Starting phenix.real_space_refine on Sat Jan 20 02:39:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dnh_7112/01_2024/6dnh_7112.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dnh_7112/01_2024/6dnh_7112.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dnh_7112/01_2024/6dnh_7112.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dnh_7112/01_2024/6dnh_7112.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dnh_7112/01_2024/6dnh_7112.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dnh_7112/01_2024/6dnh_7112.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.014 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 7 5.49 5 S 89 5.16 5 C 8574 2.51 5 N 2338 2.21 5 O 2431 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 616": "NH1" <-> "NH2" Residue "A TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 702": "NH1" <-> "NH2" Residue "A PHE 877": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1274": "NH1" <-> "NH2" Residue "A PHE 1338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 47": "NH1" <-> "NH2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "B PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 265": "OD1" <-> "OD2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13442 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 9337 Classifications: {'peptide': 1177} Link IDs: {'PTRANS': 66, 'TRANS': 1110} Chain breaks: 12 Chain: "B" Number of atoms: 3035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3035 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 15, 'TRANS': 360} Chain: "C" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 917 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain: "E" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 150 Classifications: {'RNA': 7} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 1, 'rna3p_pyr': 1} Link IDs: {'rna2p': 6} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12682 SG CYS C 41 65.500 35.700 17.405 1.00 39.96 S ATOM 12746 SG CYS C 49 69.488 33.242 16.962 1.00 39.96 S ATOM 12781 SG CYS C 55 68.567 33.935 21.043 1.00 39.96 S ATOM 12953 SG CYS C 76 53.386 24.077 22.615 1.00 69.54 S ATOM 13119 SG CYS C 96 33.280 21.341 18.350 1.00 39.93 S ATOM 13237 SG CYS C 110 33.552 24.825 20.217 1.00 37.40 S Time building chain proxies: 7.54, per 1000 atoms: 0.56 Number of scatterers: 13442 At special positions: 0 Unit cell: (87.74, 135.89, 102.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 89 16.00 P 7 15.00 O 2431 8.00 N 2338 7.00 C 8574 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 - 3.50 Amino acid : False - 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: 5.45 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 59 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 49 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 41 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 55 " pdb=" ZN C 302 " pdb="ZN ZN C 302 " - pdb=" NE2 HIS C 86 " pdb="ZN ZN C 302 " - pdb=" SG CYS C 76 " pdb=" ZN C 303 " pdb="ZN ZN C 303 " - pdb=" NE2 HIS C 114 " pdb="ZN ZN C 303 " - pdb=" SG CYS C 110 " pdb="ZN ZN C 303 " - pdb=" SG CYS C 96 " Number of angles added : 3 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3120 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 32 sheets defined 7.5% alpha, 32.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 487 through 491 removed outlier: 3.616A pdb=" N GLN A 491 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 509 Processing helix chain 'A' and resid 1153 through 1156 Processing helix chain 'A' and resid 1352 through 1369 removed outlier: 3.743A pdb=" N ARG A1358 " --> pdb=" O LYS A1354 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A1359 " --> pdb=" O THR A1355 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET A1361 " --> pdb=" O ARG A1357 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A1362 " --> pdb=" O ARG A1358 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A1365 " --> pdb=" O MET A1361 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1376 Processing helix chain 'A' and resid 1403 through 1407 Processing helix chain 'A' and resid 1411 through 1423 removed outlier: 3.737A pdb=" N SER A1416 " --> pdb=" O THR A1412 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU A1417 " --> pdb=" O MET A1413 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A1418 " --> pdb=" O GLU A1414 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A1419 " --> pdb=" O ARG A1415 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1434 removed outlier: 3.820A pdb=" N ILE A1429 " --> pdb=" O THR A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1439 removed outlier: 3.508A pdb=" N VAL A1439 " --> pdb=" O GLU A1435 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 73 removed outlier: 3.659A pdb=" N LYS B 65 " --> pdb=" O PRO B 61 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N TRP B 72 " --> pdb=" O GLU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 removed outlier: 3.590A pdb=" N ASP B 91 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU B 92 " --> pdb=" O TYR B 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 88 through 92' Processing helix chain 'B' and resid 101 through 106 removed outlier: 3.544A pdb=" N ALA B 105 " --> pdb=" O PRO B 102 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B 106 " --> pdb=" O MET B 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 19 Processing helix chain 'C' and resid 42 through 47 Processing helix chain 'C' and resid 70 through 74 removed outlier: 3.537A pdb=" N ARG C 73 " --> pdb=" O HIS C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.855A pdb=" N GLN C 81 " --> pdb=" O LYS C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 101 removed outlier: 3.638A pdb=" N SER C 100 " --> pdb=" O CYS C 96 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1312 through 1315 removed outlier: 6.898A pdb=" N HIS A1334 " --> pdb=" O PRO A1350 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ILE A1345 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 6 " --> pdb=" O LEU A1347 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 20 removed outlier: 6.641A pdb=" N ALA A 33 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER A 17 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL A 31 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N TYR A 19 " --> pdb=" O ASN A 29 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ASN A 29 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN A 37 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU A 38 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER A 71 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL A 40 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 84 removed outlier: 3.612A pdb=" N LYS A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU A 103 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU A 120 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL A 105 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 143 removed outlier: 3.716A pdb=" N ARG A 140 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 202 through 208 removed outlier: 5.937A pdb=" N ILE A 203 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLU A 222 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP A 205 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE A 240 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER A 257 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 255 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 270 removed outlier: 4.418A pdb=" N GLN A 267 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER A 285 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N GLY A 297 " --> pdb=" O ARG A 313 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 326 through 328 removed outlier: 6.792A pdb=" N THR A 348 " --> pdb=" O PHE A 360 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N PHE A 360 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE A 350 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 326 through 328 removed outlier: 4.685A pdb=" N ILE A 344 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 375 through 376 removed outlier: 3.566A pdb=" N LEU A 392 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER A 391 " --> pdb=" O SER A 468 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N SER A 468 " --> pdb=" O SER A 391 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU A 393 " --> pdb=" O CYS A 466 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 478 through 481 Processing sheet with id=AB2, first strand: chain 'A' and resid 522 through 526 removed outlier: 5.238A pdb=" N VAL A 523 " --> pdb=" O VAL A1000 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A1000 " --> pdb=" O VAL A 523 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR A 525 " --> pdb=" O ILE A 998 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR A 989 " --> pdb=" O ARG A 997 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER A 974 " --> pdb=" O PHE A 990 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 534 through 539 removed outlier: 3.857A pdb=" N ASP A 534 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 578 " --> pdb=" O ASP A 534 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 608 through 612 removed outlier: 3.591A pdb=" N PHE A 608 " --> pdb=" O VAL A 621 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR A 617 " --> pdb=" O ILE A 612 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 648 through 652 removed outlier: 3.820A pdb=" N GLN A 648 " --> pdb=" O MET A 659 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 695 through 702 removed outlier: 6.946A pdb=" N VAL A 788 " --> pdb=" O ILE A 696 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU A 698 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU A 786 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU A 700 " --> pdb=" O TRP A 784 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TRP A 784 " --> pdb=" O LEU A 700 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N MET A 794 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU A 807 " --> pdb=" O MET A 794 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE A 796 " --> pdb=" O VAL A 805 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 846 through 854 removed outlier: 6.633A pdb=" N HIS A 866 " --> pdb=" O LYS A 847 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL A 849 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU A 864 " --> pdb=" O VAL A 849 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU A 851 " --> pdb=" O TYR A 862 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TYR A 862 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ALA A 853 " --> pdb=" O ARG A 860 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG A 860 " --> pdb=" O ALA A 853 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 865 " --> pdb=" O LEU A 872 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 872 " --> pdb=" O VAL A 865 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 877 through 878 Processing sheet with id=AB9, first strand: chain 'A' and resid 931 through 937 removed outlier: 5.705A pdb=" N TYR A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1024 through 1028 removed outlier: 3.661A pdb=" N TYR A1024 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1046 through 1047 Processing sheet with id=AC3, first strand: chain 'A' and resid 1098 through 1106 removed outlier: 6.745A pdb=" N GLY A1124 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N MET A1103 " --> pdb=" O ALA A1122 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA A1122 " --> pdb=" O MET A1103 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR A1105 " --> pdb=" O TYR A1120 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N TYR A1120 " --> pdb=" O THR A1105 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLY A1137 " --> pdb=" O GLU A1167 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLU A1167 " --> pdb=" O GLY A1137 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE A1139 " --> pdb=" O GLU A1165 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU A1165 " --> pdb=" O ILE A1139 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE A1141 " --> pdb=" O LEU A1163 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1172 through 1177 removed outlier: 4.313A pdb=" N ALA A1174 " --> pdb=" O ALA A1185 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE A1190 " --> pdb=" O PHE A1205 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE A1205 " --> pdb=" O ILE A1190 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU A1192 " --> pdb=" O MET A1203 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1212 through 1217 removed outlier: 3.558A pdb=" N GLN A1214 " --> pdb=" O ALA A1225 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE A1231 " --> pdb=" O ARG A1248 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG A1248 " --> pdb=" O ILE A1231 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU A1233 " --> pdb=" O VAL A1246 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN A1237 " --> pdb=" O THR A1242 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR A1242 " --> pdb=" O GLN A1237 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1255 through 1258 removed outlier: 6.857A pdb=" N SER A1272 " --> pdb=" O TYR A1256 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL A1258 " --> pdb=" O LEU A1270 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU A1270 " --> pdb=" O VAL A1258 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1255 through 1258 removed outlier: 6.857A pdb=" N SER A1272 " --> pdb=" O TYR A1256 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL A1258 " --> pdb=" O LEU A1270 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU A1270 " --> pdb=" O VAL A1258 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU A1278 " --> pdb=" O ASP A1301 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP A1301 " --> pdb=" O LEU A1278 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A1280 " --> pdb=" O ARG A1299 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 109 through 113 removed outlier: 6.644A pdb=" N PHE B 401 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR B 113 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N SER B 399 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS B 400 " --> pdb=" O SER B 392 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE B 389 " --> pdb=" O TRP B 383 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TRP B 383 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N CYS B 391 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU B 381 " --> pdb=" O CYS B 391 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY B 393 " --> pdb=" O TRP B 379 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 124 through 127 removed outlier: 3.517A pdb=" N VAL B 124 " --> pdb=" O GLY B 137 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 155 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 164 through 169 removed outlier: 3.799A pdb=" N ALA B 166 