Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 9 04:17:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5y_24843/05_2023/7s5y_24843_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5y_24843/05_2023/7s5y_24843.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/7s5y_24843/05_2023/7s5y_24843.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5y_24843/05_2023/7s5y_24843.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5y_24843/05_2023/7s5y_24843_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s5y_24843/05_2023/7s5y_24843_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.075 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 119 5.16 5 C 13639 2.51 5 N 3594 2.21 5 O 3747 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 GLU 51": "OE1" <-> "OE2" Residue "A ASP 65": "OD1" <-> "OD2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A ASP 237": "OD1" <-> "OD2" Residue "A ASP 280": "OD1" <-> "OD2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A ASP 323": "OD1" <-> "OD2" Residue "A TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 51": "OE1" <-> "OE2" Residue "B ASP 65": "OD1" <-> "OD2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B ASP 237": "OD1" <-> "OD2" Residue "B ASP 280": "OD1" <-> "OD2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "B TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 51": "OE1" <-> "OE2" Residue "C ASP 65": "OD1" <-> "OD2" Residue "C GLU 141": "OE1" <-> "OE2" Residue "C PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 195": "NH1" <-> "NH2" Residue "C ASP 237": "OD1" <-> "OD2" Residue "C ASP 280": "OD1" <-> "OD2" Residue "C GLU 282": "OE1" <-> "OE2" Residue "C ASP 323": "OD1" <-> "OD2" Residue "C TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 32": "NH1" <-> "NH2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 51": "OE1" <-> "OE2" Residue "D ASP 65": "OD1" <-> "OD2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 195": "NH1" <-> "NH2" Residue "D ASP 237": "OD1" <-> "OD2" Residue "D ASP 280": "OD1" <-> "OD2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "D ASP 323": "OD1" <-> "OD2" Residue "D TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 10": "OE1" <-> "OE2" Residue "E ARG 17": "NH1" <-> "NH2" Residue "E ASP 30": "OD1" <-> "OD2" Residue "E ARG 75": "NH1" <-> "NH2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E ASP 97": "OD1" <-> "OD2" Residue "E TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 269": "OE1" <-> "OE2" Residue "E PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 307": "NH1" <-> "NH2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 425": "OD1" <-> "OD2" Residue "E TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 524": "OE1" <-> "OE2" Residue "E ARG 528": "NH1" <-> "NH2" Residue "E PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 613": "OE1" <-> "OE2" Residue "E TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 703": "NH1" <-> "NH2" Residue "E PHE 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 842": "NH1" <-> "NH2" Residue "E ASP 854": "OD1" <-> "OD2" Residue "E ASP 855": "OD1" <-> "OD2" Residue "E ASP 866": "OD1" <-> "OD2" Residue "E ASP 916": "OD1" <-> "OD2" Residue "E PHE 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 938": "OE1" <-> "OE2" Residue "E GLU 940": "OE1" <-> "OE2" Residue "E TYR 1004": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1031": "OD1" <-> "OD2" Residue "E TYR 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1124": "NH1" <-> "NH2" Residue "E ASP 1128": "OD1" <-> "OD2" Residue "E GLU 1141": "OE1" <-> "OE2" Residue "E ASP 1194": "OD1" <-> "OD2" Residue "E PHE 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1222": "NH1" <-> "NH2" Residue "E GLU 1229": "OE1" <-> "OE2" Residue "E ASP 1232": "OD1" <-> "OD2" Residue "E TYR 1294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1314": "NH1" <-> "NH2" Residue "E TYR 1326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1327": "OE1" <-> "OE2" Residue "E TYR 1354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1406": "OD1" <-> "OD2" Residue "E ARG 1419": "NH1" <-> "NH2" Residue "E ARG 1437": "NH1" <-> "NH2" Residue "E ASP 1441": "OD1" <-> "OD2" 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 1530": "OD1" <-> "OD2" Residue "E PHE 1560": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 21106 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: 11030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1406, 11030 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'peptide': 1402, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 42, 'TRANS': 1359, 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: 103 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 64 Time building chain proxies: 11.18, per 1000 atoms: 0.53 Number of scatterers: 21106 At special positions: 0 Unit cell: (143, 145.6, 136.5, 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 119 16.00 P 5 15.00 Mg 2 11.99 O 3747 8.00 N 3594 7.00 C 13639 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS E 27 " 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: 9.21 Conformation dependent library (CDL) restraints added in 3.3 seconds 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5068 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 78 helices and 15 sheets defined 43.3% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.90 Creating SS restraints... Processing helix chain 'A' and resid 60 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 144 through 171 Processing helix chain 'A' and resid 174 through 180 Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'B' and resid 60 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 144 through 171 Processing helix chain 'B' and resid 174 through 180 Processing helix chain 'B' and resid 272 through 274 No H-bonds generated for 'chain 'B' and resid 272 through 274' Processing helix chain 'C' and resid 60 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 144 through 171 Processing helix chain 'C' and resid 174 through 180 Processing helix chain 'C' and resid 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 through 274' Processing helix chain 'D' and resid 60 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 144 through 171 Processing helix chain 'D' and resid 174 through 180 Processing helix chain 'D' and resid 272 through 274 No H-bonds generated for 'chain 'D' and resid 272 through 274' Processing helix chain 'E' and resid 22 through 24 No H-bonds generated for 'chain 'E' and resid 22 through 24' Processing helix chain 'E' and resid 26 through 50 removed outlier: 4.238A pdb=" N VAL E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 4.833A 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 75 through 93 removed outlier: 3.812A pdb=" N CYS E 88 " --> pdb=" O PHE E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 138 through 160 removed outlier: 5.941A pdb=" N PHE E 148 " --> pdb=" O THR E 145 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL E 156 " --> pdb=" O ILE E 153 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP E 160 " --> pdb=" O LYS E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 193 removed outlier: 3.656A pdb=" N LEU E 175 " --> pdb=" O CYS E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 229 Processing helix chain 'E' and resid 239 through 243 removed outlier: 3.975A pdb=" N LYS E 243 " --> pdb=" O LYS E 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 239 through 243' Processing helix chain 'E' and resid 260 through 273 removed outlier: 3.711A pdb=" N ALA E 273 " --> pdb=" O GLU E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 312 removed outlier: 6.294A pdb=" N ARG E 298 " --> pdb=" O HIS E 294 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASP E 311 " --> pdb=" O ARG E 307 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU E 312 " --> pdb=" O ILE E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 329 Proline residue: E 318 - end of helix removed outlier: 3.612A pdb=" N PHE E 322 " --> pdb=" O LEU E 319 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL E 325 " --> pdb=" O PHE E 322 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP E 326 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU E 328 " --> pdb=" O VAL E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 354 Processing helix chain 'E' and resid 356 through 400 Processing helix chain 'E' and resid 406 through 409 No H-bonds generated for 'chain 'E' and resid 406 through 409' Processing helix chain 'E' and resid 415 through 423 Processing helix chain 'E' and resid 427 through 460 Proline residue: E 437 - end of helix Proline residue: E 443 - end of helix removed outlier: 3.654A pdb=" N VAL E 448 " --> pdb=" O VAL E 444 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N VAL E 459 " --> pdb=" O TYR E 455 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N SER E 460 " --> pdb=" O ILE E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 466 through 505 removed outlier: 5.963A pdb=" N ALA E 472 " --> pdb=" O ILE E 468 " (cutoff:3.500A) Proline residue: E 473 - end of helix Processing helix chain 'E' and resid 507 through 511 Processing helix chain 'E' and resid 516 through 564 Proline residue: E 552 - end of helix removed outlier: 3.519A pdb=" N VAL E 564 " --> pdb=" O PHE E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 599 Proline residue: E 590 - end of helix removed outlier: 4.478A pdb=" N LEU E 593 " --> pdb=" O THR E 589 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER E 595 " --> pdb=" O LEU E 591 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER E 596 " --> pdb=" O PHE E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 602 through 615 Processing helix chain 'E' and resid 720 through 727 removed outlier: 4.156A 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 813 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 841 Processing helix chain 'E' and resid 862 through 870 Processing helix chain 'E' and resid 891 through 895 Proline residue: E 895 - end of helix Processing helix chain 'E' and resid 914 through 919 Processing helix chain 'E' and resid 924 through 931 Processing helix chain 'E' and resid 1000 through 1008 Processing helix chain 'E' and resid 1010 through 1038 Processing helix chain 'E' and resid 1063 through 1096 Processing helix chain 'E' and resid 1101 through 1105 Processing helix chain 'E' and resid 1110 through 1115 Processing helix chain 'E' and resid 1118 through 1133 removed outlier: 4.160A pdb=" N ASP E1128 " --> pdb=" O ARG E1124 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N CYS E1129 " --> pdb=" O PHE E1125 " (cutoff:3.500A) Processing helix chain 'E' and resid 1136 through 1160 removed outlier: 3.538A pdb=" N VAL E1160 " --> pdb=" O VAL E1156 " (cutoff:3.500A) Processing helix chain 'E' and resid 1162 through 1169 Processing helix chain 'E' and resid 1171 through 1196 removed outlier: 4.338A pdb=" N VAL E1184 " --> pdb=" O LYS E1180 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ALA E1185 " --> pdb=" O TYR E1181 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLN E1191 " --> pdb=" O ARG E1187 " (cutoff:3.500A) Processing helix chain 'E' and resid 1200 through 1206 Processing helix chain 'E' and resid 1211 through 1217 Processing helix chain 'E' and resid 1220 through 1272 Processing helix chain 'E' and resid 1280 through 1319 removed outlier: 5.926A pdb=" N ASN E1296 " --> pdb=" O SER E1292 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N TRP E1297 " --> pdb=" O ASN E1293 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA E1311 " --> pdb=" O LEU E1307 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL E1312 " --> pdb=" O GLN E1308 " (cutoff:3.500A) Processing helix chain 'E' and resid 1385 through 1392 removed outlier: 3.848A pdb=" N LEU E1390 " --> pdb=" O SER E1386 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE E1392 " --> pdb=" O PHE E1388 " (cutoff:3.500A) Processing helix chain 'E' and resid 1415 through 1420 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 1495 Processing helix chain 'E' and resid 1508 through 1510 No H-bonds generated for 'chain 'E' and resid 1508 through 1510' Processing helix chain 'E' and resid 1514 through 1527 Processing helix chain 'E' and resid 1563 through 1568 Processing helix chain 'E' and resid 1573 through 1581 Processing sheet with id= A, first strand: chain 'A' and resid 309 through 311 removed outlier: 6.707A pdb=" N ALA A 187 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 234 through 238 removed outlier: 4.364A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 319 through 322 Processing sheet with id= D, first strand: chain 'B' and resid 309 through 311 removed outlier: 6.707A pdb=" N ALA B 187 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 234 through 238 removed outlier: 4.364A pdb=" N MET B 217 " --> pdb=" O ILE B 238 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 319 through 322 Processing sheet with id= G, first strand: chain 'C' and resid 309 through 311 removed outlier: 6.708A pdb=" N ALA C 187 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 234 through 238 removed outlier: 4.363A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 319 through 322 Processing sheet with id= J, first strand: chain 'D' and resid 309 through 311 removed outlier: 6.707A pdb=" N ALA D 187 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 234 through 238 removed outlier: 4.364A pdb=" N MET D 217 " --> pdb=" O ILE D 238 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 319 through 322 Processing sheet with id= M, first strand: chain 'E' and resid 907 through 912 removed outlier: 3.606A pdb=" N THR E 907 " --> pdb=" O LYS E 904 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ALA E 902 " --> pdb=" O GLN E 909 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLU E 911 " --> pdb=" O ILE E 900 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE E 900 " --> pdb=" O GLU E 911 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL E 887 " --> pdb=" O LEU E 853 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA E 771 " --> pdb=" O PHE E 852 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 1345 through 1348 Processing sheet with id= O, first strand: chain 'E' and resid 1533 through 1536 removed outlier: 6.926A pdb=" N LEU E1548 " --> pdb=" O GLY E1376 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N CYS E1378 " --> pdb=" O LEU E1548 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE E1550 " --> pdb=" O CYS E1378 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP E1561 " --> pdb=" O VAL E1549 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU E1559 " --> pdb=" O VAL E1551 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS E1553 " --> pdb=" O ILE E1557 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ILE E1557 " --> pdb=" O LYS E1553 " (cutoff:3.500A) 973 hydrogen bonds defined for protein. 