Starting phenix.real_space_refine on Sun Aug 9 23:19:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e5k_27913/08_2026/8e5k_27913_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e5k_27913/08_2026/8e5k_27913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8e5k_27913/08_2026/8e5k_27913_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e5k_27913/08_2026/8e5k_27913_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e5k_27913/08_2026/8e5k_27913.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e5k_27913/08_2026/8e5k_27913.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 87 5.49 5 Mg 1 5.21 5 S 113 5.16 5 C 17285 2.51 5 N 4941 2.21 5 O 5571 1.98 5 H 11229 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39229 Number of models: 1 Model: "" Number of chains: 10 Chain: "5" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 913 Classifications: {'DNA': 33} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 32} Chain breaks: 1 Chain: "6" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 1031 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "7" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 464 Classifications: {'RNA': 17} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 15} Chain: "A" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1280} Chain: "B" Number of atoms: 21000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 21000 Classifications: {'peptide': 1335} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 54, 'TRANS': 1277} Chain breaks: 2 Chain: "C" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1698 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1677 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "F" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1276 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 149} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13860 SG CYS B 70 63.703 115.009 44.860 1.00 45.60 S ATOM 14119 SG CYS B 85 60.565 116.911 41.764 1.00 49.94 S ATOM 25701 SG CYS B 814 35.180 99.275 105.275 1.00 22.38 S ATOM 26838 SG CYS B 888 38.067 98.160 101.961 1.00 20.48 S ATOM 26929 SG CYS B 895 38.676 100.534 104.649 1.00 14.28 S ATOM 26966 SG CYS B 898 38.083 97.423 106.260 1.00 16.02 S Time building chain proxies: 6.98, per 1000 atoms: 0.18 Number of scatterers: 39229 At special positions: 0 Unit cell: (157.776, 154.662, 174.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 113 16.00 P 87 15.00 Mg 1 11.99 O 5571 8.00 N 4941 7.00 C 17285 6.00 H 11229 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 72 " - pdb=" SG CYS B 88 " distance=2.27 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: 3.48 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1502 " pdb="ZN ZN B1502 " - pdb=" SG CYS B 70 " pdb="ZN ZN B1502 " - pdb=" SG CYS B 85 " pdb=" ZN B1503 " pdb="ZN ZN B1503 " - pdb=" SG CYS B 888 " pdb="ZN ZN B1503 " - pdb=" SG CYS B 895 " pdb="ZN ZN B1503 " - pdb=" SG CYS B 814 " pdb="ZN ZN B1503 " - pdb=" SG CYS B 898 " Number of angles added : 6 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6182 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 46 sheets defined 35.5% alpha, 15.1% beta 29 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 5.47 Creating SS restraints... Processing helix chain 'A' and resid 4 through 8 Processing helix chain 'A' and resid 28 through 39 Processing helix chain 'A' and resid 48 through 56 removed outlier: 4.129A pdb=" N ALA A 52 " --> pdb=" O GLY A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 163 through 167 removed outlier: 3.838A pdb=" N SER A 166 " --> pdb=" O LYS A 163 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER A 167 " --> pdb=" O THR A 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 163 through 167' Processing helix chain 'A' and resid 206 through 213 removed outlier: 4.057A pdb=" N LEU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 225 Processing helix chain 'A' and resid 242 through 247 removed outlier: 3.579A pdb=" N ARG A 247 " --> pdb=" O GLU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 280 Processing helix chain 'A' and resid 318 through 327 removed outlier: 3.688A pdb=" N GLN A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 358 through 371 Processing helix chain 'A' and resid 377 through 389 removed outlier: 4.130A pdb=" N PHE A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 408 Processing helix chain 'A' and resid 421 through 438 removed outlier: 3.757A pdb=" N ILE A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 480 removed outlier: 4.513A pdb=" N SER A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 508 Processing helix chain 'A' and resid 519 through 527 Processing helix chain 'A' and resid 609 through 614 removed outlier: 4.045A pdb=" N ASN A 613 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR A 614 " --> pdb=" O GLU A 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 609 through 614' Processing helix chain 'A' and resid 670 through 674 Processing helix chain 'A' and resid 675 through 688 Processing helix chain 'A' and resid 704 through 711 Processing helix chain 'A' and resid 738 through 741 removed outlier: 3.791A pdb=" N MET A 741 " --> pdb=" O GLU A 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 738 through 741' Processing helix chain 'A' and resid 820 through 825 Processing helix chain 'A' and resid 858 through 863 Processing helix chain 'A' and resid 942 through 979 Processing helix chain 'A' and resid 987 through 991 removed outlier: 3.828A pdb=" N ASP A 990 " --> pdb=" O GLU A 987 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS A 991 " --> pdb=" O LYS A 988 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 987 through 991' Processing helix chain 'A' and resid 1005 through 1038 Processing helix chain 'A' and resid 1101 through 1106 removed outlier: 4.548A pdb=" N SER A1105 " --> pdb=" O LEU A1101 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG A1106 " --> pdb=" O GLY A1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1101 through 1106' Processing helix chain 'A' and resid 1109 through 1134 removed outlier: 3.694A pdb=" N LEU A1113 " --> pdb=" O ILE A1109 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN A1134 " --> pdb=" O ALA A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1151 removed outlier: 3.880A pdb=" N LEU A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A1151 " --> pdb=" O ARG A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1164 removed outlier: 4.192A pdb=" N THR A1163 " --> pdb=" O ASP A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1167 through 1177 Processing helix chain 'A' and resid 1191 through 1202 removed outlier: 3.552A pdb=" N GLY A1202 " --> pdb=" O LEU A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1281 removed outlier: 3.625A pdb=" N TYR A1281 " --> pdb=" O ALA A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1292 Processing helix chain 'A' and resid 1297 through 1310 Processing helix chain 'A' and resid 1320 through 1332 removed outlier: 3.653A pdb=" N ASN A1324 " --> pdb=" O PRO A1320 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 33 Processing helix chain 'B' and resid 131 through 140 Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 180 through 191 removed outlier: 3.744A pdb=" N ALA B 184 " --> pdb=" O MET B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 207 Processing helix chain 'B' and resid 210 through 230 removed outlier: 3.777A pdb=" N ARG B 220 " --> pdb=" O LYS B 216 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU B 223 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 236 Processing helix chain 'B' and resid 246 through 250 Processing helix chain 'B' and resid 263 through 286 removed outlier: 3.807A pdb=" N ASP B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 308 Processing helix chain 'B' and resid 327 through 332 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 370 through 377 Processing helix chain 'B' and resid 377 through 389 removed outlier: 3.550A pdb=" N GLY B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 404 removed outlier: 3.689A pdb=" N ALA B 397 " --> pdb=" O THR B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 417 removed outlier: 3.567A pdb=" N ILE B 411 " --> pdb=" O VAL B 407 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG B 417 " --> pdb=" O ASP B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 432 No H-bonds generated for 'chain 'B' and resid 430 through 432' Processing helix chain 'B' and resid 450 through 458 removed outlier: 3.648A pdb=" N CYS B 454 " --> pdb=" O HIS B 450 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA B 455 " --> pdb=" O PRO B 451 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 483 Processing helix chain 'B' and resid 504 through 514 removed outlier: 3.522A pdb=" N LEU B 508 " --> pdb=" O GLN B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 539 Processing helix chain 'B' and resid 573 through 581 removed outlier: 3.612A pdb=" N ALA B 577 " --> pdb=" O THR B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 592 Processing helix chain 'B' and resid 598 through 613 Processing helix chain 'B' and resid 614 through 636 removed outlier: 3.645A pdb=" N GLY B 636 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 670 removed outlier: 3.532A pdb=" N SER B 670 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 703 Processing helix chain 'B' and resid 720 through 728 Processing helix chain 'B' and resid 733 through 742 removed outlier: 3.861A pdb=" N ILE B 737 " --> pdb=" O SER B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 805 removed outlier: 3.851A pdb=" N GLY B 782 " --> pdb=" O GLY B 778 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA B 791 " --> pdb=" O ALA B 787 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN B 792 " --> pdb=" O LEU B 788 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN B 805 " --> pdb=" O VAL B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 839 removed outlier: 3.643A pdb=" N ARG B 838 " --> pdb=" O PRO B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 876 removed outlier: 3.797A pdb=" N ASN B 875 " --> pdb=" O LEU B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 895 through 900 removed outlier: 3.521A pdb=" N TYR B 899 " --> pdb=" O CYS B 895 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY B 900 " --> pdb=" O ALA B 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 895 through 900' Processing helix chain 'B' and resid 914 through 925 removed outlier: 4.007A pdb=" N ILE B 918 " --> pdb=" O ALA B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 928 No H-bonds generated for 'chain 'B' and resid 926 through 928' Processing helix chain 'B' and resid 1137 through 1146 Processing helix chain 'B' and resid 1216 through 1224 Processing helix chain 'B' and resid 1225 through 1244 removed outlier: 4.194A pdb=" N VAL B1240 " --> pdb=" O GLU B1236 " (cutoff:3.500A) Processing helix chain 'B' and resid 1250 through 1261 Processing helix chain 'B' and resid 1282 through 1294 removed outlier: 3.544A pdb=" N ALA B1294 " --> pdb=" O ARG B1290 " (cutoff:3.500A) Processing helix chain 'B' and resid 1308 through 1315 Processing helix chain 'B' and resid 1327 through 1339 removed outlier: 3.828A pdb=" N VAL B1331 " --> pdb=" O GLU B1327 " (cutoff:3.500A) Processing helix chain 'B' and resid 1346 through 1353 removed outlier: 3.807A pdb=" N ASN B1350 " --> pdb=" O GLY B1346 " (cutoff:3.500A) Processing helix chain 'B' and resid 1361 through 1372 removed outlier: 4.421A pdb=" N TYR B1365 " --> pdb=" O THR B1361 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 50 removed outlier: 3.549A pdb=" N THR C 38 " --> pdb=" O GLY C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 87 Processing helix chain 'C' and resid 212 through 228 Processing helix chain 'C' and resid 229 through 232 removed outlier: 3.840A pdb=" N VAL C 232 " --> pdb=" O GLU C 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 229 through 232' Processing helix chain 'D' and resid 34 through 50 removed outlier: 4.040A pdb=" N THR D 38 " --> pdb=" O GLY D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 87 removed outlier: 3.560A pdb=" N GLY D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 115 No H-bonds generated for 'chain 'D' and resid 113 through 115' Processing helix chain 'D' and resid 212 through 227 Processing helix chain 'E' and resid 6 through 12 Processing helix chain 'E' and resid 17 through 32 removed outlier: 3.525A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 60 through 77 removed outlier: 3.956A pdb=" N GLN E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 33 Processing helix chain 'F' and resid 35 through 37 No H-bonds generated for 'chain 'F' and resid 35 through 37' Processing helix chain 'F' and resid 76 through 86 Processing helix chain 'F' and resid 105 through 117 removed outlier: 3.647A pdb=" N ASP F 109 " --> pdb=" O ASP F 105 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARG F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU F 115 " --> pdb=" O ILE F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 178 No H-bonds generated for 'chain 'F' and resid 176 through 178' Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 removed outlier: 6.569A pdb=" N LYS A 13 " --> pdb=" O ALA A1183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.928A pdb=" N LYS A 99 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N TYR A 73 " --> pdb=" O ARG A 97 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ARG A 97 " --> pdb=" O TYR A 73 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU A 75 " --> pdb=" O PRO A 95 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ALA A 94 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLU A 126 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU A 96 " --> pdb=" O MET A 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA4, first strand: chain 'A' and resid 451 through 454 removed outlier: 6.322A pdb=" N SER A 147 " --> pdb=" O SER A 531 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 158 removed outlier: 3.581A pdb=" N LEU A 184 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 228 through 231 Processing sheet with id=AA7, first strand: chain 'A' and resid 239 through 240 Processing sheet with id=AA8, first strand: chain 'A' and resid 255 through 257 removed outlier: 6.575A pdb=" N ALA A 257 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N VAL A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 302 removed outlier: 7.194A pdb=" N TYR A 301 " --> pdb=" O ILE A 310 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 580 through 581 removed outlier: 3.687A pdb=" N GLU A 588 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS A 593 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLU A 602 " --> pdb=" O LYS A 593 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 580 through 581 removed outlier: 3.687A pdb=" N GLU A 588 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 748 through 752 removed outlier: 6.633A pdb=" N ARG A 731 " --> pdb=" O VAL A 727 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL A 727 " --> pdb=" O ARG A 731 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A 733 " --> pdb=" O GLN A 725 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 757 through 758 removed outlier: 3.995A pdb=" N THR A 757 " --> pdb=" O ILE A 765 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 768 through 769 Processing sheet with id=AB6, first strand: chain 'A' and resid 789 through 790 removed outlier: 3.590A pdb=" N ASP A 790 " --> pdb=" O GLU A 793 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1066 through 1067 removed outlier: 4.452A pdb=" N THR A1226 " --> pdb=" O PHE A 804 " (cutoff:3.500A) removed outlier: 9.206A pdb=" N ILE A1096 " --> pdb=" O ASN A 799 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ARG A 801 " --> pdb=" O ILE A1096 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEU A1098 " --> pdb=" O ARG A 801 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA A 803 " --> pdb=" O LEU A1098 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 817 " --> pdb=" O VAL A1097 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ILE A 816 " --> pdb=" O SER A1077 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE A1079 " --> pdb=" O ILE A 816 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 818 " --> pdb=" O ILE A1079 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1066 through 1067 Processing sheet with id=AB9, first strand: chain 'A' and resid 846 through 847 removed outlier: 3.862A pdb=" N GLY A 846 " --> pdb=" O THR A 843 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR A 843 " --> pdb=" O GLY A 846 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR A 830 " --> pdb=" O LYS A1057 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LYS A1057 " --> pdb=" O THR A 830 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N HIS A 832 " --> pdb=" O ALA A1055 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA A1055 " --> pdb=" O HIS A 832 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N GLN A 834 " --> pdb=" O TYR A1053 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TYR A1053 " --> pdb=" O GLN A 834 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU A 836 " --> pdb=" O LYS A1051 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LYS A1051 " --> pdb=" O LEU A 836 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N CYS A 838 " --> pdb=" O ILE A1049 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE A1049 " --> pdb=" O CYS A 838 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER A 840 " --> pdb=" O LEU A1047 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP A 930 " --> pdb=" O TYR A1053 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA A1055 " --> pdb=" O VAL A 928 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL A 928 " --> pdb=" O ALA A1055 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LYS A1057 " --> pdb=" O GLY A 926 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N GLY A 926 " --> pdb=" O LYS A1057 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 926 " --> pdb=" O VAL A 877 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1244 through 1246 Processing sheet with id=AC2, first strand: chain 'A' and resid 1269 through 1270 Processing sheet with id=AC3, first strand: chain 'A' and resid 1335 through 1337 Processing sheet with id=AC4, first strand: chain 'B' and resid 34 through 37 removed outlier: 4.452A pdb=" N SER B 34 " --> pdb=" O MET B 102 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N HIS B 104 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY B 36 " --> pdb=" O HIS B 104 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N GLU B 106 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 107 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR B 240 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 10.939A pdb=" N SER B 109 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N ILE B 238 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AC6, first strand: chain 'B' and resid 253 through 254 removed outlier: 4.416A pdb=" N VAL B 253 " --> pdb=" O ALA B 261 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 526 through 527 Processing sheet with id=AC8, first strand: chain 'B' and resid 706 through 708 removed outlier: 3.685A pdb=" N GLU B 714 " --> pdb=" O ILE B 707 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 821 through 822 Processing sheet with id=AD1, first strand: chain 'B' and resid 849 through 850 removed outlier: 4.609A pdb=" N ASP B 855 " --> pdb=" O LYS B 850 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 957 through 961 removed outlier: 3.803A pdb=" N THR B 980 " --> pdb=" O VAL B 997 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 965 through 967 Processing sheet with id=AD4, first strand: chain 'B' and resid 1034 through 1038 removed outlier: 3.619A pdb=" N ARG B1036 " --> pdb=" O LYS B1079 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS B1079 " --> pdb=" O ARG B1036 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1046 through 1049 removed outlier: 4.087A pdb=" N GLN B1049 " --> pdb=" O SER B1058 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER B1058 " --> pdb=" O GLN B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1187 through 1190 Processing sheet with id=AD7, first strand: chain 'B' and resid 1279 through 1281 removed outlier: 7.344A pdb=" N THR B1301 " --> pdb=" O VAL B1267 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 12 through 13 removed outlier: 6.339A pdb=" N ASP C 199 " --> pdb=" O PRO C 30 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 202 " --> pdb=" O ASN C 186 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 52 through 53 removed outlier: 3.521A pdb=" N GLY C 53 " --> pdb=" O GLY C 149 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 115 through 116 removed outlier: 4.249A pdb=" N THR C 101 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N SER C 141 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ILE C 61 " --> pdb=" O SER C 141 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG C 143 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL C 59 " --> pdb=" O ARG C 143 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS C 145 " --> pdb=" O THR C 57 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 90 through 91 Processing sheet with id=AE3, first strand: chain 'C' and resid 108 through 111 removed outlier: 3.837A pdb=" N CYS C 131 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 23 through 31 removed outlier: 7.013A pdb=" N ASP D 199 " --> pdb=" O PRO D 30 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG D 182 " --> pdb=" O GLU D 206 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 53 through 61 removed outlier: 4.074A pdb=" N ALA D 55 " --> pdb=" O GLN D 147 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LYS D 145 " --> pdb=" O THR D 57 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL D 59 " --> pdb=" O ARG D 143 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ARG D 143 " --> pdb=" O VAL D 59 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 90 through 91 Processing sheet with id=AE7, first strand: chain 'D' and resid 108 through 111 removed outlier: 4.051A pdb=" N CYS D 131 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 152 through 153 removed outlier: 3.624A pdb=" N VAL D 153 " --> pdb=" O ALA D 175 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 39 through 43 removed outlier: 4.151A pdb=" N GLU F 41 " --> pdb=" O GLN F 72 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN F 72 " --> pdb=" O GLU F 41 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N VAL F 11 " --> pdb=" O PHE F 92 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N PHE F 92 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLN F 13 " --> pdb=" O MET F 90 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 133 through 134 removed outlier: 3.684A pdb=" N GLU F 149 " --> pdb=" O LYS F 159 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LYS F 159 " --> pdb=" O GLU F 149 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL F 171 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL F 162 " --> pdb=" O THR F 169 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE F 164 " --> pdb=" O ARG F 167 " (cutoff:3.500A) 1000 hydrogen bonds defined for protein. 2820 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 75 hydrogen bonds 150 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 10.68 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11214 1.03 - 1.23: 304 1.23 - 1.42: 11390 1.42 - 1.62: 16720 1.62 - 1.81: 203 Bond restraints: 39831 Sorted by residual: bond pdb=" CA THR B 93 " pdb=" C THR B 93 " ideal model delta sigma weight residual 1.523 1.687 -0.164 1.34e-02 5.57e+03 1.50e+02 bond pdb=" N1 G 7 30 " pdb=" H1 G 7 30 " ideal model delta sigma weight residual 0.860 1.040 -0.180 2.00e-02 2.50e+03 8.06e+01 bond pdb=" CA CYS B 70 " pdb=" CB CYS B 70 " ideal model delta sigma weight residual 1.527 1.405 0.122 1.38e-02 5.25e+03 7.80e+01 bond pdb=" O3' DT 5 109 " pdb=" P DA 5 110 " ideal model delta sigma weight residual 1.607 1.712 -0.105 1.20e-02 6.94e+03 7.61e+01 bond pdb=" C1' DG 6 10 " pdb=" N9 DG 6 10 " ideal model delta sigma weight residual 1.468 1.354 0.114 1.40e-02 5.10e+03 6.60e+01 ... (remaining 39826 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.67: 64596 9.67 - 19.34: 26 19.34 - 29.00: 3 29.00 - 38.67: 1 38.67 - 48.34: 2 Bond angle restraints: 64628 Sorted by residual: angle pdb=" O3' DG 6 27 " pdb=" P DA 6 28 " pdb=" O5' DA 6 28 " ideal model delta sigma weight residual 104.00 148.05 -44.05 1.90e+00 2.77e-01 5.37e+02 angle pdb=" H2' DA 5 110 " pdb=" C2' DA 5 110 " pdb="H2'' DA 5 110 " ideal model delta sigma weight residual 109.00 76.07 32.93 1.50e+00 4.44e-01 4.82e+02 angle pdb=" O3' DG 6 27 " pdb=" P DA 6 28 " pdb=" OP1 DA 6 28 " ideal model delta sigma weight residual 108.00 59.66 48.34 3.00e+00 1.11e-01 2.60e+02 angle pdb=" C VAL A 920 " pdb=" N PRO A 921 " pdb=" CA PRO A 921 " ideal model delta sigma weight residual 119.84 139.45 -19.61 1.25e+00 6.40e-01 2.46e+02 angle pdb=" C3' DA 6 28 " pdb=" O3' DA 6 28 " pdb=" P DT 6 29 " ideal model delta sigma weight residual 119.70 136.23 -16.53 1.20e+00 6.94e-01 1.90e+02 ... (remaining 64623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 19938 35.99 - 71.98: 826 71.98 - 107.98: 19 107.98 - 143.97: 1 143.97 - 179.96: 7 Dihedral angle restraints: 20791 sinusoidal: 10766 harmonic: 10025 Sorted by residual: dihedral pdb=" CA VAL C 192 " pdb=" C VAL C 192 " pdb=" N GLU C 193 " pdb=" CA GLU C 193 " ideal model delta harmonic sigma weight residual -180.00 -126.71 -53.29 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" O4' U 7 24 " pdb=" C1' U 7 24 " pdb=" N1 U 7 24 " pdb=" C2 U 7 24 " ideal model delta sinusoidal sigma weight residual 200.00 43.57 156.43 1 1.50e+01 4.44e-03 8.18e+01 dihedral pdb=" CA GLN B1326 " pdb=" C GLN B1326 " pdb=" N GLU B1327 " pdb=" CA GLU B1327 " ideal model delta harmonic sigma weight residual -180.00 -138.11 -41.89 0 5.00e+00 4.00e-02 7.02e+01 ... (remaining 20788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 4012 0.107 - 0.215: 412 0.215 - 0.322: 25 0.322 - 0.430: 2 0.430 - 0.537: 2 Chirality restraints: 4453 Sorted by residual: chirality pdb=" CB ILE A1079 " pdb=" CA ILE A1079 " pdb=" CG1 ILE A1079 " pdb=" CG2 ILE A1079 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.54 2.00e-01 2.50e+01 7.21e+00 chirality pdb=" CA TYR B 46 " pdb=" N TYR B 46 " pdb=" C TYR B 46 " pdb=" CB TYR B 46 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.92e+00 chirality pdb=" CB ILE A 765 " pdb=" CA ILE A 765 " pdb=" CG1 ILE A 765 " pdb=" CG2 ILE A 765 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.58e+00 ... (remaining 4450 not shown) Planarity restraints: 6121 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 232 " 0.210 2.00e-02 2.50e+03 2.51e-01 9.42e+02 pdb=" CG ASN B 232 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN B 232 " -0.203 2.00e-02 2.50e+03 pdb=" ND2 ASN B 232 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN B 232 " 0.385 2.00e-02 2.50e+03 pdb="HD22 ASN B 232 " -0.379 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 61 " -0.029 2.00e-02 2.50e+03 5.73e-02 3.29e+01 pdb=" N PHE B 62 " 0.098 2.00e-02 2.50e+03 pdb=" CA PHE B 62 " -0.023 2.00e-02 2.50e+03 pdb=" H PHE B 62 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 69 " 0.024 2.00e-02 2.50e+03 4.89e-02 2.40e+01 pdb=" C GLU B 69 " -0.085 2.00e-02 2.50e+03 pdb=" O GLU B 69 " 0.032 2.00e-02 2.50e+03 pdb=" N CYS B 70 " 0.029 2.00e-02 2.50e+03 ... (remaining 6118 not shown) Histogram of nonbonded interaction distances: 1.21 - 1.89: 254 1.89 - 2.57: 22949 2.57 - 3.24: 82409 3.24 - 3.92: 118943 3.92 - 4.60: 180977 Nonbonded interactions: 405532 Sorted by model distance: nonbonded pdb=" O3' DA 5 103 " pdb=" NH2 ARG A 473 " model vdw 1.211 2.950 nonbonded pdb=" H42 DC 6 18 " pdb=" H1 G 7 35 " model vdw 1.266 2.100 nonbonded pdb=" HA LYS B 222 " pdb=" HD2 LYS B 222 " model vdw 1.325 2.440 nonbonded pdb=" OE2 GLU A 641 " pdb=" HZ3 LYS B 749 " model vdw 1.340 2.450 nonbonded pdb=" HG2 ARG B 202 " pdb="HH11 ARG B 202 " model vdw 1.346 2.270 ... (remaining 405527 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 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 7 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 158 or resid 169 through 232)) selection = (chain 'D' and (resid 7 through 190 or (resid 191 through 192 and (name N or nam \ e CA or name C or name O or name CB )) or resid 193 or (resid 194 and (name N or \ name CA or name C or name O or name CB )) or resid 195 through 232)) } 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 group one per residue 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: 5.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.330 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 48.320 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5210 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 : 0.011 0.499 28609 Z= 0.546 Angle : 1.195 48.338 39010 Z= 0.695 Chirality : 0.066 0.537 4453 Planarity : 0.007 0.081 4803 Dihedral : 15.482 156.433 11233 Min Nonbonded Distance : 1.211 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.69 % Allowed : 8.74 % Favored : 90.56 % Rotamer: Outliers : 4.21 % Allowed : 4.35 % Favored : 91.44 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.71 % Twisted General : 0.19 % 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: -4.34 (0.11), residues: 3328 helix: -2.91 (0.11), residues: 1100 sheet: -2.04 (0.24), residues: 399 loop : -3.14 (0.12), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 8 TYR 0.039 0.003 TYR A1229 PHE 0.035 0.003 PHE B 620 TRP 0.043 0.004 TRP A 183 HIS 0.018 0.002 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.01004 / 0.52 (28602) covalent geometry : angle 1.17398 / 0.69 (39002) SS BOND : bond 0.23800 / 11.90 ( 1) SS BOND : angle 4.33638 / 8.27 ( 2) hydrogen bonds : bond 0.17513 / 19.07 ( 1072) hydrogen bonds : angle 7.31413 / 9.11 ( 2970) metal coordination : bond 0.27791 / 17.32 ( 6) metal coordination : angle 18.03238 / 34.64 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 491 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ILE cc_start: 0.6688 (OUTLIER) cc_final: 0.6368 (mt) REVERT: A 306 THR cc_start: 0.7952 (p) cc_final: 0.7549 (t) REVERT: A 414 ILE cc_start: 0.3961 (pt) cc_final: 0.2922 (pt) REVERT: A 913 VAL cc_start: 0.4465 (OUTLIER) cc_final: 0.4044 (p) REVERT: B 70 CYS cc_start: 0.5666 (OUTLIER) cc_final: 0.5266 (t) REVERT: B 119 SER cc_start: 0.4289 (OUTLIER) cc_final: 0.4039 (p) REVERT: B 154 LEU cc_start: 0.5989 (OUTLIER) cc_final: 0.5739 (mp) REVERT: B 299 LEU cc_start: 0.4882 (tt) cc_final: 0.4576 (tt) REVERT: C 201 LEU cc_start: 0.7360 (tp) cc_final: 0.7154 (tt) REVERT: E 10 VAL cc_start: 0.7794 (t) cc_final: 0.7569 (p) outliers start: 120 outliers final: 30 residues processed: 587 average time/residue: 0.3151 time to fit residues: 282.6929 Evaluate side-chains 311 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 276 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 HIS ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN A 330 HIS ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** A 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1268 GLN A1313 HIS B1279 GLN C 147 GLN D 66 HIS D 117 HIS D 227 GLN F 33 HIS F 117 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.062747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.047207 restraints weight = 457227.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.048883 restraints weight = 261254.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.050084 restraints weight = 174254.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.050905 restraints weight = 129455.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.051379 restraints weight = 104409.269| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.133 28609 Z= 0.160 Angle : 0.677 14.481 39010 Z= 0.366 Chirality : 0.045 0.231 4453 Planarity : 0.006 0.089 4803 Dihedral : 16.279 152.739 4686 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 22.22 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.70 % Favored : 93.06 % Rotamer: Outliers : 0.11 % Allowed : 2.11 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.71 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.13), residues: 3328 helix: -0.86 (0.14), residues: 1105 sheet: -1.84 (0.24), residues: 431 loop : -2.77 (0.13), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1373 TYR 0.021 0.002 TYR F 153 PHE 0.037 0.002 PHE F 175 TRP 0.009 0.001 TRP A 807 HIS 0.008 0.001 HIS F 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (28602) covalent geometry : angle 0.67361 / 0.37 (39002) SS BOND : bond 0.01730 / 0.86 ( 1) SS BOND : angle 6.28170 / 11.77 ( 2) hydrogen bonds : bond 0.05215 / 5.63 ( 1072) hydrogen bonds : angle 5.44377 / 6.85 ( 2970) metal coordination : bond 0.01600 / 1.25 ( 6) metal coordination : angle 4.43261 / 7.92 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 312 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 LEU cc_start: 0.8125 (mp) cc_final: 0.7279 (mp) REVERT: A 459 MET cc_start: 0.9192 (mmp) cc_final: 0.8957 (mmp) REVERT: A 622 ASN cc_start: 0.8830 (t0) cc_final: 0.8554 (t0) REVERT: A 768 MET cc_start: 0.8164 (tmm) cc_final: 0.7822 (tmm) REVERT: A 951 MET cc_start: 0.9523 (mmp) cc_final: 0.9293 (mmp) REVERT: A 1126 ASP cc_start: 0.9166 (m-30) cc_final: 0.8948 (m-30) REVERT: A 1290 MET cc_start: 0.9342 (tpt) cc_final: 0.8665 (tpp) REVERT: A 1315 MET cc_start: 0.8096 (ppp) cc_final: 0.7847 (ppp) REVERT: B 466 MET cc_start: 0.8972 (mtp) cc_final: 0.8254 (mtp) REVERT: B 497 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8753 (mp0) REVERT: B 697 MET cc_start: 0.9226 (ppp) cc_final: 0.8860 (ppp) REVERT: B 704 GLU cc_start: 0.7091 (pt0) cc_final: 0.6864 (pt0) REVERT: B 724 MET cc_start: 0.9614 (mtm) cc_final: 0.8960 (mpp) REVERT: B 1040 MET cc_start: -0.0921 (ttp) cc_final: -0.1154 (ttm) REVERT: B 1193 TRP cc_start: 0.9056 (m-10) cc_final: 0.8570 (m-90) REVERT: B 1256 ILE cc_start: 0.9099 (mm) cc_final: 0.8833 (tt) REVERT: B 1306 LEU cc_start: 0.9013 (tp) cc_final: 0.8695 (tp) REVERT: B 1332 LEU cc_start: 0.9405 (tt) cc_final: 0.9198 (tt) REVERT: B 1361 THR cc_start: 0.7015 (m) cc_final: 0.6547 (m) REVERT: C 51 MET cc_start: 0.7937 (mmp) cc_final: 0.7692 (mmm) REVERT: D 51 MET cc_start: 0.8446 (mmp) cc_final: 0.8092 (mmm) REVERT: E 26 ARG cc_start: 0.8758 (tpt90) cc_final: 0.8415 (tpm170) REVERT: E 43 ASN cc_start: 0.9200 (t0) cc_final: 0.8979 (t0) REVERT: F 35 MET cc_start: 0.8080 (mmm) cc_final: 0.7805 (mmm) REVERT: F 75 MET cc_start: 0.7067 (pmm) cc_final: 0.6228 (ttt) outliers start: 3 outliers final: 2 residues processed: 314 average time/residue: 0.3000 time to fit residues: 149.8918 Evaluate side-chains 249 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 247 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 201 optimal weight: 0.5980 chunk 36 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 142 optimal weight: 0.2980 chunk 148 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 182 optimal weight: 6.9990 chunk 253 optimal weight: 7.9990 chunk 297 optimal weight: 8.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 GLN A 688 GLN ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 GLN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 HIS ** A1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 ASN ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.059832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.044466 restraints weight = 465805.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.046082 restraints weight = 265784.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.047202 restraints weight = 177970.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.047965 restraints weight = 133408.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.048419 restraints weight = 108381.972| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 28609 Z= 0.154 Angle : 0.590 10.317 39010 Z= 0.319 Chirality : 0.042 0.226 4453 Planarity : 0.005 0.051 4803 Dihedral : 15.977 149.946 4686 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 21.96 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.82 % Favored : 93.00 % Rotamer: Outliers : 0.14 % Allowed : 1.44 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.71 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.14), residues: 3328 helix: 0.12 (0.15), residues: 1111 sheet: -1.62 (0.25), residues: 417 loop : -2.37 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 123 TYR 0.021 0.001 TYR B 631 PHE 0.029 0.002 PHE A 35 TRP 0.010 0.001 TRP F 9 HIS 0.005 0.001 HIS B 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (28602) covalent geometry : angle 0.58871 / 0.32 (39002) SS BOND : bond 0.00269 / 0.13 ( 1) SS BOND : angle 3.69188 / 7.27 ( 2) hydrogen bonds : bond 0.04301 / 4.73 ( 1072) hydrogen bonds : angle 4.95166 / 6.26 ( 2970) metal coordination : bond 0.00443 / 0.29 ( 6) metal coordination : angle 2.62596 / 5.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 275 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8900 (tt) cc_final: 0.8634 (tt) REVERT: A 213 LEU cc_start: 0.8470 (mp) cc_final: 0.7965 (mp) REVERT: A 215 TYR cc_start: 0.5852 (m-80) cc_final: 0.5449 (m-80) REVERT: A 369 MET cc_start: 0.6922 (tmm) cc_final: 0.6481 (tmm) REVERT: A 476 LYS cc_start: 0.9019 (mttt) cc_final: 0.8814 (mtmt) REVERT: A 515 MET cc_start: 0.8051 (ttp) cc_final: 0.7184 (tmm) REVERT: A 768 MET cc_start: 0.8479 (tmm) cc_final: 0.8205 (tmm) REVERT: A 951 MET cc_start: 0.9532 (mmp) cc_final: 0.9292 (mmp) REVERT: A 1126 ASP cc_start: 0.9217 (m-30) cc_final: 0.8987 (m-30) REVERT: A 1180 MET cc_start: 0.8887 (tmm) cc_final: 0.8174 (tmm) REVERT: A 1290 MET cc_start: 0.9503 (tpt) cc_final: 0.9267 (mmm) REVERT: A 1319 MET cc_start: 0.7291 (tmm) cc_final: 0.6847 (tmm) REVERT: A 1337 ILE cc_start: 0.8788 (tp) cc_final: 0.8525 (tp) REVERT: B 454 CYS cc_start: 0.8967 (m) cc_final: 0.8693 (m) REVERT: B 466 MET cc_start: 0.8981 (mtp) cc_final: 0.8324 (mtp) REVERT: B 497 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8810 (mp0) REVERT: B 704 GLU cc_start: 0.7284 (pt0) cc_final: 0.7008 (pt0) REVERT: B 724 MET cc_start: 0.9637 (mtm) cc_final: 0.8838 (mpp) REVERT: B 747 MET cc_start: 0.7789 (mmt) cc_final: 0.7267 (mmm) REVERT: B 821 MET cc_start: 0.6776 (mmm) cc_final: 0.6502 (mmm) REVERT: B 1040 MET cc_start: -0.0784 (ttp) cc_final: -0.1113 (ttm) REVERT: B 1193 TRP cc_start: 0.9127 (m-10) cc_final: 0.8613 (m-90) REVERT: C 25 LYS cc_start: 0.9529 (mtmt) cc_final: 0.9274 (mtmm) REVERT: C 51 MET cc_start: 0.8220 (mmp) cc_final: 0.7989 (mmm) REVERT: D 51 MET cc_start: 0.8822 (mmp) cc_final: 0.8301 (mmm) REVERT: E 26 ARG cc_start: 0.8968 (tpt90) cc_final: 0.8522 (tpm170) REVERT: E 43 ASN cc_start: 0.9196 (t0) cc_final: 0.8990 (t0) REVERT: E 67 ARG cc_start: 0.9194 (mmm160) cc_final: 0.8769 (mmm160) REVERT: E 71 GLU cc_start: 0.9420 (pt0) cc_final: 0.9218 (pt0) REVERT: F 165 PHE cc_start: 0.8817 (t80) cc_final: 0.8518 (t80) outliers start: 4 outliers final: 3 residues processed: 278 average time/residue: 0.2808 time to fit residues: 125.5937 Evaluate side-chains 222 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 219 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 10 optimal weight: 0.8980 chunk 290 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 293 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 128 optimal weight: 8.9990 chunk 204 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN A 463 GLN A 513 GLN A 628 HIS A 686 GLN ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 ASN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 HIS D 93 GLN ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.056416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.041247 restraints weight = 478208.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.042757 restraints weight = 269823.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.043806 restraints weight = 180775.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.044518 restraints weight = 135729.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.044920 restraints weight = 111013.517| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 28609 Z= 0.198 Angle : 0.624 13.890 39010 Z= 0.338 Chirality : 0.042 0.280 4453 Planarity : 0.004 0.052 4803 Dihedral : 15.880 151.068 4686 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 26.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.67 % Favored : 93.18 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.61 (0.14), residues: 3328 helix: 0.58 (0.16), residues: 1118 sheet: -1.21 (0.26), residues: 392 loop : -2.19 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 52 TYR 0.017 0.001 TYR B 631 PHE 0.018 0.002 PHE A 230 TRP 0.016 0.002 TRP A 183 HIS 0.008 0.001 HIS A1116 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.20 (28602) covalent geometry : angle 0.62324 / 0.34 (39002) SS BOND : bond 0.01666 / 0.83 ( 1) SS BOND : angle 2.20423 / 3.91 ( 2) hydrogen bonds : bond 0.04084 / 4.43 ( 1072) hydrogen bonds : angle 4.87994 / 6.38 ( 2970) metal coordination : bond 0.01294 / 0.96 ( 6) metal coordination : angle 2.63474 / 4.84 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 TYR cc_start: 0.7482 (m-80) cc_final: 0.7231 (m-80) REVERT: A 315 MET cc_start: 0.5856 (ppp) cc_final: 0.5023 (ppp) REVERT: A 369 MET cc_start: 0.7235 (tmm) cc_final: 0.6827 (tmm) REVERT: A 476 LYS cc_start: 0.9026 (mttt) cc_final: 0.8736 (mtpt) REVERT: A 515 MET cc_start: 0.8510 (ttp) cc_final: 0.7439 (tmm) REVERT: A 768 MET cc_start: 0.8671 (tmm) cc_final: 0.8422 (tmm) REVERT: A 951 MET cc_start: 0.9502 (mmp) cc_final: 0.9205 (mmp) REVERT: A 1066 MET cc_start: 0.9192 (mmm) cc_final: 0.8826 (mmm) REVERT: A 1126 ASP cc_start: 0.9274 (m-30) cc_final: 0.9039 (m-30) REVERT: A 1290 MET cc_start: 0.9630 (tpt) cc_final: 0.8712 (tpp) REVERT: A 1315 MET cc_start: 0.8366 (ppp) cc_final: 0.8092 (tmm) REVERT: A 1326 LEU cc_start: 0.9506 (tt) cc_final: 0.9267 (tt) REVERT: A 1329 GLU cc_start: 0.9251 (mt-10) cc_final: 0.8630 (mt-10) REVERT: B 20 ILE cc_start: 0.8886 (tp) cc_final: 0.8665 (tp) REVERT: B 127 LEU cc_start: 0.9132 (tp) cc_final: 0.8751 (tp) REVERT: B 454 CYS cc_start: 0.8899 (m) cc_final: 0.8666 (m) REVERT: B 466 MET cc_start: 0.9174 (mtp) cc_final: 0.8676 (mtp) REVERT: B 485 MET cc_start: 0.8760 (mmm) cc_final: 0.8505 (mmm) REVERT: B 704 GLU cc_start: 0.7546 (pt0) cc_final: 0.7210 (pt0) REVERT: B 724 MET cc_start: 0.9652 (mtm) cc_final: 0.8933 (mpp) REVERT: B 747 MET cc_start: 0.8058 (mmt) cc_final: 0.7489 (mmm) REVERT: B 1040 MET cc_start: -0.0488 (ttp) cc_final: -0.0812 (ttm) REVERT: B 1193 TRP cc_start: 0.9170 (m-10) cc_final: 0.8609 (m-90) REVERT: B 1260 MET cc_start: 0.7835 (tpt) cc_final: 0.7274 (tpt) REVERT: B 1361 THR cc_start: 0.7769 (m) cc_final: 0.7453 (m) REVERT: C 25 LYS cc_start: 0.9611 (mtmt) cc_final: 0.9342 (mtmm) REVERT: D 51 MET cc_start: 0.9054 (mmp) cc_final: 0.8575 (mmm) REVERT: E 26 ARG cc_start: 0.9115 (tpt90) cc_final: 0.8543 (tpm170) REVERT: E 30 MET cc_start: 0.8600 (mmm) cc_final: 0.8336 (mmm) REVERT: E 36 ASP cc_start: 0.8988 (p0) cc_final: 0.8784 (p0) REVERT: E 39 VAL cc_start: 0.9164 (t) cc_final: 0.8685 (t) REVERT: F 90 MET cc_start: 0.7314 (mmp) cc_final: 0.6954 (mmm) REVERT: F 165 PHE cc_start: 0.8845 (t80) cc_final: 0.8539 (t80) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.2849 time to fit residues: 114.8606 Evaluate side-chains 203 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 282 optimal weight: 8.9990 chunk 256 optimal weight: 0.9990 chunk 334 optimal weight: 9.9990 chunk 148 optimal weight: 0.9980 chunk 275 optimal weight: 3.9990 chunk 281 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 chunk 83 optimal weight: 0.6980 chunk 60 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 HIS ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 HIS A1136 GLN ** A1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.055688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.040585 restraints weight = 475123.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.042091 restraints weight = 265683.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.043127 restraints weight = 177388.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.043839 restraints weight = 133223.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.044251 restraints weight = 108980.428| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 28609 Z= 0.134 Angle : 0.524 11.232 39010 Z= 0.285 Chirality : 0.041 0.162 4453 Planarity : 0.004 0.045 4803 Dihedral : 15.725 151.400 4686 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 25.84 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.10 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.71 % Twisted General : 0.06 % 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: -1.29 (0.14), residues: 3328 helix: 0.95 (0.16), residues: 1117 sheet: -1.18 (0.25), residues: 412 loop : -2.04 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 123 TYR 0.015 0.001 TYR F 68 PHE 0.014 0.001 PHE A1187 TRP 0.012 0.001 TRP F 9 HIS 0.025 0.001 HIS A1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (28602) covalent geometry : angle 0.52314 / 0.28 (39002) SS BOND : bond 0.05009 / 2.50 ( 1) SS BOND : angle 3.51870 / 6.24 ( 2) hydrogen bonds : bond 0.03779 / 4.11 ( 1072) hydrogen bonds : angle 4.61105 / 5.98 ( 2970) metal coordination : bond 0.00761 / 0.97 ( 6) metal coordination : angle 1.86567 / 3.58 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 TYR cc_start: 0.7466 (m-80) cc_final: 0.7170 (m-80) REVERT: A 515 MET cc_start: 0.8582 (ttp) cc_final: 0.7522 (tmm) REVERT: A 685 MET cc_start: 0.9122 (mtm) cc_final: 0.8884 (mtt) REVERT: A 768 MET cc_start: 0.8694 (tmm) cc_final: 0.8420 (tmm) REVERT: A 951 MET cc_start: 0.9498 (mmp) cc_final: 0.9186 (mmp) REVERT: A 1066 MET cc_start: 0.8832 (mmm) cc_final: 0.8045 (mmm) REVERT: A 1085 MET cc_start: 0.9674 (mmp) cc_final: 0.9377 (mmt) REVERT: A 1126 ASP cc_start: 0.9223 (m-30) cc_final: 0.8954 (m-30) REVERT: A 1290 MET cc_start: 0.9634 (tpt) cc_final: 0.9139 (mmm) REVERT: A 1315 MET cc_start: 0.8361 (ppp) cc_final: 0.8116 (tmm) REVERT: A 1325 VAL cc_start: 0.9604 (t) cc_final: 0.9374 (t) REVERT: A 1326 LEU cc_start: 0.9489 (tt) cc_final: 0.9252 (tt) REVERT: A 1329 GLU cc_start: 0.9192 (mt-10) cc_final: 0.8532 (mt-10) REVERT: B 102 MET cc_start: 0.6584 (ppp) cc_final: 0.6348 (ppp) REVERT: B 454 CYS cc_start: 0.8845 (m) cc_final: 0.8583 (m) REVERT: B 485 MET cc_start: 0.8795 (mmm) cc_final: 0.8497 (mmm) REVERT: B 581 MET cc_start: 0.8987 (tpp) cc_final: 0.8706 (tpp) REVERT: B 704 GLU cc_start: 0.7557 (pt0) cc_final: 0.7283 (pt0) REVERT: B 724 MET cc_start: 0.9651 (mtm) cc_final: 0.8937 (mpp) REVERT: B 747 MET cc_start: 0.8166 (mmt) cc_final: 0.7674 (mmm) REVERT: B 1040 MET cc_start: -0.0432 (ttp) cc_final: -0.0699 (ttm) REVERT: B 1193 TRP cc_start: 0.9166 (m-10) cc_final: 0.8679 (m-90) REVERT: B 1260 MET cc_start: 0.7583 (tpt) cc_final: 0.7353 (tpt) REVERT: B 1361 THR cc_start: 0.7771 (m) cc_final: 0.7520 (m) REVERT: C 25 LYS cc_start: 0.9623 (mtmt) cc_final: 0.9316 (mtmm) REVERT: D 51 MET cc_start: 0.9103 (mmp) cc_final: 0.8575 (mmm) REVERT: E 8 ASP cc_start: 0.9252 (p0) cc_final: 0.8992 (p0) REVERT: E 26 ARG cc_start: 0.9154 (tpt90) cc_final: 0.8582 (tpm170) REVERT: E 30 MET cc_start: 0.8576 (mmm) cc_final: 0.8325 (mmm) REVERT: E 36 ASP cc_start: 0.8934 (p0) cc_final: 0.8726 (p0) REVERT: F 13 GLN cc_start: 0.9136 (tt0) cc_final: 0.8801 (tm-30) REVERT: F 26 LEU cc_start: 0.9074 (tp) cc_final: 0.8744 (mt) REVERT: F 75 MET cc_start: 0.7923 (pmm) cc_final: 0.7695 (pmm) REVERT: F 165 PHE cc_start: 0.8860 (t80) cc_final: 0.8569 (t80) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.2875 time to fit residues: 108.4443 Evaluate side-chains 201 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 303 optimal weight: 0.9980 chunk 248 optimal weight: 0.5980 chunk 176 optimal weight: 7.9990 chunk 240 optimal weight: 7.9990 chunk 247 optimal weight: 9.9990 chunk 179 optimal weight: 5.9990 chunk 271 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 291 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 239 optimal weight: 0.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN ** A 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 HIS A1220 GLN ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN B1259 GLN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN E 70 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.053115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.038263 restraints weight = 486067.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.039684 restraints weight = 271324.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.040661 restraints weight = 181458.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.041288 restraints weight = 136658.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.041751 restraints weight = 112736.604| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.5526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 28609 Z= 0.195 Angle : 0.589 14.373 39010 Z= 0.312 Chirality : 0.041 0.241 4453 Planarity : 0.004 0.047 4803 Dihedral : 15.711 152.012 4686 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 29.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.12 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.27 (0.14), residues: 3328 helix: 0.89 (0.16), residues: 1127 sheet: -1.04 (0.26), residues: 402 loop : -2.02 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 123 TYR 0.024 0.002 TYR B 631 PHE 0.020 0.001 PHE A 35 TRP 0.010 0.001 TRP F 9 HIS 0.004 0.001 HIS A 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.20 (28602) covalent geometry : angle 0.58794 / 0.31 (39002) SS BOND : bond 0.00508 / 0.25 ( 1) SS BOND : angle 3.06796 / 5.66 ( 2) hydrogen bonds : bond 0.03789 / 4.14 ( 1072) hydrogen bonds : angle 4.69426 / 6.13 ( 2970) metal coordination : bond 0.00504 / 0.52 ( 6) metal coordination : angle 1.38755 / 2.63 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 MET cc_start: 0.8459 (ttp) cc_final: 0.7505 (tmm) REVERT: A 685 MET cc_start: 0.9271 (mtm) cc_final: 0.8968 (mtt) REVERT: A 768 MET cc_start: 0.8834 (tmm) cc_final: 0.8596 (tmm) REVERT: A 951 MET cc_start: 0.9504 (mmp) cc_final: 0.9206 (mmp) REVERT: A 1126 ASP cc_start: 0.9257 (m-30) cc_final: 0.9028 (m-30) REVERT: A 1170 MET cc_start: 0.9454 (mmp) cc_final: 0.9251 (mmp) REVERT: A 1180 MET cc_start: 0.8881 (tmm) cc_final: 0.8377 (tmm) REVERT: A 1290 MET cc_start: 0.9639 (tpt) cc_final: 0.9387 (mmm) REVERT: A 1315 MET cc_start: 0.8461 (ppp) cc_final: 0.8258 (tmm) REVERT: A 1326 LEU cc_start: 0.9597 (tt) cc_final: 0.9364 (tt) REVERT: A 1329 GLU cc_start: 0.9282 (mt-10) cc_final: 0.8624 (mt-10) REVERT: B 102 MET cc_start: 0.6648 (ppp) cc_final: 0.6395 (ppp) REVERT: B 454 CYS cc_start: 0.8900 (m) cc_final: 0.8650 (m) REVERT: B 485 MET cc_start: 0.8926 (mmm) cc_final: 0.8705 (mmm) REVERT: B 581 MET cc_start: 0.9113 (tpp) cc_final: 0.8824 (tpp) REVERT: B 704 GLU cc_start: 0.7747 (pt0) cc_final: 0.7530 (pt0) REVERT: B 724 MET cc_start: 0.9656 (mtm) cc_final: 0.9009 (mpp) REVERT: B 747 MET cc_start: 0.8200 (mmt) cc_final: 0.7751 (mmm) REVERT: B 1040 MET cc_start: -0.0415 (ttp) cc_final: -0.0771 (ttm) REVERT: B 1193 TRP cc_start: 0.9151 (m-10) cc_final: 0.8678 (m-90) REVERT: B 1361 THR cc_start: 0.8027 (m) cc_final: 0.7778 (m) REVERT: C 25 LYS cc_start: 0.9657 (mtmt) cc_final: 0.9289 (mtmm) REVERT: D 51 MET cc_start: 0.9137 (mmp) cc_final: 0.8597 (mmm) REVERT: D 142 MET cc_start: 0.8164 (pmm) cc_final: 0.7946 (pmm) REVERT: E 26 ARG cc_start: 0.9237 (tpt90) cc_final: 0.8648 (tpm170) REVERT: E 36 ASP cc_start: 0.8983 (p0) cc_final: 0.8710 (p0) REVERT: F 90 MET cc_start: 0.8207 (mmp) cc_final: 0.7490 (mpp) REVERT: F 93 ILE cc_start: 0.6528 (tp) cc_final: 0.5446 (tp) REVERT: F 112 MET cc_start: 0.7810 (mpp) cc_final: 0.7486 (mmm) REVERT: F 116 GLN cc_start: 0.8625 (mp10) cc_final: 0.8296 (mp10) REVERT: F 165 PHE cc_start: 0.8963 (t80) cc_final: 0.8705 (t80) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.2721 time to fit residues: 99.6024 Evaluate side-chains 193 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 88 optimal weight: 9.9990 chunk 228 optimal weight: 7.9990 chunk 109 optimal weight: 0.7980 chunk 252 optimal weight: 0.4980 chunk 303 optimal weight: 10.0000 chunk 211 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 318 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 295 optimal weight: 0.7980 chunk 329 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.053689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.038749 restraints weight = 471829.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.040216 restraints weight = 262472.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.041213 restraints weight = 175116.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.041902 restraints weight = 131698.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.042312 restraints weight = 107814.619| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.5632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.094 28609 Z= 0.098 Angle : 0.492 17.936 39010 Z= 0.264 Chirality : 0.040 0.151 4453 Planarity : 0.003 0.046 4803 Dihedral : 15.631 152.559 4686 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 27.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.10 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.94 (0.15), residues: 3328 helix: 1.27 (0.16), residues: 1126 sheet: -0.98 (0.25), residues: 427 loop : -1.88 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1301 TYR 0.011 0.001 TYR B 723 PHE 0.013 0.001 PHE B 620 TRP 0.013 0.001 TRP B 115 HIS 0.006 0.001 HIS B 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (28602) covalent geometry : angle 0.49102 / 0.26 (39002) SS BOND : bond 0.00680 / 0.34 ( 1) SS BOND : angle 2.17690 / 4.03 ( 2) hydrogen bonds : bond 0.03419 / 3.70 ( 1072) hydrogen bonds : angle 4.39608 / 5.72 ( 2970) metal coordination : bond 0.00288 / 0.33 ( 6) metal coordination : angle 1.89365 / 3.71 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.9351 (tt) cc_final: 0.8529 (mp) REVERT: A 369 MET cc_start: 0.7733 (tmm) cc_final: 0.7495 (tmm) REVERT: A 515 MET cc_start: 0.8411 (ttp) cc_final: 0.7567 (tmm) REVERT: A 685 MET cc_start: 0.9220 (mtm) cc_final: 0.8927 (mtt) REVERT: A 768 MET cc_start: 0.8808 (tmm) cc_final: 0.8590 (tmm) REVERT: A 951 MET cc_start: 0.9511 (mmp) cc_final: 0.9248 (mmp) REVERT: A 1066 MET cc_start: 0.8654 (mmm) cc_final: 0.8104 (mmm) REVERT: A 1126 ASP cc_start: 0.9208 (m-30) cc_final: 0.8947 (m-30) REVERT: A 1170 MET cc_start: 0.9404 (mmp) cc_final: 0.9199 (mmp) REVERT: A 1290 MET cc_start: 0.9636 (tpt) cc_final: 0.9039 (tmm) REVERT: A 1315 MET cc_start: 0.8409 (ppp) cc_final: 0.8188 (tmm) REVERT: A 1319 MET cc_start: 0.8382 (tmm) cc_final: 0.7804 (tmm) REVERT: A 1326 LEU cc_start: 0.9581 (tt) cc_final: 0.9347 (tt) REVERT: A 1329 GLU cc_start: 0.9399 (mt-10) cc_final: 0.8779 (mt-10) REVERT: B 102 MET cc_start: 0.6526 (ppp) cc_final: 0.6222 (ppp) REVERT: B 115 TRP cc_start: 0.8864 (m-10) cc_final: 0.8613 (m-10) REVERT: B 454 CYS cc_start: 0.8862 (m) cc_final: 0.8599 (m) REVERT: B 485 MET cc_start: 0.8881 (mmm) cc_final: 0.8650 (mmm) REVERT: B 581 MET cc_start: 0.9077 (tpp) cc_final: 0.8765 (tpp) REVERT: B 724 MET cc_start: 0.9647 (mtm) cc_final: 0.8909 (mtp) REVERT: B 747 MET cc_start: 0.8155 (mmt) cc_final: 0.7696 (mmm) REVERT: B 1040 MET cc_start: -0.0327 (ttp) cc_final: -0.0675 (ttm) REVERT: B 1193 TRP cc_start: 0.9148 (m-10) cc_final: 0.8673 (m-90) REVERT: B 1260 MET cc_start: 0.7744 (tpt) cc_final: 0.7477 (tpt) REVERT: B 1361 THR cc_start: 0.7939 (m) cc_final: 0.7690 (m) REVERT: C 25 LYS cc_start: 0.9645 (mtmt) cc_final: 0.9258 (mtmm) REVERT: D 51 MET cc_start: 0.9114 (mmp) cc_final: 0.8633 (mmm) REVERT: D 142 MET cc_start: 0.8239 (pmm) cc_final: 0.8010 (pmm) REVERT: E 26 ARG cc_start: 0.9297 (tpt90) cc_final: 0.8704 (tpm170) REVERT: E 36 ASP cc_start: 0.8958 (p0) cc_final: 0.8698 (p0) REVERT: E 43 ASN cc_start: 0.9276 (t0) cc_final: 0.9045 (t0) REVERT: F 43 MET cc_start: 0.4574 (tpp) cc_final: 0.4314 (tpt) REVERT: F 90 MET cc_start: 0.7727 (mmp) cc_final: 0.7402 (mpp) REVERT: F 112 MET cc_start: 0.7967 (mpp) cc_final: 0.7623 (mmm) REVERT: F 116 GLN cc_start: 0.8676 (mp10) cc_final: 0.8335 (mp10) REVERT: F 165 PHE cc_start: 0.8955 (t80) cc_final: 0.8678 (t80) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.2911 time to fit residues: 103.5101 Evaluate side-chains 190 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 91 optimal weight: 0.0570 chunk 320 optimal weight: 6.9990 chunk 303 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 184 optimal weight: 0.9980 chunk 291 optimal weight: 5.9990 chunk 331 optimal weight: 5.9990 chunk 186 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 329 optimal weight: 0.6980 chunk 185 optimal weight: 0.6980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 HIS ** A1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 HIS ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.053537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.038627 restraints weight = 475262.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.040067 restraints weight = 263415.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.041059 restraints weight = 175819.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.041728 restraints weight = 132325.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.042170 restraints weight = 108728.500| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.5784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 28609 Z= 0.095 Angle : 0.473 8.157 39010 Z= 0.256 Chirality : 0.040 0.157 4453 Planarity : 0.003 0.045 4803 Dihedral : 15.546 153.072 4686 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 27.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.22 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.73 (0.15), residues: 3328 helix: 1.39 (0.16), residues: 1134 sheet: -0.86 (0.25), residues: 420 loop : -1.72 (0.14), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1301 TYR 0.027 0.001 TYR A 742 PHE 0.015 0.001 PHE F 92 TRP 0.011 0.001 TRP F 9 HIS 0.005 0.001 HIS B 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 (28602) covalent geometry : angle 0.47169 / 0.26 (39002) SS BOND : bond 0.01564 / 0.78 ( 1) SS BOND : angle 3.31187 / 5.52 ( 2) hydrogen bonds : bond 0.03253 / 3.54 ( 1072) hydrogen bonds : angle 4.26817 / 5.59 ( 2970) metal coordination : bond 0.00208 / 0.24 ( 6) metal coordination : angle 1.67587 / 3.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 TYR cc_start: 0.7172 (m-80) cc_final: 0.6965 (m-80) REVERT: A 96 LEU cc_start: 0.9354 (tt) cc_final: 0.8537 (mp) REVERT: A 369 MET cc_start: 0.7533 (tmm) cc_final: 0.7327 (tmm) REVERT: A 515 MET cc_start: 0.8370 (ttp) cc_final: 0.7482 (tmm) REVERT: A 681 MET cc_start: 0.8873 (mtm) cc_final: 0.8380 (mtm) REVERT: A 685 MET cc_start: 0.9236 (mtm) cc_final: 0.8960 (mtt) REVERT: A 768 MET cc_start: 0.8833 (tmm) cc_final: 0.8600 (tmm) REVERT: A 951 MET cc_start: 0.9536 (mmp) cc_final: 0.9209 (mmp) REVERT: A 1066 MET cc_start: 0.8626 (mmm) cc_final: 0.8161 (mmm) REVERT: A 1126 ASP cc_start: 0.9201 (m-30) cc_final: 0.8939 (m-30) REVERT: A 1170 MET cc_start: 0.9399 (mmp) cc_final: 0.9186 (mmp) REVERT: A 1290 MET cc_start: 0.9627 (tpt) cc_final: 0.9327 (tpt) REVERT: A 1319 MET cc_start: 0.8385 (tmm) cc_final: 0.7829 (tmm) REVERT: A 1326 LEU cc_start: 0.9551 (tt) cc_final: 0.9332 (tt) REVERT: A 1329 GLU cc_start: 0.9387 (mt-10) cc_final: 0.8788 (mt-10) REVERT: B 372 MET cc_start: 0.8744 (mmm) cc_final: 0.8398 (mmt) REVERT: B 454 CYS cc_start: 0.8849 (m) cc_final: 0.8586 (m) REVERT: B 485 MET cc_start: 0.8889 (mmm) cc_final: 0.8662 (mmm) REVERT: B 697 MET cc_start: 0.9463 (ptm) cc_final: 0.8920 (ppp) REVERT: B 724 MET cc_start: 0.9642 (mtm) cc_final: 0.8892 (mtp) REVERT: B 747 MET cc_start: 0.8148 (mmt) cc_final: 0.7715 (mmm) REVERT: B 1040 MET cc_start: -0.0473 (ttp) cc_final: -0.0807 (ttm) REVERT: B 1193 TRP cc_start: 0.9155 (m-10) cc_final: 0.8680 (m-90) REVERT: B 1260 MET cc_start: 0.7769 (tpt) cc_final: 0.7535 (tpt) REVERT: C 25 LYS cc_start: 0.9638 (mtmt) cc_final: 0.9247 (mtmm) REVERT: D 51 MET cc_start: 0.9083 (mmp) cc_final: 0.8579 (mmm) REVERT: D 142 MET cc_start: 0.8286 (pmm) cc_final: 0.8042 (pmm) REVERT: E 8 ASP cc_start: 0.9300 (p0) cc_final: 0.9047 (p0) REVERT: E 36 ASP cc_start: 0.9000 (p0) cc_final: 0.8751 (p0) REVERT: E 43 ASN cc_start: 0.9299 (t0) cc_final: 0.9067 (t0) REVERT: F 73 MET cc_start: 0.7221 (tpp) cc_final: 0.7004 (tpp) REVERT: F 165 PHE cc_start: 0.8989 (t80) cc_final: 0.8717 (t80) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.2815 time to fit residues: 96.2970 Evaluate side-chains 188 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 147 optimal weight: 1.9990 chunk 206 optimal weight: 8.9990 chunk 11 optimal weight: 0.0770 chunk 270 optimal weight: 0.9990 chunk 198 optimal weight: 4.9990 chunk 320 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 161 optimal weight: 0.8980 chunk 318 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 GLN ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 GLN ** A 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.052934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.038118 restraints weight = 480655.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.039544 restraints weight = 267672.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.040512 restraints weight = 178645.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.041104 restraints weight = 134851.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.041576 restraints weight = 112362.737| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.6060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 28609 Z= 0.099 Angle : 0.475 8.056 39010 Z= 0.256 Chirality : 0.040 0.152 4453 Planarity : 0.003 0.046 4803 Dihedral : 15.461 153.293 4686 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 27.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.13 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.15), residues: 3328 helix: 1.51 (0.16), residues: 1137 sheet: -0.66 (0.25), residues: 412 loop : -1.64 (0.15), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 150 TYR 0.022 0.001 TYR A 742 PHE 0.022 0.001 PHE C 8 TRP 0.010 0.001 TRP B 115 HIS 0.005 0.001 HIS B 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (28602) covalent geometry : angle 0.47410 / 0.26 (39002) SS BOND : bond 0.00483 / 0.24 ( 1) SS BOND : angle 3.37902 / 5.66 ( 2) hydrogen bonds : bond 0.03198 / 3.48 ( 1072) hydrogen bonds : angle 4.18742 / 5.49 ( 2970) metal coordination : bond 0.00230 / 0.27 ( 6) metal coordination : angle 1.53859 / 3.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 TYR cc_start: 0.7139 (m-80) cc_final: 0.6921 (m-80) REVERT: A 369 MET cc_start: 0.7611 (tmm) cc_final: 0.7410 (tmm) REVERT: A 515 MET cc_start: 0.8461 (ttp) cc_final: 0.7424 (tmm) REVERT: A 681 MET cc_start: 0.8912 (mtm) cc_final: 0.7999 (mtm) REVERT: A 685 MET cc_start: 0.9248 (mtm) cc_final: 0.8945 (mtt) REVERT: A 768 MET cc_start: 0.8875 (tmm) cc_final: 0.8622 (tmm) REVERT: A 951 MET cc_start: 0.9548 (mmp) cc_final: 0.9217 (mmp) REVERT: A 1066 MET cc_start: 0.8680 (mmm) cc_final: 0.8189 (mmm) REVERT: A 1126 ASP cc_start: 0.9207 (m-30) cc_final: 0.8950 (m-30) REVERT: A 1170 MET cc_start: 0.9407 (mmp) cc_final: 0.9173 (mmm) REVERT: A 1180 MET cc_start: 0.8777 (tmm) cc_final: 0.8251 (tmm) REVERT: A 1290 MET cc_start: 0.9626 (tpt) cc_final: 0.8927 (tmm) REVERT: A 1329 GLU cc_start: 0.9363 (mt-10) cc_final: 0.8790 (mt-10) REVERT: B 49 PHE cc_start: 0.7975 (m-80) cc_final: 0.7669 (m-80) REVERT: B 242 LEU cc_start: 0.9384 (tt) cc_final: 0.9020 (tt) REVERT: B 454 CYS cc_start: 0.8848 (m) cc_final: 0.8617 (m) REVERT: B 466 MET cc_start: 0.9319 (mtp) cc_final: 0.9027 (mtp) REVERT: B 485 MET cc_start: 0.8943 (mmm) cc_final: 0.8711 (mmm) REVERT: B 724 MET cc_start: 0.9649 (mtm) cc_final: 0.8939 (mtp) REVERT: B 747 MET cc_start: 0.8234 (mmt) cc_final: 0.7795 (mmm) REVERT: B 1040 MET cc_start: -0.0349 (ttp) cc_final: -0.0662 (ttm) REVERT: B 1193 TRP cc_start: 0.9188 (m-10) cc_final: 0.8702 (m-90) REVERT: B 1260 MET cc_start: 0.7774 (tpt) cc_final: 0.7480 (tpt) REVERT: B 1306 LEU cc_start: 0.9374 (mt) cc_final: 0.9146 (mt) REVERT: C 25 LYS cc_start: 0.9639 (mtmt) cc_final: 0.9352 (mtmm) REVERT: D 51 MET cc_start: 0.9000 (mmp) cc_final: 0.8480 (mmm) REVERT: D 142 MET cc_start: 0.8257 (pmm) cc_final: 0.7995 (pmm) REVERT: E 26 ARG cc_start: 0.9287 (tpt90) cc_final: 0.9010 (tpp80) REVERT: E 36 ASP cc_start: 0.8963 (p0) cc_final: 0.8714 (p0) REVERT: E 43 ASN cc_start: 0.9247 (t0) cc_final: 0.9030 (t0) REVERT: F 73 MET cc_start: 0.7288 (tpp) cc_final: 0.7059 (tpp) REVERT: F 165 PHE cc_start: 0.9049 (t80) cc_final: 0.8775 (t80) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.2556 time to fit residues: 89.3445 Evaluate side-chains 187 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 31 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 295 optimal weight: 1.9990 chunk 316 optimal weight: 9.9990 chunk 302 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 299 optimal weight: 0.9990 chunk 281 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 238 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 GLN ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN A 618 GLN ** A 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1367 GLN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 HIS ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.050729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.036185 restraints weight = 488536.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.037532 restraints weight = 270731.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.038446 restraints weight = 181097.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.039057 restraints weight = 137065.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.039412 restraints weight = 113631.596| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.6655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 28609 Z= 0.167 Angle : 0.542 16.871 39010 Z= 0.287 Chirality : 0.040 0.308 4453 Planarity : 0.004 0.045 4803 Dihedral : 15.459 152.919 4686 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 31.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.06 % Favored : 92.79 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.15), residues: 3328 helix: 1.30 (0.16), residues: 1141 sheet: -0.68 (0.25), residues: 440 loop : -1.63 (0.15), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 270 TYR 0.021 0.001 TYR B 269 PHE 0.017 0.001 PHE B 176 TRP 0.013 0.001 TRP F 9 HIS 0.005 0.001 HIS B 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 (28602) covalent geometry : angle 0.54184 / 0.29 (39002) SS BOND : bond 0.00576 / 0.29 ( 1) SS BOND : angle 2.96312 / 4.97 ( 2) hydrogen bonds : bond 0.03425 / 3.75 ( 1072) hydrogen bonds : angle 4.36602 / 5.79 ( 2970) metal coordination : bond 0.00373 / 0.39 ( 6) metal coordination : angle 1.21940 / 2.31 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.7666 (tmm) cc_final: 0.7465 (ppp) REVERT: A 429 MET cc_start: 0.9296 (mtm) cc_final: 0.9009 (mtt) REVERT: A 515 MET cc_start: 0.8635 (ttp) cc_final: 0.7611 (tmm) REVERT: A 681 MET cc_start: 0.8993 (mtm) cc_final: 0.8095 (mtm) REVERT: A 685 MET cc_start: 0.9344 (mtm) cc_final: 0.8987 (mtt) REVERT: A 704 MET cc_start: 0.9378 (mmm) cc_final: 0.9100 (mmm) REVERT: A 768 MET cc_start: 0.8949 (tmm) cc_final: 0.8737 (tmm) REVERT: A 951 MET cc_start: 0.9525 (mmp) cc_final: 0.9191 (mmp) REVERT: A 1126 ASP cc_start: 0.9219 (m-30) cc_final: 0.9003 (m-30) REVERT: A 1170 MET cc_start: 0.9455 (mmp) cc_final: 0.9154 (mmm) REVERT: A 1290 MET cc_start: 0.9625 (tpt) cc_final: 0.9331 (mmm) REVERT: A 1326 LEU cc_start: 0.9650 (tt) cc_final: 0.9439 (tt) REVERT: A 1329 GLU cc_start: 0.9404 (mt-10) cc_final: 0.8863 (mt-10) REVERT: B 49 PHE cc_start: 0.7961 (m-80) cc_final: 0.7651 (m-80) REVERT: B 180 MET cc_start: 0.8155 (ptp) cc_final: 0.7936 (ptp) REVERT: B 454 CYS cc_start: 0.8859 (m) cc_final: 0.8643 (m) REVERT: B 466 MET cc_start: 0.9428 (mtp) cc_final: 0.9170 (mtp) REVERT: B 485 MET cc_start: 0.9062 (mmm) cc_final: 0.8775 (mmm) REVERT: B 513 MET cc_start: 0.9704 (mtp) cc_final: 0.9358 (mmm) REVERT: B 581 MET cc_start: 0.9194 (tpp) cc_final: 0.8891 (tpp) REVERT: B 697 MET cc_start: 0.9491 (ptm) cc_final: 0.8903 (ppp) REVERT: B 724 MET cc_start: 0.9662 (mtm) cc_final: 0.9011 (mtp) REVERT: B 747 MET cc_start: 0.8319 (mmt) cc_final: 0.7817 (mmm) REVERT: B 1040 MET cc_start: -0.0052 (ttp) cc_final: -0.0338 (ttm) REVERT: B 1193 TRP cc_start: 0.9183 (m-10) cc_final: 0.8742 (m-90) REVERT: B 1260 MET cc_start: 0.8067 (tpt) cc_final: 0.7765 (tpt) REVERT: B 1306 LEU cc_start: 0.9380 (mt) cc_final: 0.9170 (mt) REVERT: C 25 LYS cc_start: 0.9657 (mtmt) cc_final: 0.9283 (mtmm) REVERT: D 51 MET cc_start: 0.9099 (mmp) cc_final: 0.8642 (mmm) REVERT: D 142 MET cc_start: 0.8465 (pmm) cc_final: 0.8017 (pmm) REVERT: E 7 GLN cc_start: 0.8888 (tp40) cc_final: 0.8639 (tp40) REVERT: E 26 ARG cc_start: 0.9328 (tpt90) cc_final: 0.9047 (tpp80) REVERT: E 36 ASP cc_start: 0.8998 (p0) cc_final: 0.8778 (p0) REVERT: E 43 ASN cc_start: 0.9296 (t0) cc_final: 0.9072 (t0) REVERT: F 73 MET cc_start: 0.7552 (tpp) cc_final: 0.7296 (tpp) REVERT: F 116 GLN cc_start: 0.8685 (mp10) cc_final: 0.8391 (mp10) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.2812 time to fit residues: 92.7924 Evaluate side-chains 177 residues out of total 2857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 285 optimal weight: 8.9990 chunk 339 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 243 optimal weight: 7.9990 chunk 297 optimal weight: 0.2980 chunk 313 optimal weight: 10.0000 chunk 192 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 187 optimal weight: 6.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.049975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.035399 restraints weight = 493394.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.036746 restraints weight = 269211.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.037643 restraints weight = 179069.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.038268 restraints weight = 135737.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.038618 restraints weight = 112261.228| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.7068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 28609 Z= 0.137 Angle : 0.508 8.681 39010 Z= 0.275 Chirality : 0.040 0.185 4453 Planarity : 0.004 0.102 4803 Dihedral : 15.444 153.116 4686 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 30.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.89 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.59 (0.15), residues: 3328 helix: 1.35 (0.16), residues: 1147 sheet: -0.48 (0.26), residues: 406 loop : -1.61 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1345 TYR 0.014 0.001 TYR A 742 PHE 0.017 0.001 PHE A 972 TRP 0.015 0.001 TRP F 9 HIS 0.005 0.001 HIS B1227 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (28602) covalent geometry : angle 0.50767 / 0.27 (39002) SS BOND : bond 0.00652 / 0.33 ( 1) SS BOND : angle 2.68943 / 4.48 ( 2) hydrogen bonds : bond 0.03293 / 3.60 ( 1072) hydrogen bonds : angle 4.29732 / 5.66 ( 2970) metal coordination : bond 0.00523 / 0.50 ( 6) metal coordination : angle 1.74600 / 3.39 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7666.64 seconds wall clock time: 131 minutes 59.95 seconds (7919.95 seconds total)