Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 10 17:01:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5z_24844/10_2023/7s5z_24844_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5z_24844/10_2023/7s5z_24844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5z_24844/10_2023/7s5z_24844.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5z_24844/10_2023/7s5z_24844.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5z_24844/10_2023/7s5z_24844_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5z_24844/10_2023/7s5z_24844_updated.pdb" } resolution = 3.9 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= -0.005 sd= 0.078 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 P 5 5.49 5 Mg 2 5.21 5 S 121 5.16 5 C 13673 2.51 5 N 3597 2.21 5 O 3750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 32": "NH1" <-> "NH2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A ASP 280": "OD1" <-> "OD2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A GLU 288": "OE1" <-> "OE2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "B GLU 179": "OE1" <-> "OE2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B ASP 280": "OD1" <-> "OD2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B GLU 288": "OE1" <-> "OE2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C GLU 141": "OE1" <-> "OE2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C ARG 195": "NH1" <-> "NH2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C ASP 280": "OD1" <-> "OD2" Residue "C GLU 282": "OE1" <-> "OE2" Residue "C GLU 288": "OE1" <-> "OE2" Residue "D ARG 32": "NH1" <-> "NH2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D ARG 195": "NH1" <-> "NH2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "D ASP 280": "OD1" <-> "OD2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "D GLU 288": "OE1" <-> "OE2" Residue "E GLU 10": "OE1" <-> "OE2" Residue "E ASP 30": "OD1" <-> "OD2" Residue "E ARG 75": "NH1" <-> "NH2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "E GLU 101": "OE1" <-> "OE2" Residue "E TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 307": "NH1" <-> "NH2" Residue "E PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 516": "OE1" <-> "OE2" Residue "E PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 528": "NH1" <-> "NH2" Residue "E PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 569": "OE1" <-> "OE2" Residue "E ASP 571": "OD1" <-> "OD2" Residue "E ASP 676": "OD1" <-> "OD2" Residue "E ARG 703": "NH1" <-> "NH2" Residue "E PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 819": "OD1" <-> "OD2" Residue "E ARG 842": "NH1" <-> "NH2" Residue "E ASP 854": "OD1" <-> "OD2" Residue "E ASP 861": "OD1" <-> "OD2" Residue "E ASP 905": "OD1" <-> "OD2" Residue "E GLU 911": "OE1" <-> "OE2" Residue "E ASP 916": "OD1" <-> "OD2" Residue "E GLU 938": "OE1" <-> "OE2" Residue "E GLU 942": "OE1" <-> "OE2" Residue "E ASP 1031": "OD1" <-> "OD2" Residue "E TYR 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1068": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1124": "NH1" <-> "NH2" Residue "E ASP 1133": "OD1" <-> "OD2" Residue "E GLU 1141": "OE1" <-> "OE2" Residue "E TYR 1181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1206": "OE1" <-> "OE2" Residue "E PHE 1217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1222": "NH1" <-> "NH2" Residue "E GLU 1275": "OE1" <-> "OE2" Residue "E TYR 1287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1304": "OD1" <-> "OD2" Residue "E ARG 1314": "NH1" <-> "NH2" Residue "E GLU 1322": "OE1" <-> "OE2" Residue "E TYR 1326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1327": "OE1" <-> "OE2" Residue "E PHE 1393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1406": "OD1" <-> "OD2" Residue "E ARG 1419": "NH1" <-> "NH2" Residue "E ARG 1437": "NH1" <-> "NH2" Residue "E PHE 1438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1480": "OE1" <-> "OE2" Residue "E ARG 1487": "NH1" <-> "NH2" Residue "E ARG 1494": "NH1" <-> "NH2" Residue "E ARG 1498": "NH1" <-> "NH2" Residue "E PHE 1503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1507": "OE1" <-> "OE2" Residue "E ASP 1513": "OD1" <-> "OD2" Residue "E PHE 1528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1560": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 21148 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2519 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain: "B" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2519 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain: "C" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2519 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain: "D" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2519 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain: "E" Number of atoms: 11072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1407, 11072 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'peptide': 1403, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 42, 'TRANS': 1360, None: 4} Not linked: pdbres="LYS E1582 " pdbres="ADP E1601 " Not linked: pdbres="ADP E1601 " pdbres=" MG E1602 " Not linked: pdbres=" MG E1602 " pdbres=" MG E1603 " Not linked: pdbres=" MG E1603 " pdbres="ATP E1604 " Chain breaks: 7 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 53 Time building chain proxies: 10.92, per 1000 atoms: 0.52 Number of scatterers: 21148 At special positions: 0 Unit cell: (130, 154.7, 141.7, 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) S 121 16.00 P 5 15.00 Mg 2 11.99 O 3750 8.00 N 3597 7.00 C 13673 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " distance=2.03 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: 8.86 Conformation dependent library (CDL) restraints added in 3.3 seconds 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5070 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 87 helices and 26 sheets defined 46.0% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.55 Creating SS restraints... Processing helix chain 'A' and resid 53 through 56 No H-bonds generated for 'chain 'A' and resid 53 through 56' Processing helix chain 'A' and resid 59 through 64 Processing helix chain 'A' and resid 68 through 96 Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 143 through 172 Processing helix chain 'A' and resid 177 through 180 Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.794A pdb=" N ASP A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 346 through 350' Processing helix chain 'B' and resid 53 through 56 No H-bonds generated for 'chain 'B' and resid 53 through 56' Processing helix chain 'B' and resid 59 through 64 Processing helix chain 'B' and resid 68 through 96 Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 143 through 172 Processing helix chain 'B' and resid 177 through 180 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 330 through 332 No H-bonds generated for 'chain 'B' and resid 330 through 332' Processing helix chain 'B' and resid 346 through 350 removed outlier: 3.794A pdb=" N ASP B 350 " --> pdb=" O ALA B 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 346 through 350' Processing helix chain 'C' and resid 53 through 56 No H-bonds generated for 'chain 'C' and resid 53 through 56' Processing helix chain 'C' and resid 59 through 64 Processing helix chain 'C' and resid 68 through 96 Processing helix chain 'C' and resid 117 through 128 Processing helix chain 'C' and resid 143 through 172 Processing helix chain 'C' and resid 177 through 180 Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 330 through 332 No H-bonds generated for 'chain 'C' and resid 330 through 332' Processing helix chain 'C' and resid 346 through 350 removed outlier: 3.793A pdb=" N ASP C 350 " --> pdb=" O ALA C 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 346 through 350' Processing helix chain 'D' and resid 53 through 56 No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 59 through 64 Processing helix chain 'D' and resid 68 through 96 Processing helix chain 'D' and resid 117 through 128 Processing helix chain 'D' and resid 143 through 172 Processing helix chain 'D' and resid 177 through 180 Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 346 through 350 removed outlier: 3.793A pdb=" N ASP D 350 " --> pdb=" O ALA D 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 346 through 350' Processing helix chain 'E' and resid 14 through 16 No H-bonds generated for 'chain 'E' and resid 14 through 16' Processing helix chain 'E' and resid 26 through 51 removed outlier: 3.563A pdb=" N VAL E 35 " --> pdb=" O ALA E 31 " (cutoff:3.500A) Proline residue: E 36 - end of helix Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 72 through 96 Processing helix chain 'E' and resid 109 through 130 Processing helix chain 'E' and resid 138 through 161 Processing helix chain 'E' and resid 168 through 192 Processing helix chain 'E' and resid 225 through 230 Processing helix chain 'E' and resid 232 through 239 removed outlier: 3.568A pdb=" N ILE E 238 " --> pdb=" O ASN E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 274 removed outlier: 5.837A pdb=" N LEU E 267 " --> pdb=" O ASN E 263 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA E 273 " --> pdb=" O GLU E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 309 removed outlier: 5.631A pdb=" N ARG E 298 " --> pdb=" O HIS E 294 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ARG E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 327 Proline residue: E 318 - end of helix removed outlier: 3.792A pdb=" N VAL E 325 " --> pdb=" O PHE E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 354 Processing helix chain 'E' and resid 356 through 401 removed outlier: 4.001A pdb=" N THR E 394 " --> pdb=" O GLY E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 409 Processing helix chain 'E' and resid 415 through 455 removed outlier: 5.293A pdb=" N ASN E 427 " --> pdb=" O ALA E 423 " (cutoff:3.500A) Proline residue: E 437 - end of helix Proline residue: E 443 - end of helix Processing helix chain 'E' and resid 458 through 505 removed outlier: 3.613A pdb=" N ALA E 461 " --> pdb=" O GLY E 458 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA E 466 " --> pdb=" O ILE E 463 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL E 467 " --> pdb=" O GLY E 464 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA E 472 " --> pdb=" O ILE E 469 " (cutoff:3.500A) Proline residue: E 473 - end of helix removed outlier: 3.599A pdb=" N VAL E 478 " --> pdb=" O GLN E 475 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU E 482 " --> pdb=" O ALA E 479 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU E 490 " --> pdb=" O ARG E 487 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG E 496 " --> pdb=" O SER E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 507 through 512 Processing helix chain 'E' and resid 516 through 548 removed outlier: 3.530A pdb=" N SER E 533 " --> pdb=" O LYS E 529 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA E 536 " --> pdb=" O THR E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 551 through 564 Processing helix chain 'E' and resid 574 through 588 Processing helix chain 'E' and resid 594 through 615 Processing helix chain 'E' and resid 720 through 727 removed outlier: 3.620A pdb=" N LEU E 724 " --> pdb=" O LYS E 720 " (cutoff:3.500A) Processing helix chain 'E' and resid 784 through 789 Processing helix chain 'E' and resid 796 through 805 Processing helix chain 'E' and resid 809 through 814 Processing helix chain 'E' and resid 818 through 820 No H-bonds generated for 'chain 'E' and resid 818 through 820' Processing helix chain 'E' and resid 833 through 846 removed outlier: 3.768A pdb=" N GLN E 846 " --> pdb=" O ARG E 842 " (cutoff:3.500A) Processing helix chain 'E' and resid 862 through 870 Processing helix chain 'E' and resid 894 through 896 No H-bonds generated for 'chain 'E' and resid 894 through 896' Processing helix chain 'E' and resid 914 through 919 Processing helix chain 'E' and resid 922 through 932 Processing helix chain 'E' and resid 999 through 1008 Processing helix chain 'E' and resid 1010 through 1038 Processing helix chain 'E' and resid 1067 through 1097 Processing helix chain 'E' and resid 1101 through 1106 Processing helix chain 'E' and resid 1110 through 1115 Processing helix chain 'E' and resid 1118 through 1134 removed outlier: 4.984A pdb=" N CYS E1129 " --> pdb=" O PHE E1125 " (cutoff:3.500A) Processing helix chain 'E' and resid 1136 through 1160 removed outlier: 3.544A pdb=" N SER E1146 " --> pdb=" O CYS E1142 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU E1148 " --> pdb=" O SER E1144 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU E1149 " --> pdb=" O ARG E1145 " (cutoff:3.500A) Processing helix chain 'E' and resid 1162 through 1216 removed outlier: 4.265A pdb=" N LEU E1165 " --> pdb=" O PRO E1162 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL E1166 " --> pdb=" O VAL E1163 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU E1169 " --> pdb=" O VAL E1166 " (cutoff:3.500A) Proline residue: E1170 - end of helix removed outlier: 3.530A pdb=" N VAL E1174 " --> pdb=" O LEU E1171 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE E1178 " --> pdb=" O CYS E1175 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG E1183 " --> pdb=" O LYS E1180 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL E1184 " --> pdb=" O TYR E1181 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG E1187 " --> pdb=" O VAL E1184 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU E1189 " --> pdb=" O SER E1186 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR E1196 " --> pdb=" O ASP E1193 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU E1198 " --> pdb=" O THR E1195 " (cutoff:3.500A) Proline residue: E1199 - end of helix removed outlier: 3.911A pdb=" N VAL E1208 " --> pdb=" O ALA E1205 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU E1209 " --> pdb=" O GLU E1206 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY E1210 " --> pdb=" O THR E1207 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU E1211 " --> pdb=" O VAL E1208 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR E1212 " --> pdb=" O GLU E1209 " (cutoff:3.500A) Processing helix chain 'E' and resid 1220 through 1272 removed outlier: 4.029A pdb=" N VAL E1260 " --> pdb=" O GLY E1256 " (cutoff:3.500A) Processing helix chain 'E' and resid 1280 through 1319 removed outlier: 5.342A pdb=" N ASN E1296 " --> pdb=" O SER E1292 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N TRP E1297 " --> pdb=" O ASN E1293 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA E1311 " --> pdb=" O LEU E1307 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL E1312 " --> pdb=" O GLN E1308 " (cutoff:3.500A) Processing helix chain 'E' and resid 1385 through 1392 removed outlier: 3.859A pdb=" N SER E1389 " --> pdb=" O LYS E1385 " (cutoff:3.500A) Processing helix chain 'E' and resid 1415 through 1421 Processing helix chain 'E' and resid 1436 through 1440 Processing helix chain 'E' and resid 1448 through 1456 Processing helix chain 'E' and resid 1461 through 1466 Processing helix chain 'E' and resid 1484 through 1497 Processing helix chain 'E' and resid 1514 through 1523 Processing helix chain 'E' and resid 1540 through 1543 No H-bonds generated for 'chain 'E' and resid 1540 through 1543' Processing helix chain 'E' and resid 1563 through 1567 Processing helix chain 'E' and resid 1573 through 1581 Processing sheet with id= A, first strand: chain 'A' and resid 181 through 183 removed outlier: 3.670A pdb=" N VAL A 202 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 255 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 188 through 192 Processing sheet with id= C, first strand: chain 'A' and resid 234 through 238 removed outlier: 3.777A pdb=" N ARG A 221 " --> pdb=" O HIS A 234 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 313 through 315 Processing sheet with id= E, first strand: chain 'A' and resid 319 through 322 Processing sheet with id= F, first strand: chain 'B' and resid 181 through 183 removed outlier: 3.670A pdb=" N VAL B 202 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 255 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 188 through 192 Processing sheet with id= H, first strand: chain 'B' and resid 234 through 238 removed outlier: 3.777A pdb=" N ARG B 221 " --> pdb=" O HIS B 234 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N MET B 217 " --> pdb=" O ILE B 238 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 313 through 315 Processing sheet with id= J, first strand: chain 'B' and resid 319 through 322 Processing sheet with id= K, first strand: chain 'C' and resid 181 through 183 removed outlier: 3.670A pdb=" N VAL C 202 " --> pdb=" O LEU C 255 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 255 " --> pdb=" O VAL C 202 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 188 through 192 Processing sheet with id= M, first strand: chain 'C' and resid 234 through 238 removed outlier: 3.777A pdb=" N ARG C 221 " --> pdb=" O HIS C 234 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 313 through 315 Processing sheet with id= O, first strand: chain 'C' and resid 319 through 322 Processing sheet with id= P, first strand: chain 'D' and resid 181 through 183 removed outlier: 3.670A pdb=" N VAL D 202 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D 255 " --> pdb=" O VAL D 202 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 188 through 192 Processing sheet with id= R, first strand: chain 'D' and resid 234 through 238 removed outlier: 3.777A pdb=" N ARG D 221 " --> pdb=" O HIS D 234 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N MET D 217 " --> pdb=" O ILE D 238 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 313 through 315 Processing sheet with id= T, first strand: chain 'D' and resid 319 through 322 Processing sheet with id= U, first strand: chain 'E' and resid 899 through 903 removed outlier: 6.733A pdb=" N VAL E 884 " --> pdb=" O THR E 710 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE E 712 " --> pdb=" O VAL E 884 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU E 886 " --> pdb=" O ILE E 712 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N GLY E 714 " --> pdb=" O LEU E 886 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ALA E 771 " --> pdb=" O PHE E 852 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 1376 through 1379 removed outlier: 3.528A pdb=" N VAL E1551 " --> pdb=" O GLU E1559 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU E1559 " --> pdb=" O VAL E1551 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LYS E1553 " --> pdb=" O ILE E1557 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ILE E1557 " --> pdb=" O LYS E1553 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 1502 through 1505 removed outlier: 6.154A pdb=" N THR E1532 " --> pdb=" O PHE E1503 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N MET E1505 " --> pdb=" O THR E1532 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL E1534 " --> pdb=" O MET E1505 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'E' and resid 686 through 688 removed outlier: 3.758A pdb=" N TYR E 686 " --> pdb=" O SER E 735 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER E 735 " --> pdb=" O TYR E 686 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR E 688 " --> pdb=" O LYS E 733 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LYS E 733 " --> pdb=" O THR E 688 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'E' and resid 1345 through 1350 removed outlier: 5.368A pdb=" N VAL E1365 " --> pdb=" O ASN E1349 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 1351 through 1353 removed outlier: 3.670A pdb=" N SER E1351 " --> pdb=" O GLU E1400 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG E1353 " --> pdb=" O THR E1398 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N THR E1398 " --> pdb=" O ARG E1353 " (cutoff:3.500A) 996 hydrogen bonds defined for protein. 2682 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: 7.66 Time building geometry restraints manager: 9.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6588 1.34 - 1.46: 4241 1.46 - 1.58: 10580 1.58 - 1.70: 8 1.70 - 1.81: 194 Bond restraints: 21611 Sorted by residual: bond pdb=" C4 ATP E1604 " pdb=" C5 ATP E1604 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.98e+01 bond pdb=" C5 ATP E1604 " pdb=" C6 ATP E1604 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.87e+01 bond pdb=" C ILE E1136 " pdb=" N PRO E1137 " ideal model delta sigma weight residual 1.336 1.403 -0.067 1.20e-02 6.94e+03 3.09e+01 bond pdb=" C4 ATP E1604 " pdb=" N9 ATP E1604 " ideal model delta sigma weight residual 1.374 1.325 0.049 1.00e-02 1.00e+04 2.42e+01 bond pdb=" C5 ATP E1604 " pdb=" N7 ATP E1604 " ideal model delta sigma weight residual 1.387 1.339 0.048 1.00e-02 1.00e+04 2.31e+01 ... (remaining 21606 not shown) Histogram of bond angle deviations from ideal: 97.62 - 105.32: 388 105.32 - 113.03: 12143 113.03 - 120.73: 9921 120.73 - 128.43: 6695 128.43 - 136.13: 218 Bond angle restraints: 29365 Sorted by residual: angle pdb=" PA ATP E1604 " pdb=" O3A ATP E1604 " pdb=" PB ATP E1604 " ideal model delta sigma weight residual 136.83 117.99 18.84 1.00e+00 1.00e+00 3.55e+02 angle pdb=" PB ATP E1604 " pdb=" O3B ATP E1604 " pdb=" PG ATP E1604 " ideal model delta sigma weight residual 139.87 125.45 14.42 1.00e+00 1.00e+00 2.08e+02 angle pdb=" C5 ATP E1604 " pdb=" C4 ATP E1604 " pdb=" N3 ATP E1604 " ideal model delta sigma weight residual 126.80 119.32 7.48 1.00e+00 1.00e+00 5.59e+01 angle pdb=" N3 ATP E1604 " pdb=" C4 ATP E1604 " pdb=" N9 ATP E1604 " ideal model delta sigma weight residual 127.04 134.77 -7.73 1.15e+00 7.59e-01 4.54e+01 angle pdb=" C ASN E 263 " pdb=" N TYR E 264 " pdb=" CA TYR E 264 " ideal model delta sigma weight residual 121.54 131.73 -10.19 1.91e+00 2.74e-01 2.84e+01 ... (remaining 29360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.38: 11939 26.38 - 52.75: 757 52.75 - 79.13: 111 79.13 - 105.50: 6 105.50 - 131.88: 1 Dihedral angle restraints: 12814 sinusoidal: 5011 harmonic: 7803 Sorted by residual: dihedral pdb=" CA ILE E 61 " pdb=" C ILE E 61 " pdb=" N HIS E 62 " pdb=" CA HIS E 62 " ideal model delta harmonic sigma weight residual 180.00 141.72 38.28 0 5.00e+00 4.00e-02 5.86e+01 dihedral pdb=" CB CYS B 110 " pdb=" SG CYS B 110 " pdb=" SG CYS B 142 " pdb=" CB CYS B 142 " ideal model delta sinusoidal sigma weight residual 93.00 29.23 63.77 1 1.00e+01 1.00e-02 5.36e+01 dihedral pdb=" CB CYS C 110 " pdb=" SG CYS C 110 " pdb=" SG CYS C 142 " pdb=" CB CYS C 142 " ideal model delta sinusoidal sigma weight residual 93.00 29.25 63.75 1 1.00e+01 1.00e-02 5.35e+01 ... (remaining 12811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2639 0.062 - 0.124: 717 0.124 - 0.186: 97 0.186 - 0.249: 18 0.249 - 0.311: 3 Chirality restraints: 3474 Sorted by residual: chirality pdb=" CB ILE E 712 " pdb=" CA ILE E 712 " pdb=" CG1 ILE E 712 " pdb=" CG2 ILE E 712 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CB ILE E 704 " pdb=" CA ILE E 704 " pdb=" CG1 ILE E 704 " pdb=" CG2 ILE E 704 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB VAL E1396 " pdb=" CA VAL E1396 " pdb=" CG1 VAL E1396 " pdb=" CG2 VAL E1396 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 3471 not shown) Planarity restraints: 3650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR E 264 " -0.020 2.00e-02 2.50e+03 3.94e-02 1.56e+01 pdb=" C TYR E 264 " 0.068 2.00e-02 2.50e+03 pdb=" O TYR E 264 " -0.025 2.00e-02 2.50e+03 pdb=" N GLN E 265 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 261 " -0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C LEU E 261 " 0.061 2.00e-02 2.50e+03 pdb=" O LEU E 261 " -0.023 2.00e-02 2.50e+03 pdb=" N THR E 262 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 422 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.58e+00 pdb=" C VAL E 422 " -0.048 2.00e-02 2.50e+03 pdb=" O VAL E 422 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA E 423 " 0.016 2.00e-02 2.50e+03 ... (remaining 3647 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 342 2.64 - 3.20: 19222 3.20 - 3.77: 35768 3.77 - 4.33: 45783 4.33 - 4.90: 73806 Nonbonded interactions: 174921 Sorted by model distance: nonbonded pdb=" OE1 GLN E 775 " pdb="MG MG E1602 " model vdw 2.073 2.170 nonbonded pdb="MG MG E1602 " pdb=" O3A ATP E1604 " model vdw 2.085 2.170 nonbonded pdb=" OG SER E 721 " pdb="MG MG E1602 " model vdw 2.088 2.170 nonbonded pdb=" O1B ADP E1601 " pdb="MG MG E1603 " model vdw 2.118 2.170 nonbonded pdb=" NE2 GLN E 775 " pdb="MG MG E1602 " model vdw 2.169 2.250 ... (remaining 174916 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.150 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 55.900 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.110 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 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 : 0.005 0.077 21611 Z= 0.352 Angle : 0.960 18.839 29365 Z= 0.544 Chirality : 0.056 0.311 3474 Planarity : 0.007 0.069 3650 Dihedral : 16.761 131.879 7732 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 6.47 % Allowed : 8.33 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.30 (0.13), residues: 2663 helix: -2.12 (0.10), residues: 1327 sheet: -2.27 (0.26), residues: 274 loop : -2.02 (0.17), residues: 1062 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 532 time to evaluate : 2.427 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 outliers start: 149 outliers final: 35 residues processed: 625 average time/residue: 0.3336 time to fit residues: 320.8853 Evaluate side-chains 360 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 325 time to evaluate : 2.371 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.1973 time to fit residues: 16.0557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 4.9990 chunk 203 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 210 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 chunk 156 optimal weight: 0.9990 chunk 243 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 HIS B 279 GLN C 52 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 HIS C 277 HIS C 278 HIS D 48 ASN D 52 GLN D 153 ASN D 277 HIS E 106 HIS E 167 GLN E 407 ASN E 438 ASN E 715 GLN E 836 GLN E 923 GLN ** E 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1308 GLN E1348 GLN E1364 HIS E1427 GLN E1459 GLN E1486 GLN ** E1488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21611 Z= 0.230 Angle : 0.644 11.334 29365 Z= 0.335 Chirality : 0.043 0.210 3474 Planarity : 0.005 0.059 3650 Dihedral : 6.101 105.396 2880 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.86 % Allowed : 17.53 % Favored : 79.60 % 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: -1.65 (0.15), residues: 2663 helix: -0.50 (0.13), residues: 1356 sheet: -1.49 (0.31), residues: 242 loop : -1.65 (0.18), residues: 1065 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 354 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 35 residues processed: 398 average time/residue: 0.3099 time to fit residues: 196.9351 Evaluate side-chains 329 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 294 time to evaluate : 2.543 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.2092 time to fit residues: 17.0655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 135 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 243 optimal weight: 0.0000 chunk 263 optimal weight: 3.9990 chunk 217 optimal weight: 0.9980 chunk 241 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 195 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN C 160 ASN C 173 GLN C 335 ASN E 327 HIS E 494 ASN ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 889 HIS ** E 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21611 Z= 0.225 Angle : 0.627 11.891 29365 Z= 0.319 Chirality : 0.043 0.175 3474 Planarity : 0.004 0.064 3650 Dihedral : 5.696 95.732 2880 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.30 % Allowed : 20.40 % Favored : 77.30 % 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: -1.00 (0.16), residues: 2663 helix: 0.12 (0.14), residues: 1349 sheet: -1.00 (0.31), residues: 233 loop : -1.53 (0.18), residues: 1081 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 330 time to evaluate : 2.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 27 residues processed: 370 average time/residue: 0.3251 time to fit residues: 191.8483 Evaluate side-chains 320 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 293 time to evaluate : 2.407 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1996 time to fit residues: 13.3062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 240 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 126 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 116 optimal weight: 0.3980 chunk 163 optimal weight: 1.9990 chunk 244 optimal weight: 7.9990 chunk 259 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 231 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 242 ASN ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN ** E 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 HIS ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1197 GLN ** E1488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21611 Z= 0.225 Angle : 0.617 11.762 29365 Z= 0.313 Chirality : 0.042 0.182 3474 Planarity : 0.004 0.062 3650 Dihedral : 5.564 109.646 2880 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.39 % Allowed : 22.14 % Favored : 75.48 % 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: -0.69 (0.16), residues: 2663 helix: 0.40 (0.14), residues: 1343 sheet: -0.82 (0.32), residues: 233 loop : -1.41 (0.19), residues: 1087 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 326 time to evaluate : 2.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 25 residues processed: 360 average time/residue: 0.3134 time to fit residues: 180.8013 Evaluate side-chains 312 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 287 time to evaluate : 2.451 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1983 time to fit residues: 12.5773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 215 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 192 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 221 optimal weight: 2.9990 chunk 179 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 232 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 278 HIS B 70 HIS ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN D 46 HIS D 153 ASN ** E 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 896 HIS E 923 GLN ** E 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1316 HIS ** E1488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 21611 Z= 0.415 Angle : 0.735 11.620 29365 Z= 0.378 Chirality : 0.045 0.196 3474 Planarity : 0.004 0.063 3650 Dihedral : 5.944 125.259 2880 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.78 % Allowed : 24.48 % Favored : 72.74 % 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: -0.64 (0.16), residues: 2663 helix: 0.35 (0.14), residues: 1301 sheet: -0.94 (0.31), residues: 231 loop : -1.14 (0.19), residues: 1131 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 285 time to evaluate : 2.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 28 residues processed: 337 average time/residue: 0.3142 time to fit residues: 169.3786 Evaluate side-chains 283 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 255 time to evaluate : 2.184 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1980 time to fit residues: 13.6182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 87 optimal weight: 0.5980 chunk 233 optimal weight: 0.9980 chunk 51 optimal weight: 0.0270 chunk 152 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 259 optimal weight: 4.9990 chunk 215 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN D 153 ASN ** E 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1521 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21611 Z= 0.174 Angle : 0.641 12.481 29365 Z= 0.315 Chirality : 0.043 0.218 3474 Planarity : 0.004 0.069 3650 Dihedral : 5.555 116.858 2880 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.61 % Allowed : 25.61 % Favored : 72.79 % 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: -0.18 (0.17), residues: 2663 helix: 0.73 (0.15), residues: 1262 sheet: -0.73 (0.32), residues: 249 loop : -0.86 (0.19), residues: 1152 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 329 time to evaluate : 2.446 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 outliers start: 37 outliers final: 12 residues processed: 355 average time/residue: 0.3126 time to fit residues: 178.2605 Evaluate side-chains 303 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 291 time to evaluate : 2.366 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2031 time to fit residues: 7.8129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 249 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 218 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 258 optimal weight: 5.9990 chunk 161 optimal weight: 8.9990 chunk 157 optimal weight: 0.9980 chunk 119 optimal weight: 0.0970 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN D 97 HIS D 153 ASN ** E 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21611 Z= 0.202 Angle : 0.652 12.349 29365 Z= 0.321 Chirality : 0.043 0.257 3474 Planarity : 0.004 0.066 3650 Dihedral : 5.484 118.887 2880 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.56 % Allowed : 26.09 % Favored : 72.35 % 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: -0.07 (0.17), residues: 2663 helix: 0.81 (0.15), residues: 1257 sheet: -0.65 (0.32), residues: 249 loop : -0.79 (0.19), residues: 1157 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 306 time to evaluate : 2.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 13 residues processed: 331 average time/residue: 0.3154 time to fit residues: 166.3484 Evaluate side-chains 295 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 282 time to evaluate : 2.245 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1925 time to fit residues: 7.6783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 159 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 154 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 203 optimal weight: 1.9990 chunk 234 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN ** E 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 HIS ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 923 GLN ** E 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 21611 Z= 0.309 Angle : 0.701 12.125 29365 Z= 0.351 Chirality : 0.044 0.280 3474 Planarity : 0.004 0.063 3650 Dihedral : 5.619 122.366 2880 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.13 % Allowed : 27.17 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.04 (0.17), residues: 2663 helix: 0.72 (0.14), residues: 1264 sheet: -0.55 (0.31), residues: 253 loop : -0.66 (0.20), residues: 1146 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 284 time to evaluate : 2.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 301 average time/residue: 0.3238 time to fit residues: 156.3349 Evaluate side-chains 280 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 270 time to evaluate : 2.478 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2116 time to fit residues: 7.4144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 247 optimal weight: 20.0000 chunk 225 optimal weight: 0.7980 chunk 240 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 189 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 217 optimal weight: 9.9990 chunk 227 optimal weight: 0.0020 chunk 239 optimal weight: 2.9990 chunk 158 optimal weight: 0.6980 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN ** E 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21611 Z= 0.200 Angle : 0.668 12.687 29365 Z= 0.327 Chirality : 0.044 0.363 3474 Planarity : 0.004 0.065 3650 Dihedral : 5.502 119.576 2880 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.48 % Allowed : 27.65 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.03 (0.17), residues: 2663 helix: 0.85 (0.15), residues: 1258 sheet: -0.65 (0.31), residues: 269 loop : -0.66 (0.20), residues: 1136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 312 time to evaluate : 2.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 320 average time/residue: 0.3176 time to fit residues: 163.3858 Evaluate side-chains 295 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 292 time to evaluate : 2.366 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2183 time to fit residues: 4.4366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 254 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 176 optimal weight: 2.9990 chunk 266 optimal weight: 0.0770 chunk 245 optimal weight: 7.9990 chunk 212 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 164 optimal weight: 0.7980 chunk 130 optimal weight: 0.2980 chunk 168 optimal weight: 2.9990 overall best weight: 1.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN ** E 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 563 HIS ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21611 Z= 0.221 Angle : 0.689 12.489 29365 Z= 0.337 Chirality : 0.044 0.328 3474 Planarity : 0.004 0.065 3650 Dihedral : 5.505 120.530 2880 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.48 % Allowed : 28.34 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.09 (0.17), residues: 2663 helix: 0.88 (0.15), residues: 1257 sheet: -0.51 (0.32), residues: 249 loop : -0.65 (0.19), residues: 1157 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5326 Ramachandran restraints generated. 2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 298 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 305 average time/residue: 0.3169 time to fit residues: 156.3082 Evaluate side-chains 293 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 286 time to evaluate : 2.556 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2280 time to fit residues: 6.4088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 196 optimal weight: 0.3980 chunk 31 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 212 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 218 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 HIS D 153 ASN E 20 GLN E 60 HIS ** E 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.062499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.051935 restraints weight = 93365.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.053555 restraints weight = 47206.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.054614 restraints weight = 29646.815| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 21611 Z= 0.357 Angle : 0.749 12.292 29365 Z= 0.375 Chirality : 0.046 0.282 3474 Planarity : 0.004 0.062 3650 Dihedral : 5.754 123.496 2880 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.91 % Allowed : 28.17 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.06 (0.16), residues: 2663 helix: 0.68 (0.14), residues: 1270 sheet: -0.57 (0.33), residues: 241 loop : -0.64 (0.19), residues: 1152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4230.17 seconds wall clock time: 78 minutes 20.10 seconds (4700.10 seconds total)