Starting phenix.real_space_refine on Thu Mar 14 16:41:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eig_28155/03_2024/8eig_28155_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eig_28155/03_2024/8eig_28155.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eig_28155/03_2024/8eig_28155_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eig_28155/03_2024/8eig_28155_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eig_28155/03_2024/8eig_28155_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eig_28155/03_2024/8eig_28155.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eig_28155/03_2024/8eig_28155.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eig_28155/03_2024/8eig_28155_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eig_28155/03_2024/8eig_28155_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 47 5.16 5 C 6032 2.51 5 N 1530 2.21 5 O 1629 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 976": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1425": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9249 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9249 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1147, 9243 Unusual residues: {' MG': 2, 'ATP': 2, 'CLR': 1, 'WJX': 1} Classifications: {'peptide': 1141, 'undetermined': 6} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 30, 'TRANS': 1110, None: 6} Not linked: pdbres="LYS A1429 " pdbres=" MG A1501 " Not linked: pdbres=" MG A1501 " pdbres=" MG A1502 " Not linked: pdbres=" MG A1502 " pdbres="ATP A1503 " Not linked: pdbres="ATP A1503 " pdbres="ATP A1504 " Not linked: pdbres="ATP A1504 " pdbres="CLR A1505 " Not linked: pdbres="CLR A1505 " pdbres="WJX A1506 " Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 1147, 9243 Unusual residues: {' MG': 2, 'ATP': 2, 'CLR': 1, 'WJX': 1} Classifications: {'peptide': 1141, 'undetermined': 6} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 30, 'TRANS': 1110, None: 6} Not linked: pdbres="LYS A1429 " pdbres=" MG A1501 " Not linked: pdbres=" MG A1501 " pdbres=" MG A1502 " Not linked: pdbres=" MG A1502 " pdbres="ATP A1503 " Not linked: pdbres="ATP A1503 " pdbres="ATP A1504 " Not linked: pdbres="ATP A1504 " pdbres="CLR A1505 " Not linked: pdbres="CLR A1505 " pdbres="WJX A1506 " Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 9437 Time building chain proxies: 8.94, per 1000 atoms: 0.97 Number of scatterers: 9249 At special positions: 0 Unit cell: (76.388, 84.5, 140.608, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 47 16.00 P 6 15.00 Mg 2 11.99 F 3 9.00 O 1629 8.00 N 1530 7.00 C 6032 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.43 Conformation dependent library (CDL) restraints added in 3.0 seconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 3 sheets defined 60.0% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.64 Creating SS restraints... Processing helix chain 'A' and resid 5 through 8 No H-bonds generated for 'chain 'A' and resid 5 through 8' Processing helix chain 'A' and resid 11 through 16 removed outlier: 3.663A pdb=" N PHE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 29 Proline residue: A 22 - end of helix removed outlier: 3.517A pdb=" N ARG A 25 " --> pdb=" O PRO A 22 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY A 27 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG A 29 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 60 removed outlier: 4.174A pdb=" N ARG A 59 " --> pdb=" O ARG A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 96 removed outlier: 3.663A pdb=" N CYS A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N TRP A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ARG A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.663A pdb=" N ARG A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR A 109 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 118 No H-bonds generated for 'chain 'A' and resid 115 through 118' Processing helix chain 'A' and resid 121 through 166 removed outlier: 4.207A pdb=" N HIS A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix removed outlier: 3.789A pdb=" N LYS A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 172 No H-bonds generated for 'chain 'A' and resid 169 through 172' Processing helix chain 'A' and resid 178 through 184 removed outlier: 3.556A pdb=" N SER A 182 " --> pdb=" O GLY A 178 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 