2706 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: 6.99 Time building geometry restraints manager: 9.78 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: 6091 1.34 - 1.46: 5348 1.46 - 1.58: 9925 1.58 - 1.71: 13 1.71 - 1.83: 190 Bond restraints: 21567 Sorted by residual: bond pdb=" C4 ATP E1604 " pdb=" C5 ATP E1604 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.17e+01 bond pdb=" C4 ATP E1604 " pdb=" N9 ATP E1604 " ideal model delta sigma weight residual 1.374 1.319 0.055 1.00e-02 1.00e+04 3.02e+01 bond pdb=" C5 ATP E1604 " pdb=" N7 ATP E1604 " ideal model delta sigma weight residual 1.387 1.333 0.054 1.00e-02 1.00e+04 2.89e+01 bond pdb=" C5 ATP E1604 " pdb=" C6 ATP E1604 " ideal model delta sigma weight residual 1.409 1.462 -0.053 1.00e-02 1.00e+04 2.86e+01 bond pdb=" C ILE E1136 " pdb=" N PRO E1137 " ideal model delta sigma weight residual 1.334 1.453 -0.119 2.34e-02 1.83e+03 2.59e+01 ... (remaining 21562 not shown) Histogram of bond angle deviations from ideal: 97.24 - 105.61: 477 105.61 - 113.97: 12367 113.97 - 122.34: 12754 122.34 - 130.70: 3526 130.70 - 139.07: 186 Bond angle restraints: 29310 Sorted by residual: angle pdb=" PB ATP E1604 " pdb=" O3B ATP E1604 " pdb=" PG ATP E1604 " ideal model delta sigma weight residual 139.87 122.05 17.82 1.00e+00 1.00e+00 3.18e+02 angle pdb=" PA ATP E1604 " pdb=" O3A ATP E1604 " pdb=" PB ATP E1604 " ideal model delta sigma weight residual 136.83 124.59 12.24 1.00e+00 1.00e+00 1.50e+02 angle pdb=" C ALA E 310 " pdb=" N ASP E 311 " pdb=" CA ASP E 311 " ideal model delta sigma weight residual 121.54 135.64 -14.10 1.91e+00 2.74e-01 5.45e+01 angle pdb=" C5 ATP E1604 " pdb=" C4 ATP E1604 " pdb=" N3 ATP E1604 " ideal model delta sigma weight residual 126.80 119.74 7.06 1.00e+00 1.00e+00 4.98e+01 angle pdb=" N3 ATP E1604 " pdb=" C4 ATP E1604 " pdb=" N9 ATP E1604 " ideal model delta sigma weight residual 127.04 134.86 -7.82 1.15e+00 7.59e-01 4.64e+01 ... (remaining 29305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.98: 11719 24.98 - 49.96: 897 49.96 - 74.93: 156 74.93 - 99.91: 5 99.91 - 124.89: 1 Dihedral angle restraints: 12778 sinusoidal: 4978 harmonic: 7800 Sorted by residual: dihedral pdb=" CA GLY E 343 " pdb=" C GLY E 343 " pdb=" N VAL E 344 " pdb=" CA VAL E 344 " ideal model delta harmonic sigma weight residual -180.00 -118.48 -61.52 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" CA PHE E1182 " pdb=" C PHE E1182 " pdb=" N ARG E1183 " pdb=" CA ARG E1183 " ideal model delta harmonic sigma weight residual -180.00 -129.32 -50.68 0 5.00e+00 4.00e-02 1.03e+02 dihedral pdb=" CA LEU E 137 " pdb=" C LEU E 137 " pdb=" N ILE E 138 " pdb=" CA ILE E 138 " ideal model delta harmonic sigma weight residual -180.00 -136.18 -43.82 0 5.00e+00 4.00e-02 7.68e+01 ... (remaining 12775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 3193 0.141 - 0.282: 244 0.282 - 0.422: 23 0.422 - 0.563: 5 0.563 - 0.704: 4 Chirality restraints: 3469 Sorted by residual: chirality pdb=" CB VAL D 337 " pdb=" CA VAL D 337 " pdb=" CG1 VAL D 337 " pdb=" CG2 VAL D 337 " both_signs ideal model delta sigma weight residual False -2.63 -1.93 -0.70 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" CB VAL C 337 " pdb=" CA VAL C 337 " pdb=" CG1 VAL C 337 " pdb=" CG2 VAL C 337 " both_signs ideal model delta sigma weight residual False -2.63 -1.93 -0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CB VAL A 337 " pdb=" CA VAL A 337 " pdb=" CG1 VAL A 337 " pdb=" CG2 VAL A 337 " both_signs ideal model delta sigma weight residual False -2.63 -1.93 -0.70 2.00e-01 2.50e+01 1.23e+01 ... (remaining 3466 not shown) Planarity restraints: 3646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E1180 " 0.023 2.00e-02 2.50e+03 4.64e-02 2.16e+01 pdb=" C LYS E1180 " -0.080 2.00e-02 2.50e+03 pdb=" O LYS E1180 " 0.030 2.00e-02 2.50e+03 pdb=" N TYR E1181 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 149 " -0.023 2.00e-02 2.50e+03 4.62e-02 2.14e+01 pdb=" C ILE E 149 " 0.080 2.00e-02 2.50e+03 pdb=" O ILE E 149 " -0.030 2.00e-02 2.50e+03 pdb=" N THR E 150 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP E 144 " -0.022 2.00e-02 2.50e+03 4.49e-02 2.01e+01 pdb=" C TRP E 144 " 0.078 2.00e-02 2.50e+03 pdb=" O TRP E 144 " -0.029 2.00e-02 2.50e+03 pdb=" N THR E 145 " -0.026 2.00e-02 2.50e+03 ... (remaining 3643 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 951 2.71 - 3.26: 19201 3.26 - 3.80: 36524 3.80 - 4.35: 43921 4.35 - 4.90: 71303 Nonbonded interactions: 171900 Sorted by model distance: nonbonded pdb=" O1B ADP E1601 " pdb="MG MG E1603 " model vdw 2.160 2.170 nonbonded pdb=" OE1 GLN E 775 " pdb="MG MG E1602 " model vdw 2.166 2.170 nonbonded pdb="MG MG E1602 " pdb=" O2B ATP E1604 " model vdw 2.166 2.170 nonbonded pdb=" OG SER E1386 " pdb="MG MG E1603 " model vdw 2.172 2.170 nonbonded pdb="MG MG E1602 " pdb=" O3B ATP E1604 " model vdw 2.175 2.170 ... (remaining 171895 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: 5.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 12.340 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 54.330 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.090 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 0.119 21567 Z= 0.624 Angle : 1.484 19.636 29310 Z= 0.813 Chirality : 0.083 0.704 3469 Planarity : 0.012 0.095 3646 Dihedral : 17.609 124.888 7707 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.26 % Favored : 94.67 % Rotamer Outliers : 7.41 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.62 % 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: -5.12 (0.11), residues: 2662 helix: -4.11 (0.07), residues: 1321 sheet: -1.57 (0.30), residues: 271 loop : -2.65 (0.15), residues: 1070 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 552 time to evaluate : 2.641 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 outliers start: 170 outliers final: 39 residues processed: 669 average time/residue: 0.3253 time to fit residues: 338.2460 Evaluate side-chains 366 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 327 time to evaluate : 2.964 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.2402 time to fit residues: 21.1641 ------------------------------------------------------------------------------- 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: 3.9990 chunk 112 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 137 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 chunk 210 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 243 optimal weight: 50.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 153 ASN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS B 48 ASN B 313 GLN C 46 HIS ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN ** D 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 ASN ** E 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN E 375 GLN E 475 GLN E 486 GLN E 609 GLN ** E 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 787 ASN ** E 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 867 HIS E1301 ASN E1402 HIS E1486 GLN E1518 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 21567 Z= 0.272 Angle : 0.740 11.538 29310 Z= 0.383 Chirality : 0.046 0.247 3469 Planarity : 0.006 0.057 3646 Dihedral : 6.629 98.531 2879 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.36 % Rotamer Outliers : 3.18 % 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: -2.44 (0.14), residues: 2662 helix: -1.51 (0.12), residues: 1314 sheet: -0.51 (0.32), residues: 255 loop : -1.88 (0.17), residues: 1093 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 368 time to evaluate : 2.711 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 outliers start: 73 outliers final: 37 residues processed: 418 average time/residue: 0.3318 time to fit residues: 216.9885 Evaluate side-chains 334 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 297 time to evaluate : 2.546 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.2195 time to fit residues: 18.2908 ------------------------------------------------------------------------------- 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: 0.8980 chunk 75 optimal weight: 0.0060 chunk 202 optimal weight: 0.9980 chunk 165 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 243 optimal weight: 20.0000 chunk 263 optimal weight: 1.9990 chunk 217 optimal weight: 8.9990 chunk 241 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 195 optimal weight: 7.9990 overall best weight: 1.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 57 GLN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 57 GLN C 128 GLN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN ** D 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 HIS E 220 GLN E 428 GLN E 681 GLN ** E 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1197 GLN E1427 GLN E1439 ASN E1521 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 21567 Z= 0.262 Angle : 0.712 10.882 29310 Z= 0.362 Chirality : 0.045 0.247 3469 Planarity : 0.004 0.038 3646 Dihedral : 6.012 85.749 2879 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.40 % Favored : 95.57 % Rotamer Outliers : 2.01 % 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: -1.42 (0.15), residues: 2662 helix: -0.46 (0.14), residues: 1344 sheet: -0.30 (0.32), residues: 267 loop : -1.64 (0.18), residues: 1051 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 317 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 25 residues processed: 344 average time/residue: 0.3191 time to fit residues: 175.1040 Evaluate side-chains 308 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 283 time to evaluate : 2.424 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1889 time to fit residues: 12.2720 ------------------------------------------------------------------------------- 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: 0.7980 chunk 183 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 chunk 26 optimal weight: 0.0870 chunk 116 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 244 optimal weight: 0.3980 chunk 259 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 231 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN B 70 HIS ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN E 24 ASN ** E 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 817 HIS ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1301 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 21567 Z= 0.169 Angle : 0.660 11.810 29310 Z= 0.325 Chirality : 0.043 0.230 3469 Planarity : 0.004 0.032 3646 Dihedral : 5.573 80.675 2879 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.36 % Rotamer Outliers : 2.05 % 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: -0.75 (0.16), residues: 2662 helix: 0.13 (0.14), residues: 1323 sheet: -0.00 (0.34), residues: 256 loop : -1.32 (0.18), residues: 1083 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 335 time to evaluate : 2.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 20 residues processed: 362 average time/residue: 0.3222 time to fit residues: 185.1984 Evaluate side-chains 304 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 284 time to evaluate : 2.544 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2116 time to fit residues: 11.2547 ------------------------------------------------------------------------------- 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: 2.9990 chunk 147 optimal weight: 0.0870 chunk 3 optimal weight: 4.9990 chunk 192 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 221 optimal weight: 0.5980 chunk 179 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 65 optimal weight: 20.0000 overall best weight: 1.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 235 ASN ** E 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 548 ASN E 708 GLN ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1301 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 21567 Z= 0.234 Angle : 0.678 11.745 29310 Z= 0.339 Chirality : 0.044 0.242 3469 Planarity : 0.003 0.029 3646 Dihedral : 5.419 91.053 2879 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 2.62 % 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: -0.43 (0.16), residues: 2662 helix: 0.37 (0.14), residues: 1321 sheet: -0.03 (0.34), residues: 259 loop : -1.09 (0.18), residues: 1082 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 299 time to evaluate : 2.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 34 residues processed: 333 average time/residue: 0.3035 time to fit residues: 162.3157 Evaluate side-chains 315 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 281 time to evaluate : 2.625 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.2061 time to fit residues: 16.6977 ------------------------------------------------------------------------------- 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: 6.9990 chunk 233 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 259 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 21 optimal weight: 0.0050 chunk 85 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 HIS ** E 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 889 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 21567 Z= 0.237 Angle : 0.687 11.868 29310 Z= 0.339 Chirality : 0.044 0.255 3469 Planarity : 0.003 0.028 3646 Dihedral : 5.356 102.796 2879 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer Outliers : 1.79 % 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: -0.20 (0.16), residues: 2662 helix: 0.55 (0.14), residues: 1316 sheet: -0.08 (0.33), residues: 269 loop : -0.91 (0.18), residues: 1077 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 302 time to evaluate : 2.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 17 residues processed: 329 average time/residue: 0.3409 time to fit residues: 180.1414 Evaluate side-chains 297 residues out of total 2323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 280 time to evaluate : 2.728 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2138 time to fit residues: 10.6995 ------------------------------------------------------------------------------- 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: 10.0000 chunk 29 optimal weight: 10.0000 chunk 147 optimal weight: 0.0870 chunk 189 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 258 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 157 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 overall best weight: 2.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 HIS ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 HIS ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 445 GLN E 846 GLN E1308 GLN E1541 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.4805 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: