C 263 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 11.383A pdb=" N MET C 188 " --> pdb=" O ASP C 263 " (cutoff:3.500A) removed outlier: 9.826A pdb=" N PHE C 265 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 11.249A pdb=" N THR C 186 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 10.086A pdb=" N PHE C 267 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 11.372A pdb=" N THR C 184 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 10.125A pdb=" N VAL C 269 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 9.351A pdb=" N ALA C 182 " --> pdb=" O VAL C 269 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 126 through 127 removed outlier: 6.462A pdb=" N GLU C 161 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL C 57 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LYS C 163 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE C 55 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ARG C 165 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL C 53 " --> pdb=" O ARG C 165 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE C 167 " --> pdb=" O ASP C 51 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 118 through 121 removed outlier: 3.707A pdb=" N VAL C 154 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 220 through 222 removed outlier: 3.708A pdb=" N ASP C 221 " --> pdb=" O VAL C 230 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 230 " --> pdb=" O ASP C 221 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AB9, first strand: chain 'L' and resid 18 through 19 removed outlier: 5.395A pdb=" N VAL B 882 " --> pdb=" O LYS L 39 " (cutoff:3.500A) removed outlier: 9.447A pdb=" N GLY B 877 " --> pdb=" O VAL B 901 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N VAL B 901 " --> pdb=" O GLY B 877 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL B 879 " --> pdb=" O ARG B 899 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ARG B 899 " --> pdb=" O VAL B 879 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS B 881 " --> pdb=" O SER B 897 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 18 through 19 removed outlier: 5.395A pdb=" N VAL B 882 " --> pdb=" O LYS L 39 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY B 877 " --> pdb=" O MET B 850 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 14 through 16 Processing sheet with id=AC3, first strand: chain 'I' and resid 84 through 89 Processing sheet with id=AC4, first strand: chain 'E' and resid 93 through 96 Processing sheet with id=AC5, first strand: chain 'E' and resid 169 through 170 removed outlier: 4.452A pdb=" N TYR E 223 " --> pdb=" O TYR E 215 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 68 through 70 removed outlier: 5.454A pdb=" N VAL B 89 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N GLU B 133 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N PHE B 91 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP B 131 " --> pdb=" O PHE B 91 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLU B 93 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN B 129 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA B 124 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ARG B 169 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N MET B 126 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN B 163 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AC8, first strand: chain 'B' and resid 204 through 206 Processing sheet with id=AC9, first strand: chain 'B' and resid 394 through 397 removed outlier: 6.490A pdb=" N ALA B 215 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 225 through 226 removed outlier: 3.534A pdb=" N ILE B 245 " --> pdb=" O TYR B 267 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 535 through 536 Processing sheet with id=AD3, first strand: chain 'B' and resid 535 through 536 removed outlier: 3.530A pdb=" N CYS B 685 " --> pdb=" O LEU B 628 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 575 through 580 removed outlier: 7.081A pdb=" N VAL B 570 " --> pdb=" O VAL B 577 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL B 579 " --> pdb=" O HIS B 568 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N HIS B 568 " --> pdb=" O VAL B 579 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1011 through 1012 removed outlier: 7.132A pdb=" N ILE B 784 " --> pdb=" O GLY B 921 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE B 923 " --> pdb=" O ILE B 784 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N MET B 786 " --> pdb=" O ILE B 923 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N PHE B1028 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 855 through 857 removed outlier: 3.931A pdb=" N ILE B 857 " --> pdb=" O VAL B 869 " (cutoff:3.500A) 872 hydrogen bonds defined for protein. 2436 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 41 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 6.87 Time building geometry restraints manager: 2.52 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: 7588 1.34 - 1.46: 4863 1.46 - 1.58: 11233 1.58 - 1.70: 83 1.70 - 1.82: 217 Bond restraints: 23984 Sorted by residual: bond pdb=" C3' DT N 11 " pdb=" C2' DT N 11 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.36e+01 bond pdb=" C3' DG T 20 " pdb=" C2' DG T 20 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C1' DT N 11 " pdb=" N1 DT N 11 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.57e+00 bond pdb=" C1' DC N 14 " pdb=" N1 DC N 14 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.54e+00 bond pdb=" C3' DC N 14 " pdb=" C2' DC N 14 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.48e+00 ... (remaining 23979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 32167 2.39 - 4.79: 320 4.79 - 7.18: 32 7.18 - 9.57: 5 9.57 - 11.97: 1 Bond angle restraints: 32525 Sorted by residual: angle pdb=" N ILE I 24 " pdb=" CA ILE I 24 " pdb=" C ILE I 24 " ideal model delta sigma weight residual 113.71 108.56 5.15 9.50e-01 1.11e+00 2.94e+01 angle pdb=" C LEU E 56 " pdb=" N GLU E 57 " pdb=" CA GLU E 57 " ideal model delta sigma weight residual 121.54 129.89 -8.35 1.91e+00 2.74e-01 1.91e+01 angle pdb=" N3 DT N 28 " pdb=" C4 DT N 28 " pdb=" O4 DT N 28 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT N 11 " pdb=" C4 DT N 11 " pdb=" O4 DT N 11 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT N 15 " pdb=" C4 DT N 15 " pdb=" O4 DT N 15 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.69e+01 ... (remaining 32520 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.97: 13885 34.97 - 69.93: 584 69.93 - 104.90: 44 104.90 - 139.86: 0 139.86 - 174.83: 1 Dihedral angle restraints: 14514 sinusoidal: 6256 harmonic: 8258 Sorted by residual: dihedral pdb=" C4' DC N 18 " pdb=" C3' DC N 18 " pdb=" O3' DC N 18 " pdb=" P DA N 19 " ideal model delta sinusoidal sigma weight residual -140.00 34.83 -174.83 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA VAL A 428 " pdb=" C VAL A 428 " pdb=" N TYR A 429 " pdb=" CA TYR A 429 " ideal model delta harmonic sigma weight residual 180.00 160.76 19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLU H 111 " pdb=" C GLU H 111 " pdb=" N MET H 112 " pdb=" CA MET H 112 " ideal model delta harmonic sigma weight residual 180.00 160.79 19.21 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 14511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2470 0.038 - 0.075: 852 0.075 - 0.113: 283 0.113 - 0.150: 55 0.150 - 0.188: 4 Chirality restraints: 3664 Sorted by residual: chirality pdb=" CB THR A1057 " pdb=" CA THR A1057 " pdb=" OG1 THR A1057 " pdb=" CG2 THR A1057 " both_signs ideal model delta sigma weight residual False 2.55 2.74 -0.19 2.00e-01 2.50e+01 8.80e-01 chirality pdb=" CA GLU E 57 " pdb=" N GLU E 57 " pdb=" C GLU E 57 " pdb=" CB GLU E 57 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.14e-01 chirality pdb=" CB VAL E 111 " pdb=" CA VAL E 111 " pdb=" CG1 VAL E 111 " pdb=" CG2 VAL E 111 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.60e-01 ... (remaining 3661 not shown) Planarity restraints: 4028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 229 " 0.059 5.00e-02 4.00e+02 8.92e-02 1.27e+01 pdb=" N PRO B 230 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO B 230 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 230 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR H 107 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO H 108 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO H 108 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 108 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 433 " -0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO B 434 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 434 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 434 " -0.025 5.00e-02 4.00e+02 ... (remaining 4025 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 15 2.56 - 3.15: 17399 3.15 - 3.73: 34148 3.73 - 4.32: 46942 4.32 - 4.90: 78693 Nonbonded interactions: 177197 Sorted by model distance: nonbonded pdb=" OD1 ASP A 453 " pdb="MG MG A3000 " model vdw 1.977 2.170 nonbonded pdb=" O ASN A 950 " pdb=" ND2 ASN A 950 " model vdw 2.263 3.120 nonbonded pdb=" OD1 ASP A 451 " pdb="MG MG A3000 " model vdw 2.264 2.170 nonbonded pdb=" OD1 ASP A 449 " pdb="MG MG A3000 " model vdw 2.296 2.170 nonbonded pdb=" N GLY I 82 " pdb="ZN ZN I 201 " model vdw 2.430 2.310 ... (remaining 177192 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 30.040 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 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 0.041 24003 Z= 0.197 Angle : 0.667 11.966 32545 Z= 0.407 Chirality : 0.043 0.188 3664 Planarity : 0.004 0.089 4028 Dihedral : 17.846 174.829 9164 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.23 % Allowed : 18.59 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.16), residues: 2797 helix: 0.90 (0.18), residues: 872 sheet: -0.91 (0.23), residues: 503 loop : -1.52 (0.15), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1066 TYR 0.014 0.001 TYR H 98 PHE 0.020 0.001 PHE A 978 TRP 0.031 0.002 TRP A 855 HIS 0.010 0.001 HIS A1100 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.20 (23984) covalent geometry : angle 0.65941 / 0.41 (32525) hydrogen bonds : bond 0.20189 / 21.46 ( 903) hydrogen bonds : angle 6.56580 / 6.54 ( 2518) metal coordination : bond 0.01140 / 0.69 ( 19) metal coordination : angle 4.13249 / 6.68 ( 20) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 290 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 371 MET cc_start: 0.6958 (ptp) cc_final: 0.6494 (ptt) REVERT: A 589 MET cc_start: 0.7728 (ttp) cc_final: 0.7072 (ttt) REVERT: A 770 ARG cc_start: 0.7851 (tmm-80) cc_final: 0.7303 (tpp-160) REVERT: A 860 GLU cc_start: 0.6900 (tm-30) cc_final: 0.6575 (pt0) REVERT: A 978 PHE cc_start: 0.6884 (m-80) cc_final: 0.6645 (m-80) REVERT: A 1110 TYR cc_start: 0.7920 (t80) cc_final: 0.7696 (t80) REVERT: C 96 ASP cc_start: 0.7467 (t70) cc_final: 0.6732 (t0) REVERT: C 213 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7361 (tm-30) REVERT: F 65 MET cc_start: 0.7498 (mtp) cc_final: 0.6956 (ttt) REVERT: F 109 LYS cc_start: 0.6829 (mmmt) cc_final: 0.6242 (mmtt) REVERT: F 115 ARG cc_start: 0.6230 (mmt90) cc_final: 0.5620 (mmt180) REVERT: F 130 GLU cc_start: 0.7059 (tp30) cc_final: 0.6800 (tp30) REVERT: J 26 GLN cc_start: 0.8442 (tp40) cc_final: 0.7826 (tp40) REVERT: J 31 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8470 (mt-10) REVERT: K 22 GLU cc_start: 0.8213 (tp30) cc_final: 0.7749 (tm-30) REVERT: K 36 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8283 (mm-30) REVERT: K 93 ASP cc_start: 0.8825 (m-30) cc_final: 0.8543 (m-30) REVERT: L 17 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7544 (mp10) REVERT: H 136 ASP cc_start: 0.7110 (m-30) cc_final: 0.6758 (t70) REVERT: E 190 LEU cc_start: 0.4227 (OUTLIER) cc_final: 0.3972 (mt) REVERT: B 192 ARG cc_start: 0.6648 (tpp80) cc_final: 0.5666 (tpt-90) REVERT: B 243 ARG cc_start: 0.8068 (mmt90) cc_final: 0.7658 (mtp85) REVERT: B 279 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.6497 (t80) REVERT: B 348 GLU cc_start: 0.6800 (mp0) cc_final: 0.6076 (mm-30) REVERT: B 391 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.8320 (t80) REVERT: B 484 ILE cc_start: 0.9028 (pt) cc_final: 0.8600 (pt) outliers start: 31 outliers final: 22 residues processed: 316 average time/residue: 0.1797 time to fit residues: 87.0226 Evaluate side-chains 282 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 257 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 864 CYS Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 10 CYS Chi-restraints excluded: chain E residue 36 TYR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 985 HIS Chi-restraints excluded: chain B residue 1045 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 ASN ** A1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1226 GLN B 56 HIS B 333 GLN B 459 HIS B 652 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.160256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.104932 restraints weight = 37217.413| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.36 r_work: 0.3182 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24003 Z= 0.186 Angle : 0.641 10.452 32545 Z= 0.344 Chirality : 0.045 0.175 3664 Planarity : 0.005 0.057 4028 Dihedral : 13.433 171.264 3635 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.90 % Allowed : 16.96 % Favored : 79.14 % 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: -0.99 (0.16), residues: 2797 helix: 0.86 (0.18), residues: 891 sheet: -0.72 (0.23), residues: 489 loop : -1.66 (0.15), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 950 TYR 0.015 0.002 TYR B 235 PHE 0.024 0.002 PHE E 66 TRP 0.016 0.002 TRP A 855 HIS 0.006 0.001 HIS C 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (23984) covalent geometry : angle 0.63080 / 0.34 (32525) hydrogen bonds : bond 0.06221 / 6.73 ( 903) hydrogen bonds : angle 5.01458 / 5.18 ( 2518) metal coordination : bond 0.01149 / 0.81 ( 19) metal coordination : angle 4.64080 / 7.64 ( 20) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 273 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 MET cc_start: 0.6593 (ptp) cc_final: 0.6375 (ptp) REVERT: A 503 MET cc_start: 0.8863 (tpp) cc_final: 0.8605 (mmm) REVERT: A 589 MET cc_start: 0.7788 (ttp) cc_final: 0.7176 (ttt) REVERT: A 953 MET cc_start: 0.6114 (pmm) cc_final: 0.5659 (ppp) REVERT: A 983 LEU cc_start: 0.7634 (pt) cc_final: 0.7301 (tp) REVERT: A 991 PHE cc_start: 0.4713 (m-80) cc_final: 0.4510 (m-80) REVERT: C 96 ASP cc_start: 0.7473 (t70) cc_final: 0.6670 (t0) REVERT: C 213 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7434 (tm-30) REVERT: F 65 MET cc_start: 0.7754 (mtp) cc_final: 0.7297 (ttt) REVERT: F 88 MET cc_start: 0.6813 (tpp) cc_final: 0.6213 (tpp) REVERT: F 96 ASP cc_start: 0.8573 (t0) cc_final: 0.8253 (t0) REVERT: F 109 LYS cc_start: 0.7436 (mmmt) cc_final: 0.6287 (mmtt) REVERT: F 115 ARG cc_start: 0.6393 (mmt90) cc_final: 0.5896 (mmt180) REVERT: F 130 GLU cc_start: 0.7092 (tp30) cc_final: 0.6887 (tp30) REVERT: J 26 GLN cc_start: 0.8510 (tp40) cc_final: 0.7977 (tp40) REVERT: K 22 GLU cc_start: 0.8161 (tp30) cc_final: 0.7796 (tt0) REVERT: K 93 ASP cc_start: 0.9044 (m-30) cc_final: 0.8819 (m-30) REVERT: H 136 ASP cc_start: 0.6879 (m-30) cc_final: 0.6620 (t70) REVERT: B 192 ARG cc_start: 0.6741 (tpp80) cc_final: 0.5835 (tpt-90) REVERT: B 243 ARG cc_start: 0.8036 (mmt90) cc_final: 0.7613 (mtp85) REVERT: B 279 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.6570 (t80) REVERT: B 391 PHE cc_start: 0.9189 (OUTLIER) cc_final: 0.8043 (t80) REVERT: B 484 ILE cc_start: 0.9041 (pt) cc_final: 0.8611 (pt) REVERT: B 550 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8205 (m-30) outliers start: 98 outliers final: 69 residues processed: 350 average time/residue: 0.1760 time to fit residues: 96.2050 Evaluate side-chains 317 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 245 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 774 GLU Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 901 ASN Chi-restraints excluded: chain A residue 959 ARG Chi-restraints excluded: chain A residue 1047 ASN Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1135 SER Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 138 ARG Chi-restraints excluded: chain I residue 10 CYS Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain E residue 36 TYR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 134 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 279 PHE Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 985 HIS Chi-restraints excluded: chain B residue 1045 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 94 optimal weight: 0.4980 chunk 130 optimal weight: 6.9990 chunk 137 optimal weight: 0.7980 chunk 216 optimal weight: 5.9990 chunk 280 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 chunk 201 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 505 GLN ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 ASN E 158 ASN B 334 GLN B 491 GLN B 652 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.160847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.113480 restraints weight = 37019.568| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.68 r_work: 0.3180 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 24003 Z= 0.126 Angle : 0.553 10.751 32545 Z= 0.298 Chirality : 0.042 0.178 3664 Planarity : 0.004 0.055 4028 Dihedral : 13.235 172.280 3619 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.34 % Allowed : 18.23 % Favored : 78.42 % 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: -0.79 (0.16), residues: 2797 helix: 1.11 (0.18), residues: 892 sheet: -0.57 (0.24), residues: 483 loop : -1.62 (0.15), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1067 TYR 0.012 0.001 TYR J 43 PHE 0.018 0.001 PHE A 411 TRP 0.013 0.001 TRP A1058 HIS 0.005 0.001 HIS H 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (23984) covalent geometry : angle 0.54214 / 0.30 (32525) hydrogen bonds : bond 0.04983 / 5.37 ( 903) hydrogen bonds : angle 4.67336 / 4.78 ( 2518) metal coordination : bond 0.01067 / 0.69 ( 19) metal coordination : angle 4.41148 / 7.00 ( 20) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 271 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8677 (tp) REVERT: A 493 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7695 (mt) REVERT: A 503 MET cc_start: 0.8870 (tpp) cc_final: 0.8618 (mmm) REVERT: A 518 MET cc_start: 0.9175 (mmm) cc_final: 0.7648 (mmm) REVERT: A 589 MET cc_start: 0.7649 (ttp) cc_final: 0.7096 (ttt) REVERT: A 953 MET cc_start: 0.6245 (pmm) cc_final: 0.5873 (ppp) REVERT: A 983 LEU cc_start: 0.7724 (pt) cc_final: 0.7381 (tp) REVERT: F 65 MET cc_start: 0.7635 (mtp) cc_final: 0.7207 (ttt) REVERT: F 94 GLU cc_start: 0.5264 (mp0) cc_final: 0.4993 (mp0) REVERT: F 100 ILE cc_start: 0.8154 (mt) cc_final: 0.7720 (tp) REVERT: F 109 LYS cc_start: 0.7430 (mmmt) cc_final: 0.6320 (mmtt) REVERT: F 115 ARG cc_start: 0.6539 (mmt90) cc_final: 0.6233 (mmt180) REVERT: F 130 GLU cc_start: 0.7150 (tp30) cc_final: 0.6949 (tp30) REVERT: J 26 GLN cc_start: 0.8531 (tp40) cc_final: 0.7971 (tp40) REVERT: K 22 GLU cc_start: 0.8180 (tp30) cc_final: 0.7772 (tt0) REVERT: K 93 ASP cc_start: 0.9065 (m-30) cc_final: 0.8783 (m-30) REVERT: L 17 GLN cc_start: 0.8155 (mm-40) cc_final: 0.7504 (mp10) REVERT: H 66 LEU cc_start: 0.7880 (mm) cc_final: 0.7532 (mm) REVERT: H 136 ASP cc_start: 0.6977 (m-30) cc_final: 0.6629 (t70) REVERT: I 19 ASP cc_start: 0.4343 (t70) cc_final: 0.4132 (t70) REVERT: E 201 ARG cc_start: 0.4915 (mmm-85) cc_final: 0.4537 (ttm-80) REVERT: B 192 ARG cc_start: 0.6750 (tpp80) cc_final: 0.5842 (tpt-90) REVERT: B 243 ARG cc_start: 0.8147 (mmt90) cc_final: 0.7729 (mtp85) REVERT: B 279 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7121 (t80) REVERT: B 348 GLU cc_start: 0.6481 (mp0) cc_final: 0.5545 (mm-30) REVERT: B 391 PHE cc_start: 0.9196 (OUTLIER) cc_final: 0.8006 (t80) REVERT: B 416 ARG cc_start: 0.6659 (ttp-110) cc_final: 0.6232 (ttp80) REVERT: B 422 MET cc_start: 0.7505 (tpt) cc_final: 0.7162 (tpt) REVERT: B 550 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8229 (m-30) outliers start: 84 outliers final: 53 residues processed: 332 average time/residue: 0.1729 time to fit residues: 90.5990 Evaluate side-chains 313 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 255 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 901 ASN Chi-restraints excluded: chain A residue 959 ARG Chi-restraints excluded: chain A residue 1004 CYS Chi-restraints excluded: chain A residue 1037 ILE Chi-restraints excluded: chain A residue 1047 ASN Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1135 SER Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain E residue 36 TYR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 199 VAL 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 279 PHE Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 985 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 95 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 180 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 245 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 490 GLN A 936 HIS ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 ASN ** I 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 HIS ** B 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 873 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.151284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.103254 restraints weight = 36772.550| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.82 r_work: 0.3033 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.102 24003 Z= 0.350 Angle : 0.853 9.869 32545 Z= 0.457 Chirality : 0.053 0.266 3664 Planarity : 0.007 0.082 4028 Dihedral : 13.714 173.344 3617 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 5.37 % Allowed : 17.20 % Favored : 77.43 % 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: -1.52 (0.15), residues: 2797 helix: 0.29 (0.17), residues: 892 sheet: -0.72 (0.23), residues: 480 loop : -2.02 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1066 TYR 0.028 0.003 TYR J 43 PHE 0.032 0.003 PHE C 101 TRP 0.027 0.003 TRP B 576 HIS 0.010 0.002 HIS B 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00861 / 0.35 (23984) covalent geometry : angle 0.84323 / 0.46 (32525) hydrogen bonds : bond 0.08514 / 9.22 ( 903) hydrogen bonds : angle 5.27630 / 5.57 ( 2518) metal coordination : bond 0.01811 / 1.18 ( 19) metal coordination : angle 5.21233 / 8.77 ( 20) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 276 time to evaluate : 0.952 Fit side-chains REVERT: A 493 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7662 (mt) REVERT: A 503 MET cc_start: 0.8958 (tpp) cc_final: 0.8754 (mmm) REVERT: A 568 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7424 (mm) REVERT: A 589 MET cc_start: 0.8087 (ttp) cc_final: 0.7538 (ttt) REVERT: A 953 MET cc_start: 0.6370 (pmm) cc_final: 0.6059 (ppp) REVERT: A 981 MET cc_start: 0.7753 (ptt) cc_final: 0.7382 (ptp) REVERT: A 1050 TRP cc_start: 0.6354 (t-100) cc_final: 0.5730 (t-100) REVERT: A 1066 ARG cc_start: 0.4450 (OUTLIER) cc_final: 0.3734 (ttt180) REVERT: A 1165 ASN cc_start: 0.6459 (OUTLIER) cc_final: 0.6207 (p0) REVERT: F 94 GLU cc_start: 0.6027 (mp0) cc_final: 0.5713 (mp0) REVERT: F 100 ILE cc_start: 0.8327 (mt) cc_final: 0.7851 (tp) REVERT: F 102 MET cc_start: 0.7040 (mtt) cc_final: 0.6824 (mtm) REVERT: F 109 LYS cc_start: 0.7657 (mmmt) cc_final: 0.6764 (mmtt) REVERT: F 115 ARG cc_start: 0.7193 (mmt90) cc_final: 0.6824 (mmt180) REVERT: H 39 MET cc_start: 0.5808 (mmt) cc_final: 0.5501 (mmt) REVERT: H 66 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7985 (mp) REVERT: E 185 ILE cc_start: 0.1719 (OUTLIER) cc_final: 0.1409 (tt) REVERT: B 192 ARG cc_start: 0.6848 (tpp80) cc_final: 0.5846 (tpt-90) REVERT: B 279 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.7478 (t80) REVERT: B 288 LYS cc_start: 0.7452 (ptmt) cc_final: 0.7208 (tttt) REVERT: B 348 GLU cc_start: 0.6746 (mp0) cc_final: 0.5973 (mm-30) REVERT: B 391 PHE cc_start: 0.9219 (OUTLIER) cc_final: 0.7817 (t80) REVERT: B 416 ARG cc_start: 0.6661 (ttp-110) cc_final: 0.6363 (ttp80) REVERT: B 418 MET cc_start: 0.8130 (tmm) cc_final: 0.7572 (ttp) REVERT: B 484 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8723 (pt) REVERT: B 550 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8138 (m-30) REVERT: B 692 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8578 (mp) outliers start: 135 outliers final: 81 residues processed: 383 average time/residue: 0.1653 time to fit residues: 100.8132 Evaluate side-chains 334 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 242 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 1004 CYS Chi-restraints excluded: chain A residue 1066 ARG Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1165 ASN Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 137 TRP Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 143 MET Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 134 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 279 PHE Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 461 PHE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 1045 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 218 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 235 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 chunk 207 optimal weight: 0.0570 chunk 158 optimal weight: 6.9990 chunk 215 optimal weight: 0.6980 chunk 260 optimal weight: 0.9990 chunk 223 optimal weight: 0.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1153 ASN B 873 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.154454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.107711 restraints weight = 36636.653| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.56 r_work: 0.3108 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24003 Z= 0.128 Angle : 0.597 11.598 32545 Z= 0.320 Chirality : 0.043 0.188 3664 Planarity : 0.004 0.054 4028 Dihedral : 13.430 172.236 3611 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.14 % Allowed : 19.79 % Favored : 77.07 % 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: -1.03 (0.15), residues: 2797 helix: 0.91 (0.18), residues: 891 sheet: -0.61 (0.23), residues: 501 loop : -1.82 (0.15), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 80 TYR 0.026 0.001 TYR E 202 PHE 0.038 0.001 PHE C 101 TRP 0.016 0.001 TRP B 113 HIS 0.013 0.001 HIS B 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (23984) covalent geometry : angle 0.58464 / 0.32 (32525) hydrogen bonds : bond 0.05377 / 5.85 ( 903) hydrogen bonds : angle 4.78870 / 4.98 ( 2518) metal coordination : bond 0.01596 / 0.93 ( 19) metal coordination : angle 4.96738 / 7.61 ( 20) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 263 time to evaluate : 0.864 Fit side-chains REVERT: A 493 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7669 (mt) REVERT: A 518 MET cc_start: 0.9151 (mmm) cc_final: 0.7831 (mmm) REVERT: A 568 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7336 (mm) REVERT: A 589 MET cc_start: 0.7917 (ttp) cc_final: 0.7400 (ttt) REVERT: A 953 MET cc_start: 0.6426 (pmm) cc_final: 0.6001 (ppp) REVERT: F 94 GLU cc_start: 0.5660 (mp0) cc_final: 0.5347 (mp0) REVERT: F 102 MET cc_start: 0.6760 (mtt) cc_final: 0.6555 (mtm) REVERT: F 109 LYS cc_start: 0.7739 (mmmt) cc_final: 0.6823 (mttm) REVERT: F 115 ARG cc_start: 0.7167 (mmt90) cc_final: 0.6684 (mmt180) REVERT: F 124 GLU cc_start: 0.6184 (mt-10) cc_final: 0.5742 (tm-30) REVERT: K 22 GLU cc_start: 0.8223 (tp30) cc_final: 0.7785 (tt0) REVERT: K 93 ASP cc_start: 0.9131 (m-30) cc_final: 0.8912 (m-30) REVERT: H 66 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7963 (mp) REVERT: I 5 LYS cc_start: 0.6996 (mmmt) cc_final: 0.6777 (mttp) REVERT: I 24 ILE cc_start: 0.5766 (OUTLIER) cc_final: 0.5378 (mt) REVERT: I 98 THR cc_start: 0.2101 (OUTLIER) cc_final: 0.1673 (t) REVERT: E 185 ILE cc_start: 0.1719 (OUTLIER) cc_final: 0.1281 (tt) REVERT: B 192 ARG cc_start: 0.6821 (tpp80) cc_final: 0.5884 (tpt-90) REVERT: B 279 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.7554 (t80) REVERT: B 288 LYS cc_start: 0.7081 (ptmt) cc_final: 0.6820 (tttt) REVERT: B 348 GLU cc_start: 0.6720 (mp0) cc_final: 0.5976 (mm-30) REVERT: B 382 LYS cc_start: 0.8505 (mtmt) cc_final: 0.8301 (mmmm) REVERT: B 391 PHE cc_start: 0.9206 (OUTLIER) cc_final: 0.7789 (t80) REVERT: B 416 ARG cc_start: 0.6748 (ttp-110) cc_final: 0.6464 (ttp80) REVERT: B 425 HIS cc_start: 0.7026 (OUTLIER) cc_final: 0.6796 (m-70) REVERT: B 824 GLN cc_start: 0.7196 (mt0) cc_final: 0.6934 (tt0) outliers start: 79 outliers final: 55 residues processed: 320 average time/residue: 0.1577 time to fit residues: 81.7367 Evaluate side-chains 311 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 247 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 850 ASN Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 143 MET Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 461 PHE Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 919 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 196 optimal weight: 0.0770 chunk 5 optimal weight: 0.3980 chunk 25 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 276 optimal weight: 0.9980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.155045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.108521 restraints weight = 36730.443| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.51 r_work: 0.3127 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24003 Z= 0.117 Angle : 0.561 11.181 32545 Z= 0.300 Chirality : 0.042 0.236 3664 Planarity : 0.004 0.051 4028 Dihedral : 13.301 171.426 3611 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.34 % Allowed : 19.51 % Favored : 77.15 % 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: -0.81 (0.16), residues: 2797 helix: 1.20 (0.18), residues: 893 sheet: -0.56 (0.23), residues: 505 loop : -1.74 (0.15), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 450 TYR 0.023 0.001 TYR E 202 PHE 0.033 0.001 PHE C 101 TRP 0.017 0.001 TRP A1050 HIS 0.007 0.001 HIS B 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (23984) covalent geometry : angle 0.55037 / 0.30 (32525) hydrogen bonds : bond 0.04566 / 4.94 ( 903) hydrogen bonds : angle 4.52879 / 4.69 ( 2518) metal coordination : bond 0.01239 / 0.80 ( 19) metal coordination : angle 4.38266 / 6.77 ( 20) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 264 time to evaluate : 1.148 Fit side-chains REVERT: A 432 GLU cc_start: 0.8224 (pm20) cc_final: 0.7885 (pm20) REVERT: A 493 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7640 (mt) REVERT: A 589 MET cc_start: 0.8009 (ttp) cc_final: 0.7492 (ttt) REVERT: A 953 MET cc_start: 0.6496 (pmm) cc_final: 0.6071 (ppp) REVERT: C 213 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7550 (tm-30) REVERT: F 94 GLU cc_start: 0.5718 (mp0) cc_final: 0.5378 (mp0) REVERT: F 102 MET cc_start: 0.6791 (mtt) cc_final: 0.6570 (mtm) REVERT: F 109 LYS cc_start: 0.7722 (mmmt) cc_final: 0.7241 (mtpt) REVERT: F 124 GLU cc_start: 0.6394 (mt-10) cc_final: 0.5775 (tm-30) REVERT: K 22 GLU cc_start: 0.8215 (tp30) cc_final: 0.7764 (tt0) REVERT: K 93 ASP cc_start: 0.9104 (m-30) cc_final: 0.8830 (m-30) REVERT: H 9 GLU cc_start: 0.8301 (pt0) cc_final: 0.7860 (pt0) REVERT: H 66 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8073 (mp) REVERT: I 35 GLN cc_start: 0.7194 (OUTLIER) cc_final: 0.6366 (mp-120) REVERT: I 98 THR cc_start: 0.2299 (OUTLIER) cc_final: 0.1895 (t) REVERT: E 46 MET cc_start: 0.5450 (tmm) cc_final: 0.5101 (tmm) REVERT: E 185 ILE cc_start: 0.1634 (OUTLIER) cc_final: 0.1256 (tt) REVERT: B 192 ARG cc_start: 0.6843 (tpp80) cc_final: 0.5951 (tpt-90) REVERT: B 279 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.7595 (t80) REVERT: B 288 LYS cc_start: 0.7085 (ptmt) cc_final: 0.6797 (tttt) REVERT: B 348 GLU cc_start: 0.6647 (mp0) cc_final: 0.6143 (mm-30) REVERT: B 391 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.7801 (t80) REVERT: B 415 ARG cc_start: 0.7307 (ttm170) cc_final: 0.7095 (mtp180) REVERT: B 416 ARG cc_start: 0.6797 (ttp-110) cc_final: 0.6487 (ttp80) REVERT: B 425 HIS cc_start: 0.7243 (OUTLIER) cc_final: 0.6627 (t70) REVERT: B 824 GLN cc_start: 0.7269 (mt0) cc_final: 0.7019 (tt0) REVERT: B 875 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7220 (mt-10) outliers start: 84 outliers final: 65 residues processed: 324 average time/residue: 0.1650 time to fit residues: 85.3120 Evaluate side-chains 318 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 245 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 850 ASN Chi-restraints excluded: chain A residue 1004 CYS Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain K residue 14 GLU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 143 MET Chi-restraints excluded: chain I residue 10 CYS Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 134 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 279 PHE Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 461 PHE Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 985 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 95 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 100 optimal weight: 0.0050 chunk 136 optimal weight: 2.9990 chunk 221 optimal weight: 8.9990 chunk 90 optimal weight: 0.5980 chunk 77 optimal weight: 0.0870 chunk 259 optimal weight: 10.0000 chunk 190 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.5174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.155743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.108560 restraints weight = 36762.022| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.66 r_work: 0.3135 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 24003 Z= 0.106 Angle : 0.544 10.775 32545 Z= 0.289 Chirality : 0.042 0.175 3664 Planarity : 0.004 0.057 4028 Dihedral : 13.204 171.763 3611 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.07 % Allowed : 20.06 % Favored : 76.87 % 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: -0.61 (0.16), residues: 2797 helix: 1.39 (0.18), residues: 888 sheet: -0.44 (0.23), residues: 496 loop : -1.63 (0.15), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 416 TYR 0.022 0.001 TYR E 202 PHE 0.034 0.001 PHE C 101 TRP 0.013 0.001 TRP A1058 HIS 0.005 0.001 HIS I 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.11 (23984) covalent geometry : angle 0.53393 / 0.29 (32525) hydrogen bonds : bond 0.04083 / 4.44 ( 903) hydrogen bonds : angle 4.36437 / 4.49 ( 2518) metal coordination : bond 0.01207 / 0.76 ( 19) metal coordination : angle 4.19591 / 6.42 ( 20) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 260 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 493 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7378 (mt) REVERT: A 589 MET cc_start: 0.7923 (ttp) cc_final: 0.7367 (ttt) REVERT: A 953 MET cc_start: 0.6361 (pmm) cc_final: 0.6053 (ppp) REVERT: A 1002 MET cc_start: 0.3616 (pmm) cc_final: 0.3024 (mpp) REVERT: A 1050 TRP cc_start: 0.6772 (t-100) cc_final: 0.6036 (t-100) REVERT: F 94 GLU cc_start: 0.5519 (mp0) cc_final: 0.5198 (mp0) REVERT: F 102 MET cc_start: 0.6647 (mtt) cc_final: 0.6445 (mtm) REVERT: F 109 LYS cc_start: 0.7702 (mmmt) cc_final: 0.7217 (mtpt) REVERT: F 124 GLU cc_start: 0.6183 (mt-10) cc_final: 0.5710 (tm-30) REVERT: K 22 GLU cc_start: 0.8027 (tp30) cc_final: 0.7668 (tt0) REVERT: K 93 ASP cc_start: 0.8966 (m-30) cc_final: 0.8641 (m-30) REVERT: H 9 GLU cc_start: 0.8193 (pt0) cc_final: 0.7741 (pt0) REVERT: H 66 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.8027 (mp) REVERT: I 5 LYS cc_start: 0.6787 (mttp) cc_final: 0.6515 (mmmt) REVERT: I 33 ASP cc_start: 0.7458 (p0) cc_final: 0.7217 (m-30) REVERT: I 35 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6377 (mp-120) REVERT: I 98 THR cc_start: 0.2311 (OUTLIER) cc_final: 0.1901 (t) REVERT: E 46 MET cc_start: 0.5178 (tmm) cc_final: 0.4858 (tmm) REVERT: E 162 HIS cc_start: 0.8412 (OUTLIER) cc_final: 0.8157 (t-90) REVERT: E 185 ILE cc_start: 0.1668 (OUTLIER) cc_final: 0.1322 (tt) REVERT: B 192 ARG cc_start: 0.6756 (tpp80) cc_final: 0.5951 (tpt-90) REVERT: B 260 LYS cc_start: 0.6723 (mttt) cc_final: 0.6520 (mtmt) REVERT: B 279 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.6953 (t80) REVERT: B 288 LYS cc_start: 0.6973 (ptmt) cc_final: 0.6677 (tttt) REVERT: B 348 GLU cc_start: 0.6347 (mp0) cc_final: 0.5976 (mm-30) REVERT: B 391 PHE cc_start: 0.9180 (OUTLIER) cc_final: 0.7714 (t80) REVERT: B 416 ARG cc_start: 0.6764 (ttp-110) cc_final: 0.6337 (ttp80) REVERT: B 418 MET cc_start: 0.7971 (tmm) cc_final: 0.7403 (tmm) REVERT: B 651 ASP cc_start: 0.8639 (t0) cc_final: 0.8410 (m-30) REVERT: B 824 GLN cc_start: 0.7161 (mt0) cc_final: 0.6949 (tt0) outliers start: 77 outliers final: 57 residues processed: 312 average time/residue: 0.1487 time to fit residues: 74.3436 Evaluate side-chains 312 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 247 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 818 ASN Chi-restraints excluded: chain A residue 1004 CYS Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 14 GLU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 143 MET Chi-restraints excluded: chain I residue 10 CYS Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 461 PHE Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 985 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 147 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 77 optimal weight: 0.0770 chunk 96 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 chunk 241 optimal weight: 7.9990 chunk 277 optimal weight: 1.9990 chunk 195 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 261 optimal weight: 3.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 34 HIS ** I 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.151919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.105512 restraints weight = 36642.161| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.53 r_work: 0.3081 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 24003 Z= 0.193 Angle : 0.646 10.835 32545 Z= 0.343 Chirality : 0.045 0.192 3664 Planarity : 0.005 0.055 4028 Dihedral : 13.318 172.152 3610 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.46 % Allowed : 19.94 % Favored : 76.59 % 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: -0.84 (0.16), residues: 2797 helix: 1.16 (0.18), residues: 894 sheet: -0.52 (0.22), residues: 518 loop : -1.78 (0.15), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 450 TYR 0.019 0.002 TYR A1110 PHE 0.032 0.002 PHE C 101 TRP 0.014 0.002 TRP F 126 HIS 0.005 0.001 HIS C 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 (23984) covalent geometry : angle 0.63730 / 0.34 (32525) hydrogen bonds : bond 0.05897 / 6.40 ( 903) hydrogen bonds : angle 4.60467 / 4.79 ( 2518) metal coordination : bond 0.01379 / 0.87 ( 19) metal coordination : angle 4.19653 / 6.47 ( 20) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 253 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: A 493 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7519 (mt) REVERT: A 568 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7384 (mm) REVERT: A 589 MET cc_start: 0.8046 (ttp) cc_final: 0.7505 (ttt) REVERT: A 953 MET cc_start: 0.6461 (pmm) cc_final: 0.6137 (ppp) REVERT: A 1002 MET cc_start: 0.3603 (pmm) cc_final: 0.3078 (mpp) REVERT: A 1050 TRP cc_start: 0.6773 (t-100) cc_final: 0.6135 (t-100) REVERT: C 213 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7645 (tm-30) REVERT: F 102 MET cc_start: 0.6951 (mtt) cc_final: 0.6698 (mtm) REVERT: F 109 LYS cc_start: 0.7753 (mmmt) cc_final: 0.7261 (mtpt) REVERT: F 124 GLU cc_start: 0.6394 (mt-10) cc_final: 0.5769 (tm-30) REVERT: K 93 ASP cc_start: 0.9141 (m-30) cc_final: 0.8918 (m-30) REVERT: H 39 MET cc_start: 0.5817 (mmt) cc_final: 0.5548 (mmt) REVERT: H 66 LEU cc_start: 0.8251 (mm) cc_final: 0.7968 (mp) REVERT: I 35 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.6430 (mp-120) REVERT: I 98 THR cc_start: 0.2281 (OUTLIER) cc_final: 0.1864 (t) REVERT: E 46 MET cc_start: 0.5857 (tmm) cc_final: 0.5472 (tmm) REVERT: E 185 ILE cc_start: 0.1817 (OUTLIER) cc_final: 0.1366 (tt) REVERT: B 192 ARG cc_start: 0.6899 (tpp80) cc_final: 0.5974 (tpt-90) REVERT: B 260 LYS cc_start: 0.6851 (mttt) cc_final: 0.6584 (mtmt) REVERT: B 279 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7162 (t80) REVERT: B 288 LYS cc_start: 0.7330 (ptmt) cc_final: 0.7008 (tttt) REVERT: B 391 PHE cc_start: 0.9231 (OUTLIER) cc_final: 0.7692 (t80) REVERT: B 416 ARG cc_start: 0.6833 (ttp-110) cc_final: 0.6508 (ttp80) REVERT: B 484 ILE cc_start: 0.9034 (pt) cc_final: 0.8665 (pt) REVERT: B 824 GLN cc_start: 0.7269 (mt0) cc_final: 0.7001 (tt0) outliers start: 87 outliers final: 67 residues processed: 318 average time/residue: 0.1512 time to fit residues: 77.8232 Evaluate side-chains 313 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 239 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 818 ASN Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 14 GLU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 143 MET Chi-restraints excluded: chain I residue 10 CYS Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 134 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 251 ASN Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 461 PHE Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 985 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 32 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 236 optimal weight: 0.6980 chunk 194 optimal weight: 2.9990 chunk 61 optimal weight: 0.0470 chunk 196 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.153965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.107406 restraints weight = 36911.240| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.68 r_work: 0.3114 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 24003 Z= 0.112 Angle : 0.565 10.972 32545 Z= 0.299 Chirality : 0.042 0.173 3664 Planarity : 0.004 0.053 4028 Dihedral : 13.177 171.508 3608 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.55 % Allowed : 21.26 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.16), residues: 2797 helix: 1.38 (0.18), residues: 889 sheet: -0.45 (0.23), residues: 513 loop : -1.64 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 424 TYR 0.021 0.001 TYR E 202 PHE 0.031 0.001 PHE C 101 TRP 0.014 0.001 TRP B 113 HIS 0.016 0.001 HIS B 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (23984) covalent geometry : angle 0.55462 / 0.30 (32525) hydrogen bonds : bond 0.04397 / 4.77 ( 903) hydrogen bonds : angle 4.38633 / 4.53 ( 2518) metal coordination : bond 0.01348 / 0.78 ( 19) metal coordination : angle 4.28714 / 6.45 ( 20) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 251 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 493 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7461 (mt) REVERT: A 589 MET cc_start: 0.8018 (ttp) cc_final: 0.7486 (ttt) REVERT: A 953 MET cc_start: 0.6468 (pmm) cc_final: 0.6125 (ppp) REVERT: A 1002 MET cc_start: 0.3767 (pmm) cc_final: 0.3214 (mpp) REVERT: A 1050 TRP cc_start: 0.6778 (t-100) cc_final: 0.6160 (t-100) REVERT: A 1098 VAL cc_start: 0.7224 (t) cc_final: 0.6888 (p) REVERT: C 213 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7597 (tm-30) REVERT: F 102 MET cc_start: 0.6874 (mtt) cc_final: 0.6620 (mtm) REVERT: F 109 LYS cc_start: 0.7722 (mmmt) cc_final: 0.7193 (mtpt) REVERT: F 124 GLU cc_start: 0.6306 (mt-10) cc_final: 0.5731 (tm-30) REVERT: K 22 GLU cc_start: 0.8205 (tp30) cc_final: 0.7825 (tt0) REVERT: K 93 ASP cc_start: 0.9111 (m-30) cc_final: 0.8830 (m-30) REVERT: H 9 GLU cc_start: 0.8302 (pt0) cc_final: 0.7852 (pt0) REVERT: H 23 LYS cc_start: 0.6207 (mmtp) cc_final: 0.5905 (mmmt) REVERT: H 39 MET cc_start: 0.5626 (mmt) cc_final: 0.5350 (mmt) REVERT: H 50 TYR cc_start: 0.7294 (t80) cc_final: 0.6862 (t80) REVERT: H 66 LEU cc_start: 0.8266 (mm) cc_final: 0.7973 (mp) REVERT: H 109 LYS cc_start: 0.3613 (mmmt) cc_final: 0.2660 (mmtt) REVERT: I 35 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.6445 (mp-120) REVERT: I 98 THR cc_start: 0.2278 (OUTLIER) cc_final: 0.1829 (t) REVERT: E 46 MET cc_start: 0.5828 (tmm) cc_final: 0.5460 (tmm) REVERT: E 185 ILE cc_start: 0.1768 (OUTLIER) cc_final: 0.1310 (tt) REVERT: B 192 ARG cc_start: 0.6845 (tpp80) cc_final: 0.5948 (tpt-90) REVERT: B 279 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7046 (t80) REVERT: B 288 LYS cc_start: 0.7079 (ptmt) cc_final: 0.6754 (tttt) REVERT: B 348 GLU cc_start: 0.6509 (mp0) cc_final: 0.5813 (mm-30) REVERT: B 391 PHE cc_start: 0.9210 (OUTLIER) cc_final: 0.7703 (t80) REVERT: B 416 ARG cc_start: 0.6846 (ttp-110) cc_final: 0.6619 (ttm110) REVERT: B 424 ARG cc_start: 0.7442 (tmm160) cc_final: 0.7151 (tmm-80) REVERT: B 425 HIS cc_start: 0.6832 (OUTLIER) cc_final: 0.6004 (t-90) REVERT: B 677 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8422 (mmmm) REVERT: B 824 GLN cc_start: 0.7274 (mt0) cc_final: 0.6969 (tt0) outliers start: 64 outliers final: 54 residues processed: 296 average time/residue: 0.1567 time to fit residues: 74.1005 Evaluate side-chains 303 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 241 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 818 ASN Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 14 GLU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 143 MET Chi-restraints excluded: chain I residue 10 CYS Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 213 VAL 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 279 PHE Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 461 PHE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 677 LYS Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 985 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 269 optimal weight: 0.4980 chunk 212 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 201 optimal weight: 0.0030 chunk 124 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 overall best weight: 1.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.153223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.106288 restraints weight = 36712.531| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.70 r_work: 0.3096 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24003 Z= 0.127 Angle : 0.569 10.438 32545 Z= 0.301 Chirality : 0.042 0.170 3664 Planarity : 0.004 0.051 4028 Dihedral : 13.140 171.445 3608 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.55 % Allowed : 21.34 % Favored : 76.11 % 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: -0.56 (0.16), residues: 2797 helix: 1.43 (0.18), residues: 890 sheet: -0.38 (0.23), residues: 501 loop : -1.62 (0.15), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 47 TYR 0.020 0.001 TYR E 202 PHE 0.031 0.001 PHE C 101 TRP 0.013 0.001 TRP A1058 HIS 0.005 0.001 HIS I 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (23984) covalent geometry : angle 0.55993 / 0.30 (32525) hydrogen bonds : bond 0.04553 / 4.93 ( 903) hydrogen bonds : angle 4.34550 / 4.48 ( 2518) metal coordination : bond 0.01312 / 0.77 ( 19) metal coordination : angle 4.05643 / 6.17 ( 20) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 248 time to evaluate : 0.776 Fit side-chains REVERT: A 493 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7456 (mt) REVERT: A 589 MET cc_start: 0.7977 (ttp) cc_final: 0.7447 (ttt) REVERT: A 953 MET cc_start: 0.6530 (pmm) cc_final: 0.6169 (ppp) REVERT: A 1002 MET cc_start: 0.3574 (pmm) cc_final: 0.3079 (mpp) REVERT: A 1098 VAL cc_start: 0.7389 (t) cc_final: 0.7045 (p) REVERT: C 213 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7379 (tm-30) REVERT: F 102 MET cc_start: 0.6868 (mtt) cc_final: 0.6618 (mtm) REVERT: F 109 LYS cc_start: 0.7828 (mmmt) cc_final: 0.7311 (mtpt) REVERT: F 124 GLU cc_start: 0.6266 (mt-10) cc_final: 0.5690 (tm-30) REVERT: K 22 GLU cc_start: 0.8041 (tp30) cc_final: 0.7688 (tt0) REVERT: K 93 ASP cc_start: 0.8989 (m-30) cc_final: 0.8707 (m-30) REVERT: H 9 GLU cc_start: 0.8243 (pt0) cc_final: 0.7785 (pt0) REVERT: H 23 LYS cc_start: 0.6136 (mmtp) cc_final: 0.5851 (mmmt) REVERT: H 39 MET cc_start: 0.5736 (mmt) cc_final: 0.5449 (mmt) REVERT: H 50 TYR cc_start: 0.7393 (t80) cc_final: 0.7004 (t80) REVERT: H 66 LEU cc_start: 0.8220 (mm) cc_final: 0.7942 (mp) REVERT: H 109 LYS cc_start: 0.3448 (mmmt) cc_final: 0.2475 (mmtt) REVERT: I 35 GLN cc_start: 0.7269 (OUTLIER) cc_final: 0.6436 (mp-120) REVERT: I 98 THR cc_start: 0.2311 (OUTLIER) cc_final: 0.1843 (t) REVERT: E 46 MET cc_start: 0.5653 (tmm) cc_final: 0.5302 (tmm) REVERT: E 185 ILE cc_start: 0.1627 (OUTLIER) cc_final: 0.1204 (tt) REVERT: B 192 ARG cc_start: 0.6818 (tpp80) cc_final: 0.5962 (tpt-90) REVERT: B 279 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.7017 (t80) REVERT: B 288 LYS cc_start: 0.7084 (ptmt) cc_final: 0.6789 (tttt) REVERT: B 348 GLU cc_start: 0.6467 (mp0) cc_final: 0.5855 (mm-30) REVERT: B 391 PHE cc_start: 0.9200 (OUTLIER) cc_final: 0.7640 (t80) REVERT: B 416 ARG cc_start: 0.6811 (ttp-110) cc_final: 0.6573 (ttm110) REVERT: B 424 ARG cc_start: 0.7538 (tmm160) cc_final: 0.7303 (tmm160) REVERT: B 425 HIS cc_start: 0.6970 (OUTLIER) cc_final: 0.6471 (t70) REVERT: B 438 TYR cc_start: 0.6932 (m-80) cc_final: 0.6718 (m-80) REVERT: B 677 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8373 (mmmm) REVERT: B 824 GLN cc_start: 0.7187 (mt0) cc_final: 0.6909 (tt0) outliers start: 64 outliers final: 55 residues processed: 292 average time/residue: 0.1505 time to fit residues: 71.1304 Evaluate side-chains 303 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 240 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 609 MET Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 818 ASN Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 14 GLU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 143 MET Chi-restraints excluded: chain I residue 10 CYS Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 151 GLN Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain B residue 69 LEU 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 279 PHE Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 461 PHE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 677 LYS Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 985 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 139 optimal weight: 8.9990 chunk 271 optimal weight: 0.6980 chunk 164 optimal weight: 20.0000 chunk 56 optimal weight: 0.5980 chunk 198 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 83 optimal weight: 0.0970 chunk 37 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 267 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.154111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.106973 restraints weight = 36638.735| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.64 r_work: 0.3114 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 24003 Z= 0.107 Angle : 0.543 10.626 32545 Z= 0.287 Chirality : 0.041 0.173 3664 Planarity : 0.004 0.054 4028 Dihedral : 13.063 171.312 3608 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.75 % Allowed : 21.18 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.16), residues: 2797 helix: 1.53 (0.18), residues: 891 sheet: -0.28 (0.23), residues: 491 loop : -1.57 (0.15), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 40 TYR 0.020 0.001 TYR E 202 PHE 0.033 0.001 PHE C 101 TRP 0.013 0.001 TRP B 113 HIS 0.005 0.001 HIS I 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 (23984) covalent geometry : angle 0.53382 / 0.29 (32525) hydrogen bonds : bond 0.03951 / 4.28 ( 903) hydrogen bonds : angle 4.23991 / 4.37 ( 2518) metal coordination : bond 0.01255 / 0.72 ( 19) metal coordination : angle 4.02410 / 6.09 ( 20) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7260.46 seconds wall clock time: 124 minutes 39.66 seconds (7479.66 seconds total)