218 removed outlier: 3.663A pdb=" N VAL A 201 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE A 203 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ALA A 204 " --> pdb=" O VAL A 201 " (cutoff:3.500A) Proline residue: A 205 - end of helix removed outlier: 3.902A pdb=" N ALA A 209 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET A 212 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 215 " --> pdb=" O MET A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 250 removed outlier: 3.846A pdb=" N PHE A 229 " --> pdb=" O CYS A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 267 removed outlier: 3.544A pdb=" N SER A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 278 through 309 removed outlier: 3.754A pdb=" N LEU A 288 " --> pdb=" O MET A 284 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A 309 " --> pdb=" O PHE A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 316 through 328 removed outlier: 3.639A pdb=" N LEU A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 333 through 351 removed outlier: 3.982A pdb=" N VAL A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 376 removed outlier: 3.548A pdb=" N PHE A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN A 376 " --> pdb=" O GLN A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 471 removed outlier: 3.540A pdb=" N LEU A 468 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 507 No H-bonds generated for 'chain 'A' and resid 504 through 507' Processing helix chain 'A' and resid 514 through 521 Processing helix chain 'A' and resid 527 through 532 removed outlier: 3.795A pdb=" N SER A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS A 532 " --> pdb=" O GLU A 528 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 527 through 532' Processing helix chain 'A' and resid 550 through 563 Processing helix chain 'A' and resid 574 through 576 No H-bonds generated for 'chain 'A' and resid 574 through 576' Processing helix chain 'A' and resid 580 through 589 removed outlier: 3.609A pdb=" N GLU A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 611 removed outlier: 3.853A pdb=" N LYS A 611 " --> pdb=" O MET A 607 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 607 through 611' Processing helix chain 'A' and resid 847 through 854 Processing helix chain 'A' and resid 859 through 883 Processing helix chain 'A' and resid 909 through 926 removed outlier: 3.728A pdb=" N SER A 912 " --> pdb=" O SER A 909 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N TYR A 913 " --> pdb=" O THR A 910 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A 914 " --> pdb=" O SER A 911 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ASP A 924 " --> pdb=" O GLY A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 958 removed outlier: 3.757A pdb=" N SER A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 957 " --> pdb=" O LEU A 953 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN A 958 " --> pdb=" O HIS A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 965 Processing helix chain 'A' and resid 971 through 977 removed outlier: 3.680A pdb=" N ARG A 975 " --> pdb=" O GLY A 971 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE A 976 " --> pdb=" O ILE A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 1011 removed outlier: 4.974A pdb=" N LEU A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) Proline residue: A 988 - end of helix removed outlier: 3.599A pdb=" N PHE A 992 " --> pdb=" O PRO A 988 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A1008 " --> pdb=" O ALA A1004 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA A1009 " --> pdb=" O ILE A1005 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A1010 " --> pdb=" O ALA A1006 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU A1011 " --> pdb=" O VAL A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1018 No H-bonds generated for 'chain 'A' and resid 1015 through 1018' Processing helix chain 'A' and resid 1020 through 1060 removed outlier: 3.943A pdb=" N GLN A1035 " --> pdb=" O ALA A1031 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR A1036 " --> pdb=" O TYR A1032 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN A1039 " --> pdb=" O GLN A1035 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG A1048 " --> pdb=" O GLU A1044 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N SER A1049 " --> pdb=" O SER A1045 " (cutoff:3.500A) Proline residue: A1050 - end of helix removed outlier: 3.621A pdb=" N LEU A1059 " --> pdb=" O LEU A1055 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A1060 " --> pdb=" O VAL A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1068 Processing helix chain 'A' and resid 1071 through 1121 removed outlier: 3.524A pdb=" N ASN A1088 " --> pdb=" O LEU A1084 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU A1104 " --> pdb=" O GLN A1100 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A1107 " --> pdb=" O ILE A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1167 removed outlier: 4.519A pdb=" N THR A1142 " --> pdb=" O ASN A1138 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A1143 " --> pdb=" O ILE A1139 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP A1145 " --> pdb=" O SER A1141 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A1151 " --> pdb=" O VAL A1147 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASP A1152 " --> pdb=" O ASN A1148 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A1153 " --> pdb=" O SER A1149 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG A1158 " --> pdb=" O ASP A1154 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER A1159 " --> pdb=" O SER A1155 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A1160 " --> pdb=" O LEU A1156 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE A1166 " --> pdb=" O ARG A1162 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A1167 " --> pdb=" O VAL A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1257 removed outlier: 4.079A pdb=" N LEU A1254 " --> pdb=" O LYS A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1285 removed outlier: 3.510A pdb=" N LYS A1284 " --> pdb=" O GLN A1280 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA A1285 " --> pdb=" O GLN A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1304 Processing helix chain 'A' and resid 1312 through 1322 removed outlier: 4.128A pdb=" N GLU A1321 " --> pdb=" O LYS A1317 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A1322 " --> pdb=" O VAL A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1325 through 1329 Processing helix chain 'A' and resid 1348 through 1362 Processing helix chain 'A' and resid 1378 through 1390 removed outlier: 4.770A pdb=" N ILE A1383 " --> pdb=" O VAL A1379 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE A1384 " --> pdb=" O THR A1380 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG A1385 " --> pdb=" O TYR A1381 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS A1389 " --> pdb=" O ARG A1385 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 624 through 628 removed outlier: 7.019A pdb=" N ILE A 618 " --> pdb=" O TYR A 625 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TYR A 627 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE A 616 " --> pdb=" O TYR A 627 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 615 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ARG A 600 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL A 456 " --> pdb=" O ARG A 600 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU A 602 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N GLY A 458 " --> pdb=" O LEU A 602 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TYR A 569 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N VAL A 603 " --> pdb=" O TYR A 569 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU A 571 " --> pdb=" O VAL A 603 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1266 through 1269 removed outlier: 5.321A pdb=" N ILE A1230 " --> pdb=" O ASP A1214 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1421 through 1424 removed outlier: 3.579A pdb=" N PHE A1413 " --> pdb=" O TYR A1424 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN A1412 " --> pdb=" O ARG A1239 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL A1397 " --> pdb=" O VAL A1240 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU A1242 " --> pdb=" O VAL A1397 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU A1399 " --> pdb=" O LEU A1242 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N GLY A1244 " --> pdb=" O LEU A1399 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N CYS A1400 " --> pdb=" O LEU A1369 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A1368 " --> pdb=" O GLY A1287 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1212 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: 3.22 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2854 1.34 - 1.46: 2001 1.46 - 1.58: 4506 1.58 - 1.69: 13 1.69 - 1.81: 77 Bond restraints: 9451 Sorted by residual: bond pdb=" C19 WJX A1506 " pdb=" S WJX A1506 " ideal model delta sigma weight residual 1.832 1.607 0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C1 WJX A1506 " pdb=" C2 WJX A1506 " ideal model delta sigma weight residual 1.343 1.539 -0.196 2.00e-02 2.50e+03 9.57e+01 bond pdb=" N WJX A1506 " pdb=" C5 WJX A1506 " ideal model delta sigma weight residual 1.514 1.377 0.137 2.00e-02 2.50e+03 4.72e+01 bond pdb=" N WJX A1506 " pdb=" C3 WJX A1506 " ideal model delta sigma weight residual 1.359 1.490 -0.131 2.00e-02 2.50e+03 4.32e+01 bond pdb=" C2 WJX A1506 " pdb=" C3 WJX A1506 " ideal model delta sigma weight residual 1.660 1.533 0.127 2.00e-02 2.50e+03 4.03e+01 ... (remaining 9446 not shown) Histogram of bond angle deviations from ideal: 70.03 - 82.83: 4 82.83 - 95.62: 2 95.62 - 108.42: 357 108.42 - 121.22: 10290 121.22 - 134.01: 2160 Bond angle restraints: 12813 Sorted by residual: angle pdb=" O1A ATP A1503 " pdb=" PA ATP A1503 " pdb=" O5' ATP A1503 " ideal model delta sigma weight residual 110.65 70.03 40.62 3.49e+00 8.21e-02 1.35e+02 angle pdb=" O1A ATP A1504 " pdb=" PA ATP A1504 " pdb=" O2A ATP A1504 " ideal model delta sigma weight residual 114.42 74.12 40.30 3.53e+00 8.04e-02 1.31e+02 angle pdb=" O1A ATP A1503 " pdb=" PA ATP A1503 " pdb=" O2A ATP A1503 " ideal model delta sigma weight residual 114.42 74.17 40.25 3.53e+00 8.04e-02 1.30e+02 angle pdb=" O1A ATP A1504 " pdb=" PA ATP A1504 " pdb=" O5' ATP A1504 " ideal model delta sigma weight residual 110.65 71.14 39.51 3.49e+00 8.21e-02 1.28e+02 angle pdb=" PB ATP A1503 " pdb=" O3B ATP A1503 " pdb=" PG ATP A1503 " ideal model delta sigma weight residual 139.87 130.44 9.43 1.00e+00 1.00e+00 8.89e+01 ... (remaining 12808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.54: 5521 30.54 - 61.07: 150 61.07 - 91.61: 13 91.61 - 122.14: 0 122.14 - 152.68: 1 Dihedral angle restraints: 5685 sinusoidal: 2366 harmonic: 3319 Sorted by residual: dihedral pdb=" C18 WJX A1506 " pdb=" N4 WJX A1506 " pdb=" S WJX A1506 " pdb=" C19 WJX A1506 " ideal model delta sinusoidal sigma weight residual 203.67 50.99 152.68 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" CA LYS A 532 " pdb=" C LYS A 532 " pdb=" N PHE A 533 " pdb=" CA PHE A 533 " ideal model delta harmonic sigma weight residual 180.00 -159.75 -20.25 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA ASP A1425 " pdb=" CB ASP A1425 " pdb=" CG ASP A1425 " pdb=" OD1 ASP A1425 " ideal model delta sinusoidal sigma weight residual -30.00 -88.50 58.50 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 5682 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 866 0.029 - 0.057: 417 0.057 - 0.086: 126 0.086 - 0.114: 54 0.114 - 0.143: 13 Chirality restraints: 1476 Sorted by residual: chirality pdb=" CA GLN A1371 " pdb=" N GLN A1371 " pdb=" C GLN A1371 " pdb=" CB GLN A1371 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CB ILE A 177 " pdb=" CA ILE A 177 " pdb=" CG1 ILE A 177 " pdb=" CG2 ILE A 177 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA ARG A1259 " pdb=" N ARG A1259 " pdb=" C ARG A1259 " pdb=" CB ARG A1259 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 1473 not shown) Planarity restraints: 1553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C18 WJX A1506 " -0.142 2.00e-02 2.50e+03 9.67e-02 1.17e+02 pdb=" C6 WJX A1506 " 0.109 2.00e-02 2.50e+03 pdb=" N4 WJX A1506 " -0.081 2.00e-02 2.50e+03 pdb=" O1 WJX A1506 " 0.027 2.00e-02 2.50e+03 pdb=" S WJX A1506 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N WJX A1506 " -0.056 2.00e-02 2.50e+03 6.65e-02 9.94e+01 pdb=" C18 WJX A1506 " 0.127 2.00e-02 2.50e+03 pdb=" C5 WJX A1506 " -0.012 2.00e-02 2.50e+03 pdb=" C6 WJX A1506 " -0.015 2.00e-02 2.50e+03 pdb=" C7 WJX A1506 " -0.062 2.00e-02 2.50e+03 pdb=" C8 WJX A1506 " -0.063 2.00e-02 2.50e+03 pdb=" C9 WJX A1506 " -0.017 2.00e-02 2.50e+03 pdb=" N1 WJX A1506 " -0.011 2.00e-02 2.50e+03 pdb=" N2 WJX A1506 " 0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" O WJX A1506 " 0.014 2.00e-02 2.50e+03 1.39e-02 3.40e+00 pdb=" C10 WJX A1506 " -0.004 2.00e-02 2.50e+03 pdb=" C11 WJX A1506 " 0.006 2.00e-02 2.50e+03 pdb=" C12 WJX A1506 " -0.003 2.00e-02 2.50e+03 pdb=" C9 WJX A1506 " 0.022 2.00e-02 2.50e+03 pdb=" N2 WJX A1506 " -0.015 2.00e-02 2.50e+03 pdb=" N3 WJX A1506 " -0.020 2.00e-02 2.50e+03 ... (remaining 1550 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 9 2.49 - 3.09: 6357 3.09 - 3.69: 13023 3.69 - 4.30: 19539 4.30 - 4.90: 31862 Nonbonded interactions: 70790 Sorted by model distance: nonbonded pdb="MG MG A1502 " pdb=" O2B ATP A1504 " model vdw 1.883 2.170 nonbonded pdb="MG MG A1501 " pdb=" O3G ATP A1503 " model vdw 2.010 2.170 nonbonded pdb=" OG1 THR A 465 " pdb="MG MG A1501 " model vdw 2.117 2.170 nonbonded pdb="MG MG A1502 " pdb=" O3G ATP A1504 " model vdw 2.332 2.170 nonbonded pdb=" OG SER A1251 " pdb="MG MG A1502 " model vdw 2.354 2.170 ... (remaining 70785 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 3.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 18.370 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 34.280 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 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 : 0.006 0.225 9451 Z= 0.378 Angle : 1.051 40.620 12813 Z= 0.418 Chirality : 0.039 0.143 1476 Planarity : 0.004 0.097 1553 Dihedral : 13.115 152.680 3541 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.48 % Favored : 97.44 % Rotamer: Outliers : 1.91 % Allowed : 5.84 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.23), residues: 1132 helix: 0.14 (0.19), residues: 661 sheet: -1.17 (0.68), residues: 53 loop : -1.37 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 79 HIS 0.002 0.001 HIS A 484 PHE 0.016 0.001 PHE A 81 TYR 0.014 0.001 TYR A 380 ARG 0.004 0.001 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 188 time to evaluate : 1.049 Fit side-chains REVERT: A 162 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8165 (mtpp) REVERT: A 197 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8755 (pp) REVERT: A 235 LEU cc_start: 0.8353 (mm) cc_final: 0.7371 (tp) REVERT: A 284 MET cc_start: 0.8060 (ttm) cc_final: 0.7803 (ttt) REVERT: A 332 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.6961 (pp) REVERT: A 375 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8878 (mp) REVERT: A 445 ASN cc_start: 0.7160 (OUTLIER) cc_final: 0.6900 (p0) REVERT: A 611 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7437 (ttmm) REVERT: A 1028 MET cc_start: 0.7536 (mtt) cc_final: 0.7309 (mtp) REVERT: A 1049 SER cc_start: 0.8659 (m) cc_final: 0.8303 (p) REVERT: A 1126 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6856 (mt-10) REVERT: A 1157 MET cc_start: 0.8081 (mmm) cc_final: 0.7847 (tpp) REVERT: A 1261 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7776 (pp) outliers start: 19 outliers final: 4 residues processed: 206 average time/residue: 0.2552 time to fit residues: 69.6613 Evaluate side-chains 123 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1261 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 47 optimal weight: 0.0980 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN A 369 ASN A 452 GLN A 493 GLN A 958 GLN A 965 ASN A1012 GLN A1100 GLN A1138 ASN A1144 GLN A1238 GLN A1268 GLN A1280 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9451 Z= 0.216 Angle : 0.606 10.732 12813 Z= 0.306 Chirality : 0.042 0.146 1476 Planarity : 0.004 0.032 1553 Dihedral : 9.664 175.499 1402 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.27 % Favored : 96.64 % Rotamer: Outliers : 2.62 % Allowed : 10.88 % Favored : 86.51 % 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 (0.25), residues: 1132 helix: 1.19 (0.20), residues: 674 sheet: -1.09 (0.68), residues: 53 loop : -1.55 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1274 HIS 0.004 0.001 HIS A 939 PHE 0.023 0.001 PHE A 81 TYR 0.014 0.001 TYR A 380 ARG 0.005 0.001 ARG A1325 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 127 time to evaluate : 1.142 Fit side-chains REVERT: A 74 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.5723 (mmt-90) REVERT: A 197 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8766 (pp) REVERT: A 242 ARG cc_start: 0.8012 (mmt90) cc_final: 0.7014 (ttp-110) REVERT: A 332 ILE cc_start: 0.7311 (OUTLIER) cc_final: 0.6836 (pp) REVERT: A 375 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8798 (mp) REVERT: A 445 ASN cc_start: 0.7011 (OUTLIER) cc_final: 0.6461 (p0) REVERT: A 611 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7429 (ttmm) REVERT: A 1126 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6883 (mt-10) REVERT: A 1261 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7850 (pp) outliers start: 26 outliers final: 11 residues processed: 151 average time/residue: 0.2421 time to fit residues: 49.6896 Evaluate side-chains 121 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 846 TRP Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1261 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.0270 chunk 32 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9451 Z= 0.137 Angle : 0.518 9.955 12813 Z= 0.258 Chirality : 0.039 0.169 1476 Planarity : 0.003 0.028 1553 Dihedral : 9.289 172.612 1396 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.01 % Favored : 96.91 % Rotamer: Outliers : 2.22 % Allowed : 13.29 % Favored : 84.49 % 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: 0.60 (0.25), residues: 1132 helix: 1.57 (0.21), residues: 676 sheet: -0.83 (0.69), residues: 53 loop : -1.50 (0.28), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1274 HIS 0.003 0.001 HIS A 147 PHE 0.017 0.001 PHE A 81 TYR 0.011 0.001 TYR A 380 ARG 0.003 0.000 ARG A1325 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 1.127 Fit side-chains REVERT: A 74 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.5396 (mmt-90) REVERT: A 94 THR cc_start: 0.8258 (p) cc_final: 0.7969 (m) REVERT: A 197 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8759 (pp) REVERT: A 242 ARG cc_start: 0.7975 (mmt90) cc_final: 0.6984 (ttt-90) REVERT: A 332 ILE cc_start: 0.7249 (OUTLIER) cc_final: 0.6814 (pp) REVERT: A 375 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8785 (mp) REVERT: A 488 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8046 (mt) REVERT: A 611 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7408 (ttmm) REVERT: A 1126 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6918 (mt-10) REVERT: A 1261 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7850 (pp) outliers start: 22 outliers final: 11 residues processed: 136 average time/residue: 0.2321 time to fit residues: 43.8369 Evaluate side-chains 123 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 846 TRP Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1261 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 49 optimal weight: 0.0030 chunk 69 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 110 optimal weight: 0.0970 chunk 54 optimal weight: 5.9990 chunk 98 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9451 Z= 0.118 Angle : 0.497 10.313 12813 Z= 0.245 Chirality : 0.038 0.161 1476 Planarity : 0.003 0.026 1553 Dihedral : 8.799 171.071 1394 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.27 % Favored : 96.64 % Rotamer: Outliers : 2.42 % Allowed : 14.30 % Favored : 83.28 % 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: 0.88 (0.26), residues: 1132 helix: 1.84 (0.21), residues: 678 sheet: -0.39 (0.78), residues: 43 loop : -1.53 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1274 HIS 0.003 0.001 HIS A 147 PHE 0.017 0.001 PHE A 236 TYR 0.009 0.001 TYR A 577 ARG 0.004 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 1.063 Fit side-chains REVERT: A 74 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.5388 (mmt-90) REVERT: A 197 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8733 (pp) REVERT: A 242 ARG cc_start: 0.7914 (mmt90) cc_final: 0.6951 (ttt-90) REVERT: A 332 ILE cc_start: 0.7166 (OUTLIER) cc_final: 0.6756 (pp) REVERT: A 488 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.7813 (mt) REVERT: A 611 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7438 (ttmm) REVERT: A 854 THR cc_start: 0.7542 (m) cc_final: 0.7306 (t) REVERT: A 1126 GLU cc_start: 0.7222 (mm-30) cc_final: 0.6942 (mt-10) outliers start: 24 outliers final: 14 residues processed: 135 average time/residue: 0.2404 time to fit residues: 44.8847 Evaluate side-chains 129 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 846 TRP Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1420 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.0770 chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1423 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9451 Z= 0.168 Angle : 0.514 9.969 12813 Z= 0.255 Chirality : 0.039 0.149 1476 Planarity : 0.003 0.034 1553 Dihedral : 8.657 172.622 1388 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.09 % Favored : 96.82 % Rotamer: Outliers : 3.02 % Allowed : 14.20 % Favored : 82.78 % 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: 0.85 (0.26), residues: 1132 helix: 1.83 (0.21), residues: 678 sheet: -0.36 (0.77), residues: 43 loop : -1.57 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1274 HIS 0.003 0.001 HIS A 939 PHE 0.019 0.001 PHE A 236 TYR 0.011 0.001 TYR A 380 ARG 0.002 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 109 time to evaluate : 1.100 Fit side-chains REVERT: A 74 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.5400 (mmt-90) REVERT: A 197 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8735 (pp) REVERT: A 242 ARG cc_start: 0.7952 (mmt90) cc_final: 0.6968 (ttt-90) REVERT: A 332 ILE cc_start: 0.7257 (OUTLIER) cc_final: 0.6803 (pp) REVERT: A 488 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.7832 (mt) REVERT: A 611 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7388 (ttmm) REVERT: A 1049 SER cc_start: 0.8710 (m) cc_final: 0.8323 (p) REVERT: A 1126 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6907 (mt-10) outliers start: 30 outliers final: 22 residues processed: 131 average time/residue: 0.2302 time to fit residues: 41.5180 Evaluate side-chains 132 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 105 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 846 TRP Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1354 MET Chi-restraints excluded: chain A residue 1420 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 0.0980 chunk 27 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 51 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 0.0040 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 98 GLN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9451 Z= 0.116 Angle : 0.477 10.299 12813 Z= 0.236 Chirality : 0.038 0.150 1476 Planarity : 0.003 0.027 1553 Dihedral : 8.367 171.740 1388 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.18 % Favored : 96.73 % Rotamer: Outliers : 2.32 % Allowed : 15.21 % Favored : 82.48 % 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: 1.01 (0.26), residues: 1132 helix: 1.94 (0.21), residues: 679 sheet: -0.25 (0.70), residues: 60 loop : -1.54 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1274 HIS 0.002 0.000 HIS A 147 PHE 0.016 0.001 PHE A 236 TYR 0.010 0.001 TYR A 577 ARG 0.003 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 1.064 Fit side-chains REVERT: A 74 ARG cc_start: 0.6817 (OUTLIER) cc_final: 0.5309 (mmt-90) REVERT: A 242 ARG cc_start: 0.7921 (mmt90) cc_final: 0.6940 (ttt-90) REVERT: A 332 ILE cc_start: 0.7153 (OUTLIER) cc_final: 0.6742 (pp) REVERT: A 488 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.7743 (mt) REVERT: A 611 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7405 (ttmm) REVERT: A 1049 SER cc_start: 0.8699 (m) cc_final: 0.8306 (p) REVERT: A 1126 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6922 (mt-10) outliers start: 23 outliers final: 14 residues processed: 125 average time/residue: 0.2337 time to fit residues: 40.2703 Evaluate side-chains 122 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 846 TRP Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1420 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 61 optimal weight: 0.2980 chunk 109 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9451 Z= 0.130 Angle : 0.483 10.189 12813 Z= 0.238 Chirality : 0.038 0.175 1476 Planarity : 0.003 0.027 1553 Dihedral : 8.292 171.650 1386 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.27 % Favored : 96.64 % Rotamer: Outliers : 2.22 % Allowed : 16.11 % Favored : 81.67 % 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: 1.03 (0.26), residues: 1132 helix: 1.96 (0.21), residues: 681 sheet: -0.13 (0.70), residues: 60 loop : -1.57 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1274 HIS 0.002 0.001 HIS A 147 PHE 0.017 0.001 PHE A 236 TYR 0.012 0.001 TYR A1424 ARG 0.003 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 1.196 Fit side-chains REVERT: A 74 ARG cc_start: 0.6772 (OUTLIER) cc_final: 0.5287 (mmt-90) REVERT: A 242 ARG cc_start: 0.7936 (mmt90) cc_final: 0.6953 (ttt-90) REVERT: A 332 ILE cc_start: 0.7192 (OUTLIER) cc_final: 0.6783 (pp) REVERT: A 488 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.7747 (mt) REVERT: A 611 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7410 (ttmm) REVERT: A 1049 SER cc_start: 0.8704 (m) cc_final: 0.8308 (p) REVERT: A 1126 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6934 (mt-10) REVERT: A 1140 MET cc_start: 0.7712 (mmp) