Starting phenix.real_space_refine on Mon Sep 14 22:59:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7d7d_30605/09_2026/7d7d_30605.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d7d_30605/09_2026/7d7d_30605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7d7d_30605/09_2026/7d7d_30605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d7d_30605/09_2026/7d7d_30605.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7d7d_30605/09_2026/7d7d_30605.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7d7d_30605/09_2026/7d7d_30605.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7d7d_30605/09_2026/7d7d_30605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d7d_30605/09_2026/7d7d_30605.map" } resolution = 4.5 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 94 5.49 5 Mg 1 5.21 5 S 132 5.16 5 C 20949 2.51 5 N 5888 2.21 5 O 6689 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33755 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1686 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1689 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} 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: "C" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "D" Number of atoms: 10384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10384 Classifications: {'peptide': 1335} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1279} Chain breaks: 2 Chain: "T" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 939 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain breaks: 1 Chain: "F" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1128 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 1, 'TRANS': 135} Chain breaks: 1 Chain: "N" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 990 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain breaks: 1 Chain: "K" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 558 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 67} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 564 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "G" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1749 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "H" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1749 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "I" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1749 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "D" 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 14537 SG CYS D 88 113.469 68.577 73.984 1.00202.45 S ATOM 20225 SG CYS D 814 85.986 82.912 136.182 1.00122.90 S ATOM 20790 SG CYS D 888 85.868 82.918 132.318 1.00119.14 S ATOM 20841 SG CYS D 895 84.420 80.053 134.163 1.00112.38 S ATOM 20862 SG CYS D 898 82.965 83.085 134.219 1.00109.26 S Time building chain proxies: 6.93, per 1000 atoms: 0.21 Number of scatterers: 33755 At special positions: 0 Unit cell: (167.296, 177.752, 169.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 132 16.00 P 94 15.00 Mg 1 11.99 O 6689 8.00 N 5888 7.00 C 20949 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.36 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " Number of angles added : 6 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7554 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 55 sheets defined 35.7% alpha, 16.4% beta 38 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 4.31 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.938A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'B' and resid 35 through 50 removed outlier: 4.152A pdb=" N ALA B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 removed outlier: 3.670A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'C' and resid 28 through 39 Processing helix chain 'C' and resid 47 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.588A pdb=" N ARG C 245 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 293 Processing helix chain 'C' and resid 318 through 328 removed outlier: 3.703A pdb=" N SER C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 354 removed outlier: 4.289A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR C 350 " --> pdb=" O TYR C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.561A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE C 390 " --> pdb=" O GLU C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 481 removed outlier: 3.704A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 removed outlier: 4.440A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 526 Processing helix chain 'C' and resid 551 through 555 Processing helix chain 'C' and resid 609 through 614 removed outlier: 3.738A pdb=" N ASN C 613 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 Processing helix chain 'C' and resid 705 through 710 removed outlier: 3.644A pdb=" N ALA C 709 " --> pdb=" O GLU C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 826 Processing helix chain 'C' and resid 858 through 865 removed outlier: 4.111A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU C 865 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 removed outlier: 4.604A pdb=" N LEU C 902 " --> pdb=" O GLU C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 969 removed outlier: 3.934A pdb=" N ASP C 959 " --> pdb=" O GLN C 955 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA C 969 " --> pdb=" O GLN C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 981 removed outlier: 4.349A pdb=" N ALA C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.268A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1123 Processing helix chain 'C' and resid 1124 through 1134 removed outlier: 3.621A pdb=" N ALA C1130 " --> pdb=" O ASP C1126 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 4.071A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C1151 " --> pdb=" O ARG C1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 1167 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 4.174A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1297 through 1310 Processing helix chain 'C' and resid 1321 through 1333 removed outlier: 4.186A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.680A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 129 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.725A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 191 Processing helix chain 'D' and resid 194 through 208 Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.680A pdb=" N SER D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 removed outlier: 3.733A pdb=" N LEU D 249 " --> pdb=" O PRO D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 284 removed outlier: 3.638A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 370 through 376 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 403 removed outlier: 3.571A pdb=" N ARG D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 417 removed outlier: 3.682A pdb=" N ILE D 411 " --> pdb=" O VAL D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 456 Processing helix chain 'D' and resid 473 through 484 Processing helix chain 'D' and resid 485 through 489 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 581 Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 597 through 613 removed outlier: 3.997A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.576A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.664A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 729 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.502A pdb=" N TYR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 4.221A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 874 Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.694A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 929 Processing helix chain 'D' and resid 1137 through 1146 removed outlier: 3.662A pdb=" N VAL D1141 " --> pdb=" O GLY D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1225 Processing helix chain 'D' and resid 1226 through 1243 Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.507A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1293 Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1319 through 1325 Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.994A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1351 removed outlier: 3.583A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1373 removed outlier: 3.862A pdb=" N ARG D1373 " --> pdb=" O ARG D1369 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 28 removed outlier: 3.526A pdb=" N LEU F 16 " --> pdb=" O ASN F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 56 removed outlier: 3.608A pdb=" N LYS F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 83 removed outlier: 3.564A pdb=" N GLU F 70 " --> pdb=" O SER F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 126 removed outlier: 3.718A pdb=" N HIS F 126 " --> pdb=" O SER F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 3.708A pdb=" N ASP F 141 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS F 151 " --> pdb=" O ASP F 147 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR F 153 " --> pdb=" O TYR F 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 51 removed outlier: 3.570A pdb=" N LYS K 46 " --> pdb=" O PHE K 42 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL K 48 " --> pdb=" O ILE K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 66 Processing helix chain 'K' and resid 80 through 93 removed outlier: 3.659A pdb=" N LYS K 84 " --> pdb=" O GLY K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 101 removed outlier: 3.563A pdb=" N VAL K 100 " --> pdb=" O ARG K 96 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG K 101 " --> pdb=" O PRO K 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 96 through 101' Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 32 removed outlier: 3.558A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 Processing helix chain 'E' and resid 60 through 72 Processing helix chain 'G' and resid 4 through 15 Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 96 through 100 Processing helix chain 'G' and resid 119 through 133 removed outlier: 3.821A pdb=" N ARG G 131 " --> pdb=" O LEU G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 157 Processing helix chain 'G' and resid 185 through 187 No H-bonds generated for 'chain 'G' and resid 185 through 187' Processing helix chain 'H' and resid 4 through 18 removed outlier: 3.924A pdb=" N ILE H 17 " --> pdb=" O ASN H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 67 Processing helix chain 'H' and resid 119 through 134 removed outlier: 4.590A pdb=" N ARG H 131 " --> pdb=" O LEU H 127 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY H 132 " --> pdb=" O ARG H 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 16 removed outlier: 3.642A pdb=" N THR I 16 " --> pdb=" O LYS I 12 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 67 removed outlier: 4.242A pdb=" N VAL I 67 " --> pdb=" O ILE I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 100 removed outlier: 3.560A pdb=" N VAL I 100 " --> pdb=" O PRO I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 133 removed outlier: 3.559A pdb=" N ARG I 131 " --> pdb=" O LEU I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 187 No H-bonds generated for 'chain 'I' and resid 185 through 187' Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17 removed outlier: 6.501A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 61 Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 removed outlier: 3.822A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.563A pdb=" N VAL A 153 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 15 through 18 removed outlier: 4.039A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 101 removed outlier: 6.736A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B 59 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 171 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 removed outlier: 6.102A pdb=" N GLY B 108 " --> pdb=" O HIS B 132 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N HIS B 132 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.326A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.134A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA C 94 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY C 125 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU C 96 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N TYR C 123 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL C 98 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLU C 121 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU C 100 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU C 119 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU C 102 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE C 117 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE C 104 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 143 through 144 Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 453 removed outlier: 6.825A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB6, first strand: chain 'C' and resid 228 through 230 Processing sheet with id=AB7, first strand: chain 'C' and resid 239 through 240 removed outlier: 3.724A pdb=" N MET C 239 " --> pdb=" O ILE C 285 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 250 through 251 Processing sheet with id=AB9, first strand: chain 'C' and resid 256 through 257 removed outlier: 3.535A pdb=" N ALA C 257 " --> pdb=" O LYS C 260 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AC2, first strand: chain 'C' and resid 599 through 605 removed outlier: 5.595A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG C 637 " --> pdb=" O ILE C 616 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.600A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 748 through 751 removed outlier: 6.337A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC6, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 4.358A pdb=" N LYS C1065 " --> pdb=" O LEU C1235 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY C1068 " --> pdb=" O ASN C1072 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN C1072 " --> pdb=" O GLY C1068 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL C1097 " --> pdb=" O LEU C 817 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 830 through 838 removed outlier: 3.507A pdb=" N GLN C 834 " --> pdb=" O LEU C1054 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.653A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 887 through 889 Processing sheet with id=AD2, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD3, first strand: chain 'C' and resid 1337 through 1339 Processing sheet with id=AD4, first strand: chain 'D' and resid 103 through 112 removed outlier: 10.361A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.822A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 145 through 146 Processing sheet with id=AD6, first strand: chain 'D' and resid 317 through 319 removed outlier: 6.097A pdb=" N ARG D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 366 through 369 removed outlier: 6.352A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AD9, first strand: chain 'D' and resid 809 through 811 removed outlier: 6.161A pdb=" N VAL D 894 " --> pdb=" O VAL D 809 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU D 811 " --> pdb=" O VAL D 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE2, first strand: chain 'D' and resid 848 through 849 removed outlier: 6.370A pdb=" N VAL D 848 " --> pdb=" O LEU D 857 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 957 through 959 Processing sheet with id=AE4, first strand: chain 'D' and resid 965 through 967 removed outlier: 3.630A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA D1001 " --> pdb=" O ILE D 975 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1046 through 1050 Processing sheet with id=AE6, first strand: chain 'D' and resid 1077 through 1079 removed outlier: 3.918A pdb=" N TYR D1099 " --> pdb=" O LEU D1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1162 through 1164 removed outlier: 3.869A pdb=" N TYR D1186 " --> pdb=" O ILE D1177 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.484A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 21 through 23 Processing sheet with id=AF1, first strand: chain 'G' and resid 26 through 32 removed outlier: 4.975A pdb=" N GLN G 27 " --> pdb=" O ILE G 44 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 72 through 75 Processing sheet with id=AF3, first strand: chain 'G' and resid 165 through 171 removed outlier: 3.513A pdb=" N TYR G 165 " --> pdb=" O GLY G 151 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE G 147 " --> pdb=" O LEU G 169 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL G 142 " --> pdb=" O PHE G 178 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N PHE G 178 " --> pdb=" O VAL G 142 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASN G 179 " --> pdb=" O ASP G 223 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASP G 223 " --> pdb=" O ASN G 179 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ILE G 181 " --> pdb=" O GLU G 221 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 21 through 23 Processing sheet with id=AF5, first strand: chain 'H' and resid 26 through 32 removed outlier: 4.111A pdb=" N PHE H 28 " --> pdb=" O ASP H 46 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ASP H 46 " --> pdb=" O PHE H 28 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N MET H 30 " --> pdb=" O ILE H 44 " (cutoff:3.500A) removed outlier: 10.935A pdb=" N ILE H 44 " --> pdb=" O MET H 30 " (cutoff:3.500A) removed outlier: 11.700A pdb=" N ARG H 32 " --> pdb=" O ALA H 42 " (cutoff:3.500A) removed outlier: 12.269A pdb=" N ALA H 42 " --> pdb=" O ARG H 32 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 72 through 75 Processing sheet with id=AF7, first strand: chain 'H' and resid 225 through 226 removed outlier: 5.846A pdb=" N PHE H 178 " --> pdb=" O VAL H 142 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE H 147 " --> pdb=" O LEU H 169 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU H 169 " --> pdb=" O ILE H 147 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR H 165 " --> pdb=" O GLY H 151 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N LYS H 164 " --> pdb=" O PHE I 91 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 21 through 23 Processing sheet with id=AF9, first strand: chain 'I' and resid 26 through 32 removed outlier: 5.195A pdb=" N GLN I 27 " --> pdb=" O ILE I 44 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA I 214 " --> pdb=" O GLY I 211 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 166 through 171 removed outlier: 6.467A pdb=" N ILE I 147 " --> pdb=" O LEU I 169 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL I 142 " --> pdb=" O PHE I 178 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N PHE I 178 " --> pdb=" O VAL I 142 " (cutoff:3.500A) 1329 hydrogen bonds defined for protein. 3642 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 90 hydrogen bonds 168 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 8.75 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8717 1.33 - 1.45: 6333 1.45 - 1.57: 18998 1.57 - 1.69: 185 1.69 - 1.81: 234 Bond restraints: 34467 Sorted by residual: bond pdb=" CA LEU C 448 " pdb=" C LEU C 448 " ideal model delta sigma weight residual 1.522 1.433 0.088 1.45e-02 4.76e+03 3.71e+01 bond pdb=" CA GLN C 658 " pdb=" C GLN C 658 " ideal model delta sigma weight residual 1.523 1.452 0.072 1.34e-02 5.57e+03 2.85e+01 bond pdb=" CA GLN C 659 " pdb=" C GLN C 659 " ideal model delta sigma weight residual 1.523 1.456 0.067 1.34e-02 5.57e+03 2.51e+01 bond pdb=" C CYS C 559 " pdb=" N PRO C 560 " ideal model delta sigma weight residual 1.336 1.280 0.055 1.23e-02 6.61e+03 2.03e+01 bond pdb=" CA LYS C 163 " pdb=" C LYS C 163 " ideal model delta sigma weight residual 1.523 1.471 0.053 1.34e-02 5.57e+03 1.54e+01 ... (remaining 34462 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 45611 2.38 - 4.76: 1226 4.76 - 7.14: 111 7.14 - 9.52: 21 9.52 - 11.90: 4 Bond angle restraints: 46973 Sorted by residual: angle pdb=" O4' DT T 22 " pdb=" C4' DT T 22 " pdb=" C3' DT T 22 " ideal model delta sigma weight residual 106.00 102.77 3.23 6.00e-01 2.78e+00 2.90e+01 angle pdb=" C3' DG N 5 " pdb=" C2' DG N 5 " pdb=" C1' DG N 5 " ideal model delta sigma weight residual 102.50 96.67 5.83 1.20e+00 6.94e-01 2.36e+01 angle pdb=" O4' DC N 6 " pdb=" C4' DC N 6 " pdb=" C3' DC N 6 " ideal model delta sigma weight residual 106.00 103.12 2.88 6.00e-01 2.78e+00 2.31e+01 angle pdb=" O4' DG T 1 " pdb=" C4' DG T 1 " pdb=" C3' DG T 1 " ideal model delta sigma weight residual 106.00 103.14 2.86 6.00e-01 2.78e+00 2.26e+01 angle pdb=" CA ARG C 821 " pdb=" C ARG C 821 " pdb=" N VAL C 822 " ideal model delta sigma weight residual 118.43 124.40 -5.97 1.33e+00 5.65e-01 2.01e+01 ... (remaining 46968 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.80: 18949 23.80 - 47.60: 1559 47.60 - 71.40: 323 71.40 - 95.20: 43 95.20 - 118.99: 2 Dihedral angle restraints: 20876 sinusoidal: 9149 harmonic: 11727 Sorted by residual: dihedral pdb=" CA ARG D1149 " pdb=" C ARG D1149 " pdb=" N PRO D1150 " pdb=" CA PRO D1150 " ideal model delta harmonic sigma weight residual 180.00 152.17 27.83 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N GLU B 76 " pdb=" CA GLU B 76 " ideal model delta harmonic sigma weight residual -180.00 -152.19 -27.81 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ALA C 746 " pdb=" C ALA C 746 " pdb=" N GLY C 747 " pdb=" CA GLY C 747 " ideal model delta harmonic sigma weight residual 180.00 153.10 26.90 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 20873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 4293 0.062 - 0.123: 985 0.123 - 0.185: 91 0.185 - 0.246: 6 0.246 - 0.308: 1 Chirality restraints: 5376 Sorted by residual: chirality pdb=" CB ILE G 83 " pdb=" CA ILE G 83 " pdb=" CG1 ILE G 83 " pdb=" CG2 ILE G 83 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA ILE C1079 " pdb=" N ILE C1079 " pdb=" C ILE C1079 " pdb=" CB ILE C1079 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ARG D 764 " pdb=" N ARG D 764 " pdb=" C ARG D 764 " pdb=" CB ARG D 764 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 5373 not shown) Planarity restraints: 5798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C1080 " -0.072 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO C1081 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO C1081 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO C1081 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 858 " 0.039 5.00e-02 4.00e+02 5.85e-02 5.47e+00 pdb=" N PRO D 859 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 859 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 859 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC T 28 " 0.015 2.00e-02 2.50e+03 1.54e-02 5.34e+00 pdb=" N1 DC T 28 " -0.010 2.00e-02 2.50e+03 pdb=" C2 DC T 28 " -0.030 2.00e-02 2.50e+03 pdb=" O2 DC T 28 " 0.011 2.00e-02 2.50e+03 pdb=" N3 DC T 28 " 0.009 2.00e-02 2.50e+03 pdb=" C4 DC T 28 " -0.015 2.00e-02 2.50e+03 pdb=" N4 DC T 28 " 0.018 2.00e-02 2.50e+03 pdb=" C5 DC T 28 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DC T 28 " 0.008 2.00e-02 2.50e+03 ... (remaining 5795 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 684 2.56 - 3.15: 32904 3.15 - 3.73: 55862 3.73 - 4.32: 76306 4.32 - 4.90: 115470 Nonbonded interactions: 281226 Sorted by model distance: nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 1.978 2.170 nonbonded pdb=" OG1 THR K 71 " pdb=" OE1 GLN K 72 " model vdw 2.100 3.040 nonbonded pdb=" NZ LYS B 104 " pdb=" O SER B 105 " model vdw 2.107 3.120 nonbonded pdb=" N GLU B 80 " pdb=" OE1 GLU B 80 " model vdw 2.177 3.120 nonbonded pdb=" N GLU D 913 " pdb=" OE1 GLU D 913 " model vdw 2.180 3.120 ... (remaining 281221 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 'A' and (resid 8 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 170 through 232)) selection = (chain 'B' and (resid 8 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 232)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 38.660 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 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 : 0.008 0.144 34472 Z= 0.463 Angle : 0.951 12.207 46979 Z= 0.583 Chirality : 0.050 0.308 5376 Planarity : 0.005 0.110 5798 Dihedral : 17.660 118.994 13322 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 34.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 15.62 % Favored : 84.31 % Rotamer: Outliers : 0.67 % Allowed : 11.74 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.01 (0.10), residues: 4046 helix: -3.24 (0.10), residues: 1320 sheet: -2.52 (0.20), residues: 523 loop : -3.70 (0.10), residues: 2203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 87 TYR 0.025 0.003 TYR G 55 PHE 0.018 0.002 PHE C 224 TRP 0.028 0.002 TRP C 183 HIS 0.010 0.002 HIS D1227 Details of bonding type rmsd/Z covalent geometry : bond 0.00812 / 0.46 (34467) covalent geometry : angle 0.94694 / 0.58 (46973) hydrogen bonds : bond 0.16875 / 11.31 ( 1419) hydrogen bonds : angle 7.88706 / 5.52 ( 3810) metal coordination : bond 0.08909 / 5.81 ( 5) metal coordination : angle 7.55030 / 5.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 658 time to evaluate : 1.293 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: A 23 HIS cc_start: 0.5651 (p-80) cc_final: 0.5221 (p90) REVERT: A 123 ILE cc_start: 0.9117 (mm) cc_final: 0.8819 (mt) REVERT: A 223 ILE cc_start: 0.9639 (mt) cc_final: 0.9237 (mm) REVERT: A 226 GLU cc_start: 0.8829 (tt0) cc_final: 0.8346 (mt-10) REVERT: B 10 LYS cc_start: 0.8599 (mmtm) cc_final: 0.8380 (mppt) REVERT: B 214 GLU cc_start: 0.8101 (tt0) cc_final: 0.7862 (tt0) REVERT: C 151 ARG cc_start: 0.8123 (mtp180) cc_final: 0.7257 (mtm110) REVERT: C 185 ASP cc_start: 0.7484 (t0) cc_final: 0.7239 (t0) REVERT: C 322 LEU cc_start: 0.9394 (tt) cc_final: 0.9122 (mt) REVERT: C 434 ASP cc_start: 0.9246 (m-30) cc_final: 0.8968 (m-30) REVERT: C 473 ARG cc_start: 0.8176 (mtt180) cc_final: 0.7538 (mmt180) REVERT: C 488 MET cc_start: 0.8818 (mmm) cc_final: 0.8444 (mmm) REVERT: C 515 MET cc_start: 0.7140 (ttt) cc_final: 0.6471 (ttt) REVERT: C 522 SER cc_start: 0.7572 (p) cc_final: 0.7108 (p) REVERT: C 685 MET cc_start: 0.6844 (mtm) cc_final: 0.6039 (mtt) REVERT: C 752 ASN cc_start: 0.8785 (m-40) cc_final: 0.8383 (t0) REVERT: C 768 MET cc_start: 0.7616 (mtm) cc_final: 0.6751 (ptt) REVERT: C 800 MET cc_start: 0.7791 (mtt) cc_final: 0.7467 (mmm) REVERT: C 807 TRP cc_start: 0.8430 (OUTLIER) cc_final: 0.7817 (t60) REVERT: C 817 LEU cc_start: 0.8551 (tp) cc_final: 0.8324 (tp) REVERT: C 835 GLU cc_start: 0.8145 (tt0) cc_final: 0.7460 (pp20) REVERT: C 844 LYS cc_start: 0.7639 (ptpt) cc_final: 0.7251 (ptmt) REVERT: C 853 ASP cc_start: 0.7731 (t70) cc_final: 0.7230 (t70) REVERT: C 878 THR cc_start: 0.6693 (p) cc_final: 0.6395 (t) REVERT: C 906 PHE cc_start: 0.8925 (m-80) cc_final: 0.8719 (m-80) REVERT: C 1197 GLU cc_start: 0.8739 (tp30) cc_final: 0.8531 (mt-10) REVERT: C 1230 MET cc_start: 0.5762 (ttm) cc_final: 0.4764 (ptm) REVERT: C 1235 LEU cc_start: 0.7700 (tp) cc_final: 0.7499 (mp) REVERT: C 1243 MET cc_start: 0.7228 (ttp) cc_final: 0.6937 (ttt) REVERT: C 1244 HIS cc_start: 0.7766 (t70) cc_final: 0.7431 (t70) REVERT: C 1272 GLU cc_start: 0.6812 (pm20) cc_final: 0.6404 (pt0) REVERT: C 1276 TRP cc_start: 0.8465 (m-10) cc_final: 0.7516 (m-90) REVERT: D 45 ASN cc_start: 0.8327 (t0) cc_final: 0.7857 (t0) REVERT: D 111 THR cc_start: 0.9089 (OUTLIER) cc_final: 0.8746 (m) REVERT: D 164 GLN cc_start: 0.9288 (mt0) cc_final: 0.9039 (mt0) REVERT: D 222 LYS cc_start: 0.9575 (ttpt) cc_final: 0.9100 (tptp) REVERT: D 227 PHE cc_start: 0.9057 (m-80) cc_final: 0.8694 (m-80) REVERT: D 244 VAL cc_start: 0.8060 (m) cc_final: 0.7790 (m) REVERT: D 248 ASP cc_start: 0.7575 (m-30) cc_final: 0.7199 (t0) REVERT: D 334 LYS cc_start: 0.8288 (ptpt) cc_final: 0.8006 (ptpp) REVERT: D 339 ARG cc_start: 0.6663 (mtp180) cc_final: 0.6024 (mtp85) REVERT: D 402 GLU cc_start: 0.7808 (tp30) cc_final: 0.7602 (mm-30) REVERT: D 404 GLU cc_start: 0.7219 (pm20) cc_final: 0.6860 (pp20) REVERT: D 405 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7129 (mp0) REVERT: D 466 MET cc_start: 0.8892 (mtp) cc_final: 0.8616 (mtp) REVERT: D 478 LEU cc_start: 0.8871 (mt) cc_final: 0.8565 (mt) REVERT: D 479 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7857 (mt-10) REVERT: D 484 MET cc_start: 0.7120 (mpp) cc_final: 0.6764 (mpp) REVERT: D 485 MET cc_start: 0.6804 (tpt) cc_final: 0.6332 (ttp) REVERT: D 501 VAL cc_start: 0.7561 (p) cc_final: 0.7211 (m) REVERT: D 697 MET cc_start: 0.7911 (tmm) cc_final: 0.7653 (tmm) REVERT: D 710 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7650 (m-30) REVERT: D 714 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7520 (mp0) REVERT: D 743 MET cc_start: 0.7385 (ptm) cc_final: 0.7044 (ptp) REVERT: D 795 TYR cc_start: 0.8382 (t80) cc_final: 0.8003 (t80) REVERT: D 864 LEU cc_start: 0.9104 (mt) cc_final: 0.8886 (mt) REVERT: D 925 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8636 (tm-30) REVERT: D 1349 GLU cc_start: 0.7035 (pt0) cc_final: 0.6690 (pm20) REVERT: D 1370 MET cc_start: 0.7872 (tpt) cc_final: 0.7657 (tpt) REVERT: F 113 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7527 (tp30) REVERT: F 116 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8774 (tm-30) REVERT: K 40 ASN cc_start: 0.9436 (t0) cc_final: 0.9110 (t0) REVERT: K 47 MET cc_start: 0.8772 (mmm) cc_final: 0.8461 (mmm) REVERT: K 55 TYR cc_start: 0.8844 (m-80) cc_final: 0.7981 (m-80) REVERT: K 85 ILE cc_start: 0.9256 (mm) cc_final: 0.8919 (mm) REVERT: K 86 GLN cc_start: 0.9186 (mt0) cc_final: 0.8908 (mt0) REVERT: E 30 MET cc_start: 0.8124 (mtm) cc_final: 0.7818 (mtm) REVERT: G 183 ASN cc_start: 0.9212 (t0) cc_final: 0.8966 (m-40) REVERT: G 184 MET cc_start: 0.7915 (mmm) cc_final: 0.7544 (mmm) REVERT: H 187 MET cc_start: 0.7099 (mmm) cc_final: 0.6742 (mpp) REVERT: I 165 TYR cc_start: 0.9116 (t80) cc_final: 0.8689 (t80) REVERT: I 187 MET cc_start: 0.8241 (mtp) cc_final: 0.7540 (ptm) outliers start: 23 outliers final: 12 residues processed: 679 average time/residue: 0.2478 time to fit residues: 262.2642 Evaluate side-chains 421 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 406 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 chunk 401 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 84 ASN A 93 GLN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS C 65 ASN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 ASN C 526 HIS C 618 GLN C 684 ASN C 760 ASN ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 GLN C 955 GLN C 965 GLN C1013 GLN C1116 HIS C1136 GLN C1175 ASN ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1237 HIS D 80 HIS D 365 GLN D 430 HIS D 465 GLN D 489 ASN D 495 ASN ** D 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 GLN D1023 HIS ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 ASN D1252 HIS F 18 GLN ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN K 66 ASN K 86 GLN E 43 ASN ** G 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 HIS ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 75 GLN I 186 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.136690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.117090 restraints weight = 92993.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.116491 restraints weight = 207741.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.116935 restraints weight = 176038.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.116949 restraints weight = 113923.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.118172 restraints weight = 98637.466| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 34472 Z= 0.182 Angle : 0.776 9.625 46979 Z= 0.413 Chirality : 0.049 0.278 5376 Planarity : 0.006 0.081 5798 Dihedral : 17.136 127.210 5465 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.83 % Favored : 92.14 % Rotamer: Outliers : 0.29 % Allowed : 5.64 % Favored : 94.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.12), residues: 4046 helix: -1.38 (0.13), residues: 1319 sheet: -2.03 (0.20), residues: 502 loop : -2.84 (0.12), residues: 2225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG K 101 TYR 0.035 0.002 TYR C1231 PHE 0.017 0.002 PHE H 28 TRP 0.022 0.002 TRP F 23 HIS 0.019 0.002 HIS D 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (34467) covalent geometry : angle 0.77480 / 0.41 (46973) hydrogen bonds : bond 0.06304 / 4.34 ( 1419) hydrogen bonds : angle 6.21835 / 4.41 ( 3810) metal coordination : bond 0.01113 / 0.55 ( 5) metal coordination : angle 4.18554 / 2.52 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 593 time to evaluate : 1.301 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: A 223 ILE cc_start: 0.9101 (mt) cc_final: 0.8705 (mm) REVERT: A 226 GLU cc_start: 0.6665 (tt0) cc_final: 0.6424 (tt0) REVERT: C 130 MET cc_start: 0.8357 (ttm) cc_final: 0.7287 (tpp) REVERT: C 151 ARG cc_start: 0.8103 (mtp180) cc_final: 0.7627 (mtm110) REVERT: C 171 LEU cc_start: 0.8268 (mm) cc_final: 0.8023 (mm) REVERT: C 185 ASP cc_start: 0.8402 (t0) cc_final: 0.7523 (t0) REVERT: C 685 MET cc_start: 0.7107 (mtm) cc_final: 0.6353 (mtt) REVERT: C 755 LYS cc_start: 0.8453 (mmmt) cc_final: 0.8211 (mmtt) REVERT: C 768 MET cc_start: 0.7232 (mtm) cc_final: 0.7016 (ptt) REVERT: C 835 GLU cc_start: 0.7987 (tt0) cc_final: 0.7532 (pp20) REVERT: C 902 LEU cc_start: 0.8814 (pp) cc_final: 0.8118 (pp) REVERT: C 1176 LEU cc_start: 0.9208 (mm) cc_final: 0.8914 (mm) REVERT: C 1195 ILE cc_start: 0.8673 (mm) cc_final: 0.8233 (tp) REVERT: C 1214 ASP cc_start: 0.8486 (t0) cc_final: 0.7979 (t70) REVERT: C 1230 MET cc_start: 0.7165 (ttm) cc_final: 0.6560 (ptm) REVERT: C 1232 MET cc_start: 0.8161 (mmm) cc_final: 0.7294 (mtp) REVERT: C 1276 TRP cc_start: 0.8760 (m-10) cc_final: 0.7175 (m-90) REVERT: D 201 LEU cc_start: 0.8738 (mt) cc_final: 0.7957 (tt) REVERT: D 227 PHE cc_start: 0.7962 (m-80) cc_final: 0.7740 (m-80) REVERT: D 248 ASP cc_start: 0.7872 (m-30) cc_final: 0.6966 (t0) REVERT: D 478 LEU cc_start: 0.8027 (mt) cc_final: 0.7748 (mt) REVERT: D 479 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6200 (mt-10) REVERT: D 555 TYR cc_start: 0.6556 (m-10) cc_final: 0.6328 (m-10) REVERT: D 571 ASP cc_start: 0.7825 (t0) cc_final: 0.7484 (t0) REVERT: D 574 VAL cc_start: 0.9206 (t) cc_final: 0.8999 (t) REVERT: D 625 MET cc_start: 0.8487 (ttp) cc_final: 0.8277 (tmm) REVERT: D 683 ILE cc_start: 0.8892 (mm) cc_final: 0.8567 (mm) REVERT: D 724 MET cc_start: 0.8448 (mtp) cc_final: 0.7814 (mtt) REVERT: D 1023 HIS cc_start: 0.6013 (OUTLIER) cc_final: 0.5521 (m-70) REVERT: D 1260 MET cc_start: 0.8011 (mmm) cc_final: 0.7768 (mmm) REVERT: D 1325 PHE cc_start: 0.8456 (t80) cc_final: 0.7910 (t80) REVERT: F 119 LYS cc_start: 0.8734 (pttt) cc_final: 0.8518 (pttt) REVERT: K 63 LEU cc_start: 0.9033 (mt) cc_final: 0.8796 (mt) REVERT: E 30 MET cc_start: 0.8084 (mtm) cc_final: 0.7315 (mtp) REVERT: H 187 MET cc_start: 0.4407 (mmm) cc_final: 0.4116 (mtp) outliers start: 10 outliers final: 1 residues processed: 600 average time/residue: 0.2317 time to fit residues: 221.4773 Evaluate side-chains 400 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 398 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 95 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 206 optimal weight: 0.6980 chunk 299 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 223 optimal weight: 0.0170 chunk 193 optimal weight: 0.7980 chunk 373 optimal weight: 0.2980 chunk 382 optimal weight: 8.9990 chunk 204 optimal weight: 0.9980 chunk 247 optimal weight: 5.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN C 659 GLN C1237 HIS C1256 GLN D 320 ASN D 495 ASN ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 720 ASN D 736 GLN ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 HIS ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN G 186 ASN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 HIS I 186 ASN I 213 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.137876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.118461 restraints weight = 92472.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.118005 restraints weight = 192125.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.118390 restraints weight = 180489.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.118111 restraints weight = 127009.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.118238 restraints weight = 121313.851| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 34472 Z= 0.155 Angle : 0.707 13.012 46979 Z= 0.374 Chirality : 0.047 0.330 5376 Planarity : 0.005 0.069 5798 Dihedral : 16.898 131.185 5465 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.12 % Allowed : 4.57 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.12), residues: 4046 helix: -0.58 (0.13), residues: 1320 sheet: -1.75 (0.20), residues: 539 loop : -2.47 (0.12), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG G 128 TYR 0.017 0.001 TYR C1231 PHE 0.023 0.002 PHE F 106 TRP 0.018 0.001 TRP F 23 HIS 0.007 0.001 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (34467) covalent geometry : angle 0.70479 / 0.37 (46973) hydrogen bonds : bond 0.05416 / 3.75 ( 1419) hydrogen bonds : angle 5.68405 / 4.06 ( 3810) metal coordination : bond 0.00633 / 0.42 ( 5) metal coordination : angle 4.70956 / 2.81 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 551 time to evaluate : 1.328 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: A 223 ILE cc_start: 0.9096 (mt) cc_final: 0.8859 (mm) REVERT: C 26 TYR cc_start: 0.7629 (t80) cc_final: 0.7074 (t80) REVERT: C 130 MET cc_start: 0.8230 (ttm) cc_final: 0.7292 (tpp) REVERT: C 151 ARG cc_start: 0.8100 (mtp180) cc_final: 0.7524 (mtm110) REVERT: C 185 ASP cc_start: 0.8358 (t0) cc_final: 0.7458 (t0) REVERT: C 443 ASP cc_start: 0.8363 (m-30) cc_final: 0.8145 (m-30) REVERT: C 881 ASP cc_start: 0.8161 (t0) cc_final: 0.7883 (t0) REVERT: C 1176 LEU cc_start: 0.9066 (mm) cc_final: 0.8771 (mm) REVERT: C 1230 MET cc_start: 0.7230 (ttm) cc_final: 0.6789 (ptm) REVERT: C 1232 MET cc_start: 0.8135 (mmm) cc_final: 0.7383 (mtp) REVERT: C 1273 MET cc_start: 0.6411 (mpp) cc_final: 0.6128 (mtt) REVERT: C 1276 TRP cc_start: 0.8475 (m-10) cc_final: 0.7786 (m-90) REVERT: C 1290 MET cc_start: 0.7017 (tpp) cc_final: 0.6311 (tpp) REVERT: C 1291 LEU cc_start: 0.9250 (pt) cc_final: 0.8798 (tt) REVERT: D 201 LEU cc_start: 0.8730 (mt) cc_final: 0.7873 (tt) REVERT: D 227 PHE cc_start: 0.7814 (m-80) cc_final: 0.7582 (m-80) REVERT: D 248 ASP cc_start: 0.8022 (m-30) cc_final: 0.7110 (t0) REVERT: D 334 LYS cc_start: 0.9026 (mtmm) cc_final: 0.8523 (mtmm) REVERT: D 345 LYS cc_start: 0.8323 (ptpp) cc_final: 0.7478 (ptpt) REVERT: D 405 GLU cc_start: 0.6250 (mp0) cc_final: 0.5043 (mp0) REVERT: D 438 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7831 (tm-30) REVERT: D 478 LEU cc_start: 0.7972 (mt) cc_final: 0.7726 (mt) REVERT: D 479 GLU cc_start: 0.6478 (mt-10) cc_final: 0.6102 (mt-10) REVERT: D 571 ASP cc_start: 0.7881 (t0) cc_final: 0.7557 (t0) REVERT: D 574 VAL cc_start: 0.9148 (t) cc_final: 0.8858 (t) REVERT: D 625 MET cc_start: 0.8256 (ttp) cc_final: 0.7890 (tmm) REVERT: D 795 TYR cc_start: 0.7516 (t80) cc_final: 0.7308 (t80) REVERT: D 932 MET cc_start: 0.6410 (tpt) cc_final: 0.5988 (tpt) REVERT: D 1325 PHE cc_start: 0.8445 (t80) cc_final: 0.7799 (t80) REVERT: D 1327 GLU cc_start: 0.7150 (pp20) cc_final: 0.6406 (pp20) REVERT: K 40 ASN cc_start: 0.8439 (t0) cc_final: 0.8037 (t0) REVERT: E 11 GLU cc_start: 0.7429 (mm-30) cc_final: 0.5948 (pp20) REVERT: E 42 GLU cc_start: 0.6690 (mp0) cc_final: 0.6145 (mp0) REVERT: E 52 ARG cc_start: 0.6902 (mtp180) cc_final: 0.6071 (tpp-160) REVERT: G 1 MET cc_start: 0.6043 (ptm) cc_final: 0.5838 (ptm) outliers start: 4 outliers final: 1 residues processed: 554 average time/residue: 0.2292 time to fit residues: 205.2548 Evaluate side-chains 395 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 394 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 169 optimal weight: 1.9990 chunk 365 optimal weight: 30.0000 chunk 181 optimal weight: 9.9990 chunk 160 optimal weight: 3.9990 chunk 21 optimal weight: 0.0270 chunk 59 optimal weight: 6.9990 chunk 315 optimal weight: 20.0000 chunk 398 optimal weight: 3.9990 chunk 257 optimal weight: 0.6980 chunk 333 optimal weight: 10.0000 chunk 240 optimal weight: 0.8980 overall best weight: 1.5242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS C 69 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 GLN D 340 GLN D 419 HIS ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 ASN ** D 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.136853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.115649 restraints weight = 92477.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.115428 restraints weight = 194230.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.116156 restraints weight = 171643.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.115743 restraints weight = 123239.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.116295 restraints weight = 105863.253| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34472 Z= 0.159 Angle : 0.683 9.363 46979 Z= 0.360 Chirality : 0.046 0.304 5376 Planarity : 0.005 0.076 5798 Dihedral : 16.753 131.087 5465 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.12), residues: 4046 helix: -0.29 (0.14), residues: 1323 sheet: -1.70 (0.20), residues: 578 loop : -2.33 (0.13), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 678 TYR 0.024 0.001 TYR C1229 PHE 0.017 0.001 PHE C1265 TRP 0.045 0.002 TRP F 67 HIS 0.005 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (34467) covalent geometry : angle 0.68140 / 0.36 (46973) hydrogen bonds : bond 0.05037 / 3.52 ( 1419) hydrogen bonds : angle 5.48928 / 3.90 ( 3810) metal coordination : bond 0.00532 / 0.36 ( 5) metal coordination : angle 4.15079 / 2.52 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 508 time to evaluate : 1.283 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: A 223 ILE cc_start: 0.9115 (mt) cc_final: 0.8804 (mm) REVERT: A 226 GLU cc_start: 0.6889 (tt0) cc_final: 0.6547 (tp30) REVERT: C 130 MET cc_start: 0.8375 (ttm) cc_final: 0.7573 (tpp) REVERT: C 151 ARG cc_start: 0.8052 (mtp180) cc_final: 0.7541 (mtm110) REVERT: C 185 ASP cc_start: 0.8429 (t0) cc_final: 0.7494 (t0) REVERT: C 659 GLN cc_start: 0.8368 (pp30) cc_final: 0.7835 (tm-30) REVERT: C 660 VAL cc_start: 0.8486 (t) cc_final: 0.8191 (t) REVERT: C 672 GLU cc_start: 0.8635 (pm20) cc_final: 0.8241 (pm20) REVERT: C 685 MET cc_start: 0.6567 (mtp) cc_final: 0.6087 (mtt) REVERT: C 813 GLU cc_start: 0.7204 (tp30) cc_final: 0.6692 (tt0) REVERT: C 835 GLU cc_start: 0.8302 (tt0) cc_final: 0.7156 (pp20) REVERT: C 881 ASP cc_start: 0.8285 (t0) cc_final: 0.7877 (t0) REVERT: C 902 LEU cc_start: 0.8826 (pp) cc_final: 0.8193 (pp) REVERT: C 1176 LEU cc_start: 0.9091 (mm) cc_final: 0.8773 (mm) REVERT: C 1232 MET cc_start: 0.8248 (mmm) cc_final: 0.7321 (mtp) REVERT: C 1273 MET cc_start: 0.6833 (mpp) cc_final: 0.6433 (mtt) REVERT: C 1276 TRP cc_start: 0.8721 (m-10) cc_final: 0.7310 (m-90) REVERT: C 1290 MET cc_start: 0.7131 (tpp) cc_final: 0.6784 (tpp) REVERT: C 1291 LEU cc_start: 0.9349 (pt) cc_final: 0.8785 (tt) REVERT: D 160 LEU cc_start: 0.7882 (mm) cc_final: 0.7520 (mm) REVERT: D 227 PHE cc_start: 0.7972 (m-80) cc_final: 0.7633 (m-80) REVERT: D 237 MET cc_start: 0.7426 (mtt) cc_final: 0.7197 (mtt) REVERT: D 248 ASP cc_start: 0.7976 (m-30) cc_final: 0.6949 (t0) REVERT: D 334 LYS cc_start: 0.9054 (mtmm) cc_final: 0.8572 (mtmm) REVERT: D 438 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7786 (tm-30) REVERT: D 462 ASP cc_start: 0.7568 (m-30) cc_final: 0.7268 (m-30) REVERT: D 479 GLU cc_start: 0.6768 (mt-10) cc_final: 0.6432 (mt-10) REVERT: D 544 LEU cc_start: 0.9307 (tp) cc_final: 0.9095 (tp) REVERT: D 571 ASP cc_start: 0.7921 (t0) cc_final: 0.7684 (t0) REVERT: D 1325 PHE cc_start: 0.8532 (t80) cc_final: 0.8103 (t80) REVERT: D 1349 GLU cc_start: 0.8085 (pm20) cc_final: 0.7678 (pm20) REVERT: F 74 ASP cc_start: 0.8170 (t0) cc_final: 0.7909 (t0) REVERT: F 113 GLU cc_start: 0.6322 (tp30) cc_final: 0.5851 (mm-30) REVERT: K 40 ASN cc_start: 0.8634 (t0) cc_final: 0.8016 (t0) REVERT: E 60 ASN cc_start: 0.7393 (p0) cc_final: 0.7155 (p0) REVERT: H 187 MET cc_start: 0.1308 (mtp) cc_final: 0.0916 (mtt) REVERT: I 1 MET cc_start: 0.1047 (mtp) cc_final: 0.0358 (tpp) REVERT: I 189 MET cc_start: 0.1807 (ptp) cc_final: 0.0696 (mtp) outliers start: 3 outliers final: 0 residues processed: 510 average time/residue: 0.2213 time to fit residues: 184.3039 Evaluate side-chains 378 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 163 optimal weight: 0.0770 chunk 305 optimal weight: 2.9990 chunk 159 optimal weight: 0.0000 chunk 311 optimal weight: 40.0000 chunk 92 optimal weight: 0.6980 chunk 89 optimal weight: 7.9990 chunk 121 optimal weight: 0.9980 chunk 322 optimal weight: 3.9990 chunk 238 optimal weight: 5.9990 chunk 396 optimal weight: 7.9990 chunk 53 optimal weight: 0.0020 overall best weight: 0.3550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 227 GLN C 69 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 ASN C 618 GLN C 684 ASN D 320 ASN ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 ASN D 921 GLN ** D 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.138898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.117789 restraints weight = 92329.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.117444 restraints weight = 194355.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.118234 restraints weight = 166543.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.117708 restraints weight = 125847.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.118269 restraints weight = 107527.825| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34472 Z= 0.133 Angle : 0.666 10.683 46979 Z= 0.349 Chirality : 0.046 0.345 5376 Planarity : 0.005 0.068 5798 Dihedral : 16.654 130.374 5465 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.06 % Allowed : 3.01 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.12), residues: 4046 helix: -0.13 (0.14), residues: 1334 sheet: -1.42 (0.20), residues: 560 loop : -2.21 (0.13), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 903 TYR 0.016 0.001 TYR C1229 PHE 0.028 0.001 PHE C 972 TRP 0.032 0.001 TRP F 67 HIS 0.010 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (34467) covalent geometry : angle 0.66522 / 0.35 (46973) hydrogen bonds : bond 0.04679 / 3.27 ( 1419) hydrogen bonds : angle 5.26204 / 3.73 ( 3810) metal coordination : bond 0.00349 / 0.20 ( 5) metal coordination : angle 3.25847 / 1.95 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 511 time to evaluate : 1.484 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: A 223 ILE cc_start: 0.9139 (mt) cc_final: 0.8848 (mm) REVERT: A 226 GLU cc_start: 0.6903 (tt0) cc_final: 0.6608 (tp30) REVERT: B 10 LYS cc_start: 0.7805 (mmtm) cc_final: 0.7323 (tmtt) REVERT: B 37 HIS cc_start: 0.7210 (m170) cc_final: 0.6955 (m170) REVERT: C 130 MET cc_start: 0.8344 (ttm) cc_final: 0.7505 (tpp) REVERT: C 151 ARG cc_start: 0.7890 (mtp180) cc_final: 0.7420 (mtm110) REVERT: C 185 ASP cc_start: 0.8503 (t0) cc_final: 0.7590 (t0) REVERT: C 515 MET cc_start: 0.8604 (tpt) cc_final: 0.7706 (tpt) REVERT: C 660 VAL cc_start: 0.8353 (t) cc_final: 0.7828 (t) REVERT: C 835 GLU cc_start: 0.8319 (tt0) cc_final: 0.7124 (pp20) REVERT: C 881 ASP cc_start: 0.8192 (t0) cc_final: 0.7917 (t70) REVERT: C 902 LEU cc_start: 0.8910 (pp) cc_final: 0.8413 (pp) REVERT: C 1176 LEU cc_start: 0.9081 (mm) cc_final: 0.8876 (mm) REVERT: C 1178 LYS cc_start: 0.8577 (mtpp) cc_final: 0.8296 (mmmt) REVERT: C 1207 SER cc_start: 0.8619 (p) cc_final: 0.8310 (m) REVERT: C 1232 MET cc_start: 0.8108 (mmm) cc_final: 0.7146 (mtp) REVERT: C 1273 MET cc_start: 0.6912 (mpp) cc_final: 0.6443 (mtt) REVERT: C 1276 TRP cc_start: 0.8683 (m-10) cc_final: 0.7129 (m-90) REVERT: C 1290 MET cc_start: 0.7773 (tpp) cc_final: 0.6917 (tpp) REVERT: C 1291 LEU cc_start: 0.9119 (pt) cc_final: 0.8640 (tt) REVERT: D 201 LEU cc_start: 0.8729 (mt) cc_final: 0.8489 (mt) REVERT: D 227 PHE cc_start: 0.7964 (m-80) cc_final: 0.7601 (m-10) REVERT: D 248 ASP cc_start: 0.8377 (m-30) cc_final: 0.7644 (t0) REVERT: D 334 LYS cc_start: 0.9031 (mtmm) cc_final: 0.8555 (mtmm) REVERT: D 345 LYS cc_start: 0.8144 (ptpp) cc_final: 0.7258 (ptmt) REVERT: D 479 GLU cc_start: 0.6644 (mt-10) cc_final: 0.6210 (mt-10) REVERT: D 555 TYR cc_start: 0.6659 (m-10) cc_final: 0.6398 (m-10) REVERT: D 571 ASP cc_start: 0.7891 (t0) cc_final: 0.7613 (t0) REVERT: D 1325 PHE cc_start: 0.8437 (t80) cc_final: 0.7804 (t80) REVERT: D 1349 GLU cc_start: 0.8026 (pm20) cc_final: 0.7629 (pm20) REVERT: K 40 ASN cc_start: 0.8320 (t0) cc_final: 0.8070 (t0) REVERT: K 86 GLN cc_start: 0.8631 (mt0) cc_final: 0.8287 (mt0) REVERT: E 45 LYS cc_start: 0.5329 (mttm) cc_final: 0.5004 (mttt) REVERT: E 51 LEU cc_start: 0.7794 (mp) cc_final: 0.7010 (mp) REVERT: E 67 ARG cc_start: 0.8144 (ttm110) cc_final: 0.7896 (mtm110) REVERT: G 1 MET cc_start: 0.6130 (ptm) cc_final: 0.5743 (ptm) REVERT: H 187 MET cc_start: 0.1427 (mtp) cc_final: 0.0981 (mtt) REVERT: H 191 PRO cc_start: 0.7200 (Cg_exo) cc_final: 0.6985 (Cg_endo) REVERT: I 1 MET cc_start: 0.0781 (mtp) cc_final: 0.0050 (tpt) outliers start: 2 outliers final: 0 residues processed: 513 average time/residue: 0.2178 time to fit residues: 181.8375 Evaluate side-chains 380 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 125 optimal weight: 5.9990 chunk 367 optimal weight: 50.0000 chunk 66 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 159 optimal weight: 3.9990 chunk 255 optimal weight: 4.9990 chunk 213 optimal weight: 0.0040 chunk 181 optimal weight: 9.9990 chunk 404 optimal weight: 50.0000 chunk 223 optimal weight: 1.9990 chunk 235 optimal weight: 0.0270 overall best weight: 1.6056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 69 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN C 952 GLN D 419 HIS D 495 ASN D 665 GLN D 921 GLN ** D 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.137755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.116720 restraints weight = 91676.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.116447 restraints weight = 201456.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.116989 restraints weight = 165131.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.116691 restraints weight = 116449.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.117023 restraints weight = 103993.941| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34472 Z= 0.156 Angle : 0.665 13.065 46979 Z= 0.349 Chirality : 0.045 0.270 5376 Planarity : 0.005 0.064 5798 Dihedral : 16.583 129.753 5465 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.03 % Allowed : 2.31 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.12), residues: 4046 helix: -0.00 (0.14), residues: 1331 sheet: -1.37 (0.20), residues: 579 loop : -2.19 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 162 TYR 0.031 0.002 TYR C1229 PHE 0.013 0.001 PHE C 972 TRP 0.015 0.001 TRP F 23 HIS 0.005 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (34467) covalent geometry : angle 0.66391 / 0.35 (46973) hydrogen bonds : bond 0.04618 / 3.24 ( 1419) hydrogen bonds : angle 5.23574 / 3.70 ( 3810) metal coordination : bond 0.00515 / 0.34 ( 5) metal coordination : angle 3.39850 / 2.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 490 time to evaluate : 1.284 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: A 223 ILE cc_start: 0.9165 (mt) cc_final: 0.8848 (mm) REVERT: A 226 GLU cc_start: 0.6983 (tt0) cc_final: 0.6385 (tp30) REVERT: B 205 MET cc_start: 0.7875 (tmm) cc_final: 0.7329 (tmm) REVERT: C 28 LEU cc_start: 0.8747 (mp) cc_final: 0.8461 (mt) REVERT: C 151 ARG cc_start: 0.7885 (mtp180) cc_final: 0.7473 (mtm110) REVERT: C 185 ASP cc_start: 0.8456 (t0) cc_final: 0.7512 (t0) REVERT: C 515 MET cc_start: 0.8734 (tpt) cc_final: 0.7522 (tpt) REVERT: C 813 GLU cc_start: 0.7248 (tp30) cc_final: 0.6891 (tt0) REVERT: C 835 GLU cc_start: 0.8085 (tt0) cc_final: 0.7020 (pp20) REVERT: C 881 ASP cc_start: 0.8318 (t0) cc_final: 0.7952 (t0) REVERT: C 902 LEU cc_start: 0.8956 (pp) cc_final: 0.8432 (pp) REVERT: C 931 VAL cc_start: 0.9002 (t) cc_final: 0.8730 (m) REVERT: C 1176 LEU cc_start: 0.9047 (mm) cc_final: 0.8839 (mm) REVERT: C 1207 SER cc_start: 0.8602 (p) cc_final: 0.8331 (m) REVERT: C 1232 MET cc_start: 0.7923 (mmm) cc_final: 0.7538 (mtp) REVERT: C 1273 MET cc_start: 0.6687 (mpp) cc_final: 0.6328 (mtt) REVERT: C 1276 TRP cc_start: 0.8611 (m-10) cc_final: 0.7819 (m-90) REVERT: C 1290 MET cc_start: 0.7503 (tpp) cc_final: 0.7169 (tpp) REVERT: C 1291 LEU cc_start: 0.9249 (pt) cc_final: 0.8712 (tt) REVERT: D 159 ILE cc_start: 0.7639 (pt) cc_final: 0.7337 (pt) REVERT: D 160 LEU cc_start: 0.7668 (mm) cc_final: 0.7377 (mm) REVERT: D 201 LEU cc_start: 0.8773 (mt) cc_final: 0.8512 (mt) REVERT: D 227 PHE cc_start: 0.7843 (m-80) cc_final: 0.7481 (m-10) REVERT: D 248 ASP cc_start: 0.8029 (m-30) cc_final: 0.7090 (t0) REVERT: D 334 LYS cc_start: 0.9068 (mtmm) cc_final: 0.8507 (mtmm) REVERT: D 345 LYS cc_start: 0.8294 (ptpp) cc_final: 0.7376 (ptmt) REVERT: D 544 LEU cc_start: 0.9220 (tp) cc_final: 0.8999 (tp) REVERT: D 571 ASP cc_start: 0.7948 (t0) cc_final: 0.7716 (t0) REVERT: D 1254 GLU cc_start: 0.6999 (tt0) cc_final: 0.6754 (tp30) REVERT: D 1370 MET cc_start: 0.8090 (tpt) cc_final: 0.7860 (tpp) REVERT: F 119 LYS cc_start: 0.8859 (ptmt) cc_final: 0.8235 (pttt) REVERT: K 86 GLN cc_start: 0.8642 (mt0) cc_final: 0.8348 (mt0) REVERT: E 45 LYS cc_start: 0.5234 (mttm) cc_final: 0.4791 (mttt) REVERT: E 61 ASN cc_start: 0.8578 (t0) cc_final: 0.8214 (t0) REVERT: G 1 MET cc_start: 0.6312 (ptm) cc_final: 0.6038 (ptm) REVERT: H 187 MET cc_start: 0.0868 (mtp) cc_final: 0.0600 (mtt) REVERT: H 191 PRO cc_start: 0.7131 (Cg_exo) cc_final: 0.6901 (Cg_endo) REVERT: I 1 MET cc_start: 0.0523 (mtp) cc_final: 0.0058 (tpt) outliers start: 1 outliers final: 0 residues processed: 491 average time/residue: 0.2124 time to fit residues: 170.1474 Evaluate side-chains 378 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 301 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 309 optimal weight: 40.0000 chunk 194 optimal weight: 6.9990 chunk 276 optimal weight: 30.0000 chunk 155 optimal weight: 8.9990 chunk 133 optimal weight: 7.9990 chunk 119 optimal weight: 0.8980 chunk 5 optimal weight: 0.0970 chunk 332 optimal weight: 0.4980 chunk 105 optimal weight: 0.0370 overall best weight: 1.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN C 69 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN D 430 HIS ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.137192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.115846 restraints weight = 93339.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.116212 restraints weight = 202454.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.116436 restraints weight = 156127.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.116049 restraints weight = 119835.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.116468 restraints weight = 101506.015| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 34472 Z= 0.157 Angle : 0.674 14.053 46979 Z= 0.352 Chirality : 0.046 0.272 5376 Planarity : 0.005 0.069 5798 Dihedral : 16.550 129.036 5465 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.03 % Allowed : 2.57 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.12), residues: 4046 helix: -0.01 (0.14), residues: 1356 sheet: -1.32 (0.20), residues: 588 loop : -2.20 (0.13), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 156 TYR 0.023 0.001 TYR C1229 PHE 0.016 0.001 PHE D 629 TRP 0.024 0.001 TRP F 67 HIS 0.004 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (34467) covalent geometry : angle 0.67272 / 0.35 (46973) hydrogen bonds : bond 0.04570 / 3.20 ( 1419) hydrogen bonds : angle 5.15333 / 3.64 ( 3810) metal coordination : bond 0.00565 / 0.36 ( 5) metal coordination : angle 3.55831 / 2.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 489 time to evaluate : 1.451 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: A 147 GLN cc_start: 0.7987 (pt0) cc_final: 0.7642 (pt0) REVERT: A 223 ILE cc_start: 0.9126 (mt) cc_final: 0.8861 (mm) REVERT: A 226 GLU cc_start: 0.6877 (tt0) cc_final: 0.6411 (tp30) REVERT: A 229 GLU cc_start: 0.7960 (pt0) cc_final: 0.7408 (mt-10) REVERT: B 205 MET cc_start: 0.7902 (tmm) cc_final: 0.7349 (tmm) REVERT: C 28 LEU cc_start: 0.8857 (mp) cc_final: 0.8425 (mt) REVERT: C 151 ARG cc_start: 0.7865 (mtp180) cc_final: 0.7403 (mtm110) REVERT: C 185 ASP cc_start: 0.8420 (t0) cc_final: 0.7424 (t0) REVERT: C 704 MET cc_start: 0.8049 (tmm) cc_final: 0.7286 (tmm) REVERT: C 813 GLU cc_start: 0.7416 (tp30) cc_final: 0.6875 (tt0) REVERT: C 835 GLU cc_start: 0.8176 (tt0) cc_final: 0.7105 (pp20) REVERT: C 881 ASP cc_start: 0.8323 (t0) cc_final: 0.7969 (t0) REVERT: C 902 LEU cc_start: 0.8975 (pp) cc_final: 0.8449 (pp) REVERT: C 931 VAL cc_start: 0.9032 (t) cc_final: 0.8755 (m) REVERT: C 1176 LEU cc_start: 0.9087 (mm) cc_final: 0.8878 (mm) REVERT: C 1232 MET cc_start: 0.7996 (mmm) cc_final: 0.7263 (mtp) REVERT: C 1273 MET cc_start: 0.6546 (mpp) cc_final: 0.6343 (mtt) REVERT: C 1276 TRP cc_start: 0.8191 (m-10) cc_final: 0.7705 (m-90) REVERT: C 1290 MET cc_start: 0.7664 (tpp) cc_final: 0.7198 (tpp) REVERT: C 1291 LEU cc_start: 0.9262 (pt) cc_final: 0.8820 (tt) REVERT: D 134 ASP cc_start: 0.7241 (t0) cc_final: 0.7039 (t0) REVERT: D 159 ILE cc_start: 0.7579 (pt) cc_final: 0.7292 (pt) REVERT: D 160 LEU cc_start: 0.7462 (mm) cc_final: 0.7236 (mm) REVERT: D 248 ASP cc_start: 0.8015 (m-30) cc_final: 0.6999 (t0) REVERT: D 334 LYS cc_start: 0.9054 (mtmm) cc_final: 0.8512 (mtmm) REVERT: D 345 LYS cc_start: 0.8356 (ptpp) cc_final: 0.7270 (ptmt) REVERT: D 479 GLU cc_start: 0.6711 (mt-10) cc_final: 0.6484 (mt-10) REVERT: D 571 ASP cc_start: 0.8002 (t0) cc_final: 0.7752 (t0) REVERT: D 625 MET cc_start: 0.7836 (tmm) cc_final: 0.7500 (tmm) REVERT: D 1219 ASP cc_start: 0.6948 (t0) cc_final: 0.6737 (t0) REVERT: D 1254 GLU cc_start: 0.7273 (tt0) cc_final: 0.6967 (tp30) REVERT: D 1260 MET cc_start: 0.8065 (mmm) cc_final: 0.7830 (mmm) REVERT: D 1370 MET cc_start: 0.7881 (tpt) cc_final: 0.7625 (tpp) REVERT: F 74 ASP cc_start: 0.8188 (t0) cc_final: 0.7936 (t0) REVERT: F 113 GLU cc_start: 0.5856 (tp30) cc_final: 0.5573 (tp30) REVERT: F 119 LYS cc_start: 0.8890 (ptmt) cc_final: 0.8252 (pttt) REVERT: K 86 GLN cc_start: 0.8620 (mt0) cc_final: 0.8296 (mt0) REVERT: G 1 MET cc_start: 0.6033 (ptm) cc_final: 0.5566 (ptm) REVERT: H 187 MET cc_start: 0.0794 (mtp) cc_final: 0.0463 (mtt) REVERT: H 191 PRO cc_start: 0.7202 (Cg_exo) cc_final: 0.6914 (Cg_endo) REVERT: I 1 MET cc_start: 0.1373 (mtp) cc_final: 0.0408 (tpt) REVERT: I 30 MET cc_start: 0.1587 (pmm) cc_final: 0.0468 (ttp) outliers start: 1 outliers final: 0 residues processed: 490 average time/residue: 0.2173 time to fit residues: 173.5094 Evaluate side-chains 370 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 158 optimal weight: 2.9990 chunk 397 optimal weight: 50.0000 chunk 242 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 183 optimal weight: 0.1980 chunk 175 optimal weight: 7.9990 chunk 315 optimal weight: 0.8980 chunk 352 optimal weight: 50.0000 chunk 118 optimal weight: 3.9990 chunk 312 optimal weight: 50.0000 chunk 222 optimal weight: 6.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 37 HIS C 69 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 GLN C1157 GLN D 495 ASN D 805 GLN D 875 ASN ** D 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 HIS H 213 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.136729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.116537 restraints weight = 91676.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.116189 restraints weight = 193567.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.114726 restraints weight = 131831.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.114162 restraints weight = 141382.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.113987 restraints weight = 126712.475| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 34472 Z= 0.167 Angle : 0.680 14.089 46979 Z= 0.353 Chirality : 0.046 0.317 5376 Planarity : 0.005 0.061 5798 Dihedral : 16.549 128.819 5465 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.03 % Allowed : 1.59 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.13), residues: 4046 helix: 0.04 (0.14), residues: 1354 sheet: -1.29 (0.20), residues: 611 loop : -2.18 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG K 101 TYR 0.032 0.002 TYR A 177 PHE 0.015 0.001 PHE K 42 TRP 0.021 0.001 TRP F 67 HIS 0.005 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (34467) covalent geometry : angle 0.67905 / 0.35 (46973) hydrogen bonds : bond 0.04552 / 3.20 ( 1419) hydrogen bonds : angle 5.13834 / 3.62 ( 3810) metal coordination : bond 0.00601 / 0.38 ( 5) metal coordination : angle 3.50648 / 2.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 489 time to evaluate : 1.378 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: A 223 ILE cc_start: 0.9153 (mt) cc_final: 0.8847 (mm) REVERT: B 205 MET cc_start: 0.7974 (tmm) cc_final: 0.7334 (tmm) REVERT: C 28 LEU cc_start: 0.8821 (mp) cc_final: 0.8420 (mt) REVERT: C 151 ARG cc_start: 0.7856 (mtp180) cc_final: 0.7351 (mtm110) REVERT: C 185 ASP cc_start: 0.8451 (t0) cc_final: 0.7448 (t0) REVERT: C 459 MET cc_start: 0.8806 (mtp) cc_final: 0.8520 (mtp) REVERT: C 659 GLN cc_start: 0.8786 (tt0) cc_final: 0.8225 (tm-30) REVERT: C 813 GLU cc_start: 0.7425 (tp30) cc_final: 0.6965 (tt0) REVERT: C 835 GLU cc_start: 0.8298 (tt0) cc_final: 0.7215 (pp20) REVERT: C 881 ASP cc_start: 0.8380 (t0) cc_final: 0.7978 (t0) REVERT: C 902 LEU cc_start: 0.9050 (pp) cc_final: 0.8493 (pp) REVERT: C 931 VAL cc_start: 0.9120 (t) cc_final: 0.8821 (m) REVERT: C 1232 MET cc_start: 0.8045 (mmm) cc_final: 0.6973 (mtp) REVERT: C 1276 TRP cc_start: 0.8416 (m-10) cc_final: 0.7752 (m-90) REVERT: C 1290 MET cc_start: 0.7834 (tpp) cc_final: 0.7075 (tpp) REVERT: C 1291 LEU cc_start: 0.9203 (pt) cc_final: 0.8668 (tt) REVERT: D 159 ILE cc_start: 0.7589 (pt) cc_final: 0.7293 (pt) REVERT: D 180 MET cc_start: 0.6339 (mtt) cc_final: 0.5477 (mtt) REVERT: D 227 PHE cc_start: 0.8142 (m-80) cc_final: 0.7903 (m-10) REVERT: D 237 MET cc_start: 0.6957 (mtm) cc_final: 0.6599 (mtt) REVERT: D 248 ASP cc_start: 0.8319 (m-30) cc_final: 0.7202 (t0) REVERT: D 334 LYS cc_start: 0.9015 (mtmm) cc_final: 0.8491 (mtmm) REVERT: D 345 LYS cc_start: 0.8366 (ptpp) cc_final: 0.7367 (ptmt) REVERT: D 400 MET cc_start: 0.8314 (mtm) cc_final: 0.8090 (mtm) REVERT: D 544 LEU cc_start: 0.9339 (tp) cc_final: 0.9048 (tp) REVERT: D 569 LEU cc_start: 0.8242 (tp) cc_final: 0.7882 (mp) REVERT: D 625 MET cc_start: 0.7807 (tmm) cc_final: 0.7603 (tmm) REVERT: D 1219 ASP cc_start: 0.7025 (t0) cc_final: 0.6819 (t0) REVERT: D 1254 GLU cc_start: 0.7346 (tt0) cc_final: 0.6975 (tp30) REVERT: D 1370 MET cc_start: 0.7931 (tpt) cc_final: 0.7636 (tpp) REVERT: F 16 LEU cc_start: 0.8520 (mm) cc_final: 0.8301 (mm) REVERT: F 54 LEU cc_start: 0.8737 (tt) cc_final: 0.8446 (tt) REVERT: F 71 MET cc_start: 0.8742 (ptm) cc_final: 0.8389 (ptt) REVERT: F 74 ASP cc_start: 0.8252 (t0) cc_final: 0.7995 (t0) REVERT: F 119 LYS cc_start: 0.8854 (ptmt) cc_final: 0.8145 (pttt) REVERT: F 134 ASP cc_start: 0.7990 (t70) cc_final: 0.7761 (t0) REVERT: K 86 GLN cc_start: 0.8645 (mt0) cc_final: 0.8293 (mt0) REVERT: G 1 MET cc_start: 0.5778 (ptm) cc_final: 0.5150 (ptm) REVERT: H 187 MET cc_start: 0.0794 (mtp) cc_final: 0.0451 (mtt) REVERT: H 191 PRO cc_start: 0.7254 (Cg_exo) cc_final: 0.6958 (Cg_endo) REVERT: I 1 MET cc_start: 0.1333 (mtp) cc_final: 0.0239 (tpp) REVERT: I 30 MET cc_start: 0.1634 (pmm) cc_final: 0.0498 (ttp) REVERT: I 189 MET cc_start: 0.0826 (ptp) cc_final: -0.0071 (mtp) outliers start: 1 outliers final: 0 residues processed: 490 average time/residue: 0.2294 time to fit residues: 182.7601 Evaluate side-chains 361 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 359 optimal weight: 6.9990 chunk 250 optimal weight: 0.9990 chunk 234 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 131 optimal weight: 40.0000 chunk 47 optimal weight: 0.9990 chunk 104 optimal weight: 9.9990 chunk 199 optimal weight: 0.4980 chunk 282 optimal weight: 4.9990 chunk 357 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 37 HIS C 69 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1326 GLN H 213 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.137273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.116745 restraints weight = 91639.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.116717 restraints weight = 204120.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.116523 restraints weight = 159525.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.116037 restraints weight = 122074.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.116316 restraints weight = 103141.478| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 34472 Z= 0.147 Angle : 0.679 13.778 46979 Z= 0.353 Chirality : 0.046 0.277 5376 Planarity : 0.005 0.107 5798 Dihedral : 16.516 128.551 5465 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.13), residues: 4046 helix: 0.12 (0.14), residues: 1351 sheet: -1.31 (0.20), residues: 618 loop : -2.08 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 233 TYR 0.044 0.002 TYR C1231 PHE 0.016 0.001 PHE D 629 TRP 0.037 0.001 TRP F 67 HIS 0.004 0.001 HIS C1237 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (34467) covalent geometry : angle 0.67835 / 0.35 (46973) hydrogen bonds : bond 0.04457 / 3.12 ( 1419) hydrogen bonds : angle 5.10799 / 3.59 ( 3810) metal coordination : bond 0.00482 / 0.31 ( 5) metal coordination : angle 3.30843 / 1.94 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 485 time to evaluate : 1.300 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: A 223 ILE cc_start: 0.9130 (mt) cc_final: 0.8853 (mm) REVERT: B 205 MET cc_start: 0.7932 (tmm) cc_final: 0.7292 (tmm) REVERT: C 28 LEU cc_start: 0.8692 (mp) cc_final: 0.8364 (mt) REVERT: C 151 ARG cc_start: 0.7774 (mtp180) cc_final: 0.7121 (mtm110) REVERT: C 185 ASP cc_start: 0.8327 (t0) cc_final: 0.7434 (t0) REVERT: C 459 MET cc_start: 0.8854 (mtp) cc_final: 0.8584 (mtp) REVERT: C 515 MET cc_start: 0.8754 (tpt) cc_final: 0.7639 (tpt) REVERT: C 659 GLN cc_start: 0.8750 (tt0) cc_final: 0.8150 (tm-30) REVERT: C 704 MET cc_start: 0.7949 (tmm) cc_final: 0.7492 (tmm) REVERT: C 813 GLU cc_start: 0.7441 (tp30) cc_final: 0.7131 (tt0) REVERT: C 835 GLU cc_start: 0.8157 (tt0) cc_final: 0.7097 (pp20) REVERT: C 851 THR cc_start: 0.8929 (p) cc_final: 0.8229 (p) REVERT: C 881 ASP cc_start: 0.8381 (t0) cc_final: 0.7970 (t0) REVERT: C 902 LEU cc_start: 0.9069 (pp) cc_final: 0.8446 (pp) REVERT: C 931 VAL cc_start: 0.9106 (t) cc_final: 0.8765 (m) REVERT: C 952 GLN cc_start: 0.7917 (pt0) cc_final: 0.7543 (tp40) REVERT: C 1232 MET cc_start: 0.8131 (mmm) cc_final: 0.6914 (mtp) REVERT: C 1276 TRP cc_start: 0.8660 (m-10) cc_final: 0.7695 (m-90) REVERT: C 1285 TYR cc_start: 0.7262 (m-80) cc_final: 0.6877 (m-80) REVERT: C 1291 LEU cc_start: 0.9260 (pt) cc_final: 0.8785 (tt) REVERT: D 227 PHE cc_start: 0.7900 (m-80) cc_final: 0.7667 (m-10) REVERT: D 237 MET cc_start: 0.6899 (mtm) cc_final: 0.6596 (mtt) REVERT: D 248 ASP cc_start: 0.8215 (m-30) cc_final: 0.7121 (t0) REVERT: D 334 LYS cc_start: 0.8943 (mtmm) cc_final: 0.8460 (mtmm) REVERT: D 345 LYS cc_start: 0.8301 (ptpp) cc_final: 0.7300 (ptmt) REVERT: D 400 MET cc_start: 0.8280 (mtm) cc_final: 0.8045 (mtm) REVERT: D 479 GLU cc_start: 0.6535 (mt-10) cc_final: 0.6086 (pt0) REVERT: D 544 LEU cc_start: 0.9298 (tp) cc_final: 0.9087 (tp) REVERT: D 569 LEU cc_start: 0.8218 (tp) cc_final: 0.7816 (mp) REVERT: D 1254 GLU cc_start: 0.7273 (tt0) cc_final: 0.7006 (tp30) REVERT: D 1370 MET cc_start: 0.7899 (tpt) cc_final: 0.7633 (tpp) REVERT: F 71 MET cc_start: 0.8651 (ptm) cc_final: 0.8316 (ptt) REVERT: F 74 ASP cc_start: 0.8235 (t0) cc_final: 0.7968 (t0) REVERT: F 76 ILE cc_start: 0.8354 (mp) cc_final: 0.8147 (mp) REVERT: F 134 ASP cc_start: 0.8105 (t70) cc_final: 0.7868 (t0) REVERT: K 86 GLN cc_start: 0.8555 (mt0) cc_final: 0.8221 (mt0) REVERT: E 42 GLU cc_start: 0.7034 (mp0) cc_final: 0.6796 (mp0) REVERT: G 1 MET cc_start: 0.5354 (ptm) cc_final: 0.4679 (ptm) REVERT: H 1 MET cc_start: 0.3250 (ttt) cc_final: 0.2714 (ttt) REVERT: H 187 MET cc_start: 0.0773 (mtp) cc_final: 0.0447 (mtt) REVERT: H 191 PRO cc_start: 0.7200 (Cg_exo) cc_final: 0.6947 (Cg_endo) REVERT: I 1 MET cc_start: 0.1239 (mtp) cc_final: 0.0053 (tpp) REVERT: I 30 MET cc_start: 0.1539 (pmm) cc_final: 0.0390 (ttp) REVERT: I 189 MET cc_start: 0.0899 (ptp) cc_final: -0.0062 (mtp) outliers start: 0 outliers final: 0 residues processed: 485 average time/residue: 0.2237 time to fit residues: 178.1008 Evaluate side-chains 362 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 74 optimal weight: 20.0000 chunk 301 optimal weight: 7.9990 chunk 215 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 398 optimal weight: 0.0670 chunk 108 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.1720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 37 HIS C 69 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1324 ASN ** D 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.137743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.116113 restraints weight = 92043.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.116367 restraints weight = 195257.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.116554 restraints weight = 153886.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.116350 restraints weight = 114176.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.116687 restraints weight = 98313.975| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 34472 Z= 0.137 Angle : 0.677 13.361 46979 Z= 0.352 Chirality : 0.046 0.278 5376 Planarity : 0.005 0.094 5798 Dihedral : 16.478 128.183 5465 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.13 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.13), residues: 4046 helix: 0.21 (0.14), residues: 1352 sheet: -1.27 (0.20), residues: 618 loop : -2.03 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 28 TYR 0.023 0.001 TYR A 177 PHE 0.033 0.001 PHE C 972 TRP 0.058 0.002 TRP C 997 HIS 0.004 0.001 HIS C 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (34467) covalent geometry : angle 0.67611 / 0.35 (46973) hydrogen bonds : bond 0.04370 / 3.07 ( 1419) hydrogen bonds : angle 5.05578 / 3.55 ( 3810) metal coordination : bond 0.00428 / 0.28 ( 5) metal coordination : angle 3.19229 / 1.88 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 481 time to evaluate : 1.234 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: A 223 ILE cc_start: 0.9183 (mt) cc_final: 0.8913 (mm) REVERT: B 205 MET cc_start: 0.7989 (tmm) cc_final: 0.7285 (tmm) REVERT: C 151 ARG cc_start: 0.7840 (mtp180) cc_final: 0.7118 (mtm110) REVERT: C 185 ASP cc_start: 0.8329 (t0) cc_final: 0.7455 (t0) REVERT: C 515 MET cc_start: 0.8698 (tpt) cc_final: 0.7637 (tpt) REVERT: C 659 GLN cc_start: 0.8746 (tt0) cc_final: 0.8212 (tm-30) REVERT: C 704 MET cc_start: 0.8091 (tmm) cc_final: 0.7729 (tmm) REVERT: C 813 GLU cc_start: 0.7286 (tp30) cc_final: 0.6799 (tt0) REVERT: C 835 GLU cc_start: 0.8223 (tt0) cc_final: 0.7141 (pp20) REVERT: C 851 THR cc_start: 0.8943 (p) cc_final: 0.8716 (p) REVERT: C 881 ASP cc_start: 0.8363 (t0) cc_final: 0.7952 (t0) REVERT: C 902 LEU cc_start: 0.9038 (pp) cc_final: 0.8508 (pp) REVERT: C 931 VAL cc_start: 0.9098 (t) cc_final: 0.8784 (m) REVERT: C 952 GLN cc_start: 0.7833 (pt0) cc_final: 0.7400 (tp40) REVERT: C 1066 MET cc_start: 0.7848 (ttm) cc_final: 0.7545 (ttm) REVERT: C 1170 MET cc_start: 0.7563 (mpp) cc_final: 0.6799 (mmm) REVERT: C 1232 MET cc_start: 0.8023 (mmm) cc_final: 0.7119 (mtp) REVERT: C 1276 TRP cc_start: 0.8586 (m-10) cc_final: 0.7494 (m-90) REVERT: C 1285 TYR cc_start: 0.7285 (m-80) cc_final: 0.6896 (m-80) REVERT: C 1290 MET cc_start: 0.8101 (tpp) cc_final: 0.7344 (tpp) REVERT: C 1291 LEU cc_start: 0.9155 (pt) cc_final: 0.8708 (tt) REVERT: D 237 MET cc_start: 0.6890 (mtm) cc_final: 0.6666 (mtt) REVERT: D 248 ASP cc_start: 0.8258 (m-30) cc_final: 0.7266 (t0) REVERT: D 334 LYS cc_start: 0.8937 (mtmm) cc_final: 0.8543 (mtmm) REVERT: D 345 LYS cc_start: 0.8101 (ptpp) cc_final: 0.7220 (ptmt) REVERT: D 400 MET cc_start: 0.8335 (mtm) cc_final: 0.8117 (mtm) REVERT: D 479 GLU cc_start: 0.6579 (mt-10) cc_final: 0.6057 (pt0) REVERT: D 499 ILE cc_start: 0.6532 (tp) cc_final: 0.6303 (tp) REVERT: D 544 LEU cc_start: 0.9331 (tp) cc_final: 0.9047 (tp) REVERT: D 569 LEU cc_start: 0.8254 (tp) cc_final: 0.7888 (mp) REVERT: D 625 MET cc_start: 0.7699 (tmm) cc_final: 0.7457 (tmm) REVERT: D 1254 GLU cc_start: 0.7304 (tt0) cc_final: 0.6970 (tp30) REVERT: D 1370 MET cc_start: 0.8067 (tpt) cc_final: 0.7833 (tpp) REVERT: F 16 LEU cc_start: 0.8437 (mm) cc_final: 0.8150 (mm) REVERT: F 71 MET cc_start: 0.8586 (ptm) cc_final: 0.8228 (ptt) REVERT: F 74 ASP cc_start: 0.8168 (t0) cc_final: 0.7961 (t0) REVERT: F 134 ASP cc_start: 0.8059 (t70) cc_final: 0.7831 (t0) REVERT: K 86 GLN cc_start: 0.8597 (mt0) cc_final: 0.8276 (mt0) REVERT: G 1 MET cc_start: 0.5269 (ptm) cc_final: 0.3659 (ttt) REVERT: H 187 MET cc_start: 0.0731 (mtp) cc_final: 0.0294 (ptp) REVERT: H 191 PRO cc_start: 0.7225 (Cg_exo) cc_final: 0.6939 (Cg_endo) REVERT: I 1 MET cc_start: 0.1251 (mtp) cc_final: 0.0097 (tpp) REVERT: I 30 MET cc_start: 0.1527 (pmm) cc_final: 0.0416 (ttp) REVERT: I 189 MET cc_start: 0.0938 (ptp) cc_final: -0.0003 (mtp) outliers start: 0 outliers final: 0 residues processed: 481 average time/residue: 0.2145 time to fit residues: 167.4415 Evaluate side-chains 355 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 133 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 352 optimal weight: 40.0000 chunk 2 optimal weight: 0.8980 chunk 366 optimal weight: 30.0000 chunk 41 optimal weight: 6.9990 chunk 365 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 231 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN B 37 HIS B 41 ASN C 69 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1324 ASN D 495 ASN D 736 GLN ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.135739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.114555 restraints weight = 92639.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.115112 restraints weight = 203819.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.114867 restraints weight = 160433.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.114578 restraints weight = 118716.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.114815 restraints weight = 100990.980| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 34472 Z= 0.207 Angle : 0.728 14.486 46979 Z= 0.380 Chirality : 0.047 0.277 5376 Planarity : 0.006 0.146 5798 Dihedral : 16.483 127.780 5465 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.02 % Favored : 92.96 % Rotamer: Outliers : 0.03 % Allowed : 0.72 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.13), residues: 4046 helix: 0.01 (0.14), residues: 1362 sheet: -1.27 (0.20), residues: 632 loop : -2.07 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 976 TYR 0.030 0.002 TYR C1229 PHE 0.022 0.002 PHE C 35 TRP 0.056 0.002 TRP C 997 HIS 0.007 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.21 (34467) covalent geometry : angle 0.72692 / 0.38 (46973) hydrogen bonds : bond 0.04663 / 3.29 ( 1419) hydrogen bonds : angle 5.20505 / 3.65 ( 3810) metal coordination : bond 0.00721 / 0.46 ( 5) metal coordination : angle 3.48616 / 2.08 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5221.30 seconds wall clock time: 91 minutes 37.99 seconds (5497.99 seconds total)