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL B 185 " --> pdb=" O MET B 197 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N MET B 197 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR B 187 " --> pdb=" O VAL B 195 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 205 through 210 removed outlier: 6.997A pdb=" N CYS B 220 " --> pdb=" O ARG B 206 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA B 208 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA B 218 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N PHE B 210 " --> pdb=" O LYS B 216 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LYS B 216 " --> pdb=" O PHE B 210 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG B 238 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASP B 230 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLU B 236 " --> pdb=" O ASP B 230 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 250 through 252 Processing sheet with id=AD4, first strand: chain 'B' and resid 291 through 296 removed outlier: 3.569A pdb=" N CYS B 312 " --> pdb=" O PHE B 327 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 334 through 339 removed outlier: 3.846A pdb=" N ALA B 336 " --> pdb=" O GLY B 350 " (cutoff:3.500A) 339 hydrogen bonds defined for protein. 882 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.81 Time building geometry restraints manager: 5.91 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: 3970 1.33 - 1.45: 2277 1.45 - 1.57: 7381 1.57 - 1.69: 13 1.69 - 1.81: 141 Bond restraints: 13782 Sorted by residual: bond pdb=" C ILE B 57 " pdb=" N ASP B 58 " ideal model delta sigma weight residual 1.331 1.404 -0.073 1.42e-02 4.96e+03 2.64e+01 bond pdb=" CB PHE B 210 " pdb=" CG PHE B 210 " ideal model delta sigma weight residual 1.502 1.443 0.059 2.30e-02 1.89e+03 6.50e+00 bond pdb=" N MET A 377 " pdb=" CA MET A 377 " ideal model delta sigma weight residual 1.457 1.427 0.031 1.29e-02 6.01e+03 5.63e+00 bond pdb=" CG LEU A1347 " pdb=" CD2 LEU A1347 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.29e+00 bond pdb=" N ILE A 330 " pdb=" CA ILE A 330 " ideal model delta sigma weight residual 1.459 1.431 0.028 1.24e-02 6.50e+03 5.00e+00 ... (remaining 13777 not shown) Histogram of bond angle deviations from ideal: 97.74 - 105.01: 345 105.01 - 112.28: 6890 112.28 - 119.55: 4544 119.55 - 126.82: 6684 126.82 - 134.09: 248 Bond angle restraints: 18711 Sorted by residual: angle pdb=" N CYS A 466 " pdb=" CA CYS A 466 " pdb=" C CYS A 466 " ideal model delta sigma weight residual 111.14 120.88 -9.74 1.08e+00 8.57e-01 8.13e+01 angle pdb=" N LEU A 200 " pdb=" CA LEU A 200 " pdb=" C LEU A 200 " ideal model delta sigma weight residual 111.07 119.88 -8.81 1.07e+00 8.73e-01 6.77e+01 angle pdb=" N SER B 266 " pdb=" CA SER B 266 " pdb=" C SER B 266 " ideal model delta sigma weight residual 111.28 118.10 -6.82 1.09e+00 8.42e-01 3.91e+01 angle pdb=" N ASP A1273 " pdb=" CA ASP A1273 " pdb=" C ASP A1273 " ideal model delta sigma weight residual 109.07 118.67 -9.60 1.61e+00 3.86e-01 3.55e+01 angle pdb=" C SER A 331 " pdb=" CA SER A 331 " pdb=" CB SER A 331 " ideal model delta sigma weight residual 116.63 109.83 6.80 1.16e+00 7.43e-01 3.44e+01 ... (remaining 18706 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.79: 7596 14.79 - 29.57: 495 29.57 - 44.35: 85 44.35 - 59.14: 12 59.14 - 73.92: 8 Dihedral angle restraints: 8196 sinusoidal: 3366 harmonic: 4830 Sorted by residual: dihedral pdb=" C ASP A 333 " pdb=" N ASP A 333 " pdb=" CA ASP A 333 " pdb=" CB ASP A 333 " ideal model delta harmonic sigma weight residual -122.60 -139.88 17.28 0 2.50e+00 1.60e-01 4.78e+01 dihedral pdb=" N ASP A 333 " pdb=" C ASP A 333 " pdb=" CA ASP A 333 " pdb=" CB ASP A 333 " ideal model delta harmonic sigma weight residual 122.80 139.11 -16.31 0 2.50e+00 1.60e-01 4.25e+01 dihedral pdb=" CA ASN B 100 " pdb=" C ASN B 100 " pdb=" N ASN B 101 " pdb=" CA ASN B 101 " ideal model delta harmonic sigma weight residual -180.00 -150.92 -29.08 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 8193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 1983 0.129 - 0.258: 89 0.258 - 0.386: 7 0.386 - 0.515: 0 0.515 - 0.644: 1 Chirality restraints: 2080 Sorted by residual: chirality pdb=" CA ASP A 333 " pdb=" N ASP A 333 " pdb=" C ASP A 333 " pdb=" CB ASP A 333 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" CA ILE A 330 " pdb=" N ILE A 330 " pdb=" C ILE A 330 " pdb=" CB ILE A 330 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA MET C 1 " pdb=" N MET C 1 " pdb=" C MET C 1 " pdb=" CB MET C 1 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 2077 not shown) Planarity restraints: 2362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 465 " -0.023 2.00e-02 2.50e+03 4.57e-02 2.09e+01 pdb=" C VAL A 465 " 0.079 2.00e-02 2.50e+03 pdb=" O VAL A 465 " -0.030 2.00e-02 2.50e+03 pdb=" N CYS A 466 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1312 " 0.048 2.00e-02 2.50e+03 2.60e-02 1.70e+01 pdb=" CG TRP A1312 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP A1312 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A1312 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A1312 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A1312 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A1312 " -0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1312 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1312 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A1312 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 252 " -0.024 2.00e-02 2.50e+03 1.94e-02 9.45e+00 pdb=" CG TRP B 252 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP B 252 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP B 252 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 252 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 252 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP B 252 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 252 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 252 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 252 " 0.001 2.00e-02 2.50e+03 ... (remaining 2359 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 4 1.99 - 2.71: 801 2.71 - 3.44: 17251 3.44 - 4.17: 32020 4.17 - 4.90: 57167 Nonbonded interactions: 107243 Sorted by model distance: nonbonded pdb=" OE2 GLU A 630 " pdb=" CB LEU A 635 " model vdw 1.258 3.440 nonbonded pdb=" O LEU A 628 " pdb=" CD2 LEU A 629 " model vdw 1.320 3.460 nonbonded pdb=" O ASP A1273 " pdb=" N ASP A1275 " model vdw 1.877 2.520 nonbonded pdb=" ND2 ASN A 202 " pdb=" OE1 GLN A 225 " model vdw 1.906 2.520 nonbonded pdb=" OE2 GLU A 630 " pdb=" CG LEU A 635 " model vdw 2.010 3.470 ... (remaining 107238 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.010 Extract box with map and model: 2.340 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 41.790 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.076 13782 Z= 0.633 Angle : 1.079 11.339 18711 Z= 0.610 Chirality : 0.065 0.644 2080 Planarity : 0.008 0.062 2362 Dihedral : 10.602 73.923 5076 Min Nonbonded Distance : 1.258 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.48 % Favored : 91.22 % Rotamer: Outliers : 1.10 % Allowed : 1.99 % Favored : 96.91 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.17), residues: 1640 helix: -4.77 (0.17), residues: 104 sheet: -2.46 (0.18), residues: 633 loop : -2.58 (0.18), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.005 TRP A1312 HIS 0.017 0.003 HIS A 9 PHE 0.043 0.004 PHE A1074 TYR 0.041 0.004 TYR A 2 ARG 0.012 0.001 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 350 time to evaluate : 1.654 Fit side-chains revert: symmetry clash REVERT: A 79 MET cc_start: 0.7931 (mmp) cc_final: 0.7679 (mmt) REVERT: A 1210 LEU cc_start: 0.8037 (mp) cc_final: 0.7703 (mt) REVERT: A 1253 LEU cc_start: 0.9079 (tp) cc_final: 0.8697 (tp) REVERT: B 292 MET cc_start: 0.7821 (mmm) cc_final: 0.7616 (mmt) REVERT: B 335 THR cc_start: 0.8280 (p) cc_final: 0.8072 (p) outliers start: 16 outliers final: 8 residues processed: 363 average time/residue: 0.3394 time to fit residues: 169.1162 Evaluate side-chains 191 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 183 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1176 CYS Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1316 CYS Chi-restraints excluded: chain B residue 265 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 8.9990 chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 ASN A 291 GLN A 516 GLN ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 HIS A 648 GLN A 783 HIS A 869 GLN A1309 ASN A1332 ASN B 60 ASN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN B 235 HIS B 297 ASN B 325 GLN B 416 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13782 Z= 0.206 Angle : 0.645 8.356 18711 Z= 0.337 Chirality : 0.046 0.173 2080 Planarity : 0.005 0.074 2362 Dihedral : 7.737 73.276 1907 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.89 % Favored : 92.99 % Rotamer: Outliers : 2.27 % Allowed : 8.04 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.18), residues: 1640 helix: -3.47 (0.35), residues: 102 sheet: -1.78 (0.18), residues: 644 loop : -2.32 (0.18), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 802 HIS 0.005 0.001 HIS A 680 PHE 0.013 0.002 PHE B 217 TYR 0.014 0.001 TYR A1256 ARG 0.007 0.000 ARG B 308 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 232 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.7956 (mmp) cc_final: 0.7731 (mmt) REVERT: A 264 ASP cc_start: 0.8199 (p0) cc_final: 0.7993 (p0) outliers start: 33 outliers final: 16 residues processed: 254 average time/residue: 0.2526 time to fit residues: 94.8166 Evaluate side-chains 191 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 175 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 887 ASN Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1316 CYS Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 60 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 chunk 162 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 120 optimal weight: 0.0000 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 GLN A 680 HIS ** A1209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN B 189 GLN B 235 HIS B 297 ASN ** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 ASN B 343 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 13782 Z= 0.309 Angle : 0.644 9.163 18711 Z= 0.333 Chirality : 0.046 0.173 2080 Planarity : 0.005 0.065 2362 Dihedral : 7.017 73.304 1898 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.74 % Favored : 92.13 % Rotamer: Outliers : 2.89 % Allowed : 10.86 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.19), residues: 1640 helix: -2.55 (0.42), residues: 101 sheet: -1.43 (0.19), residues: 611 loop : -2.12 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1312 HIS 0.006 0.001 HIS A 9 PHE 0.022 0.002 PHE A 600 TYR 0.017 0.001 TYR A 345 ARG 0.008 0.000 ARG B 308 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 178 time to evaluate : 1.399 Fit side-chains REVERT: A 264 ASP cc_start: 0.8219 (p0) cc_final: 0.7953 (p0) REVERT: A 707 MET cc_start: 0.7537 (ptp) cc_final: 0.7309 (ptp) REVERT: C 97 TYR cc_start: 0.8094 (t80) cc_final: 0.7810 (t80) outliers start: 42 outliers final: 27 residues processed: 209 average time/residue: 0.2406 time to fit residues: 76.0313 Evaluate side-chains 193 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 166 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 969 ASP Chi-restraints excluded: chain A residue 1103 MET Chi-restraints excluded: chain A residue 1199 GLU Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1316 CYS Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 60 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 chunk 159 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN A 246 ASN ** A1209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS B 301 ASN B 310 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.087 13782 Z= 0.623 Angle : 0.807 8.192 18711 Z= 0.413 Chirality : 0.051 0.170 2080 Planarity : 0.006 0.069 2362 Dihedral : 7.430 73.190 1898 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.94 % Favored : 89.94 % Rotamer: Outliers : 3.37 % Allowed : 13.06 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.19), residues: 1640 helix: -2.41 (0.44), residues: 103 sheet: -1.48 (0.19), residues: 639 loop : -2.05 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A1312 HIS 0.009 0.002 HIS A1099 PHE 0.029 0.003 PHE B 210 TYR 0.025 0.002 TYR A 345 ARG 0.005 0.001 ARG A1298 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 166 time to evaluate : 1.525 Fit side-chains revert: symmetry clash REVERT: A 264 ASP cc_start: 0.8336 (p0) cc_final: 0.8129 (p0) REVERT: A 707 MET cc_start: 0.7681 (ptp) cc_final: 0.7450 (ptp) REVERT: A 953 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8614 (tt) outliers start: 49 outliers final: 33 residues processed: 201 average time/residue: 0.2719 time to fit residues: 82.2110 Evaluate side-chains 194 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 160 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 887 ASN Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 969 ASP Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1199 GLU Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1316 CYS Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 60 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 2.9990 chunk 90 optimal weight: 0.1980 chunk 2 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 0 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 143 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A1071 GLN ** A1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 13782 Z= 0.161 Angle : 0.566 6.788 18711 Z= 0.292 Chirality : 0.044 0.162 2080 Planarity : 0.004 0.069 2362 Dihedral : 6.642 73.218 1898 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.07 % Favored : 92.80 % Rotamer: Outliers : 2.06 % Allowed : 14.91 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.20), residues: 1640 helix: -1.83 (0.49), residues: 103 sheet: -1.10 (0.20), residues: 603 loop : -1.91 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 72 HIS 0.003 0.001 HIS B 287 PHE 0.018 0.001 PHE A 608 TYR 0.011 0.001 TYR C 99 ARG 0.003 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 180 time to evaluate : 1.600 Fit side-chains revert: symmetry clash REVERT: A 707 MET cc_start: 0.7415 (ptp) cc_final: 0.7177 (ptp) REVERT: A 1332 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7906 (t0) outliers start: 30 outliers final: 19 residues processed: 199 average time/residue: 0.2346 time to fit residues: 70.8110 Evaluate side-chains 189 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 169 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1316 CYS Chi-restraints excluded: chain A residue 1332 ASN Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 60 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 0.8980 chunk 143 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1071 GLN ** A1209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3506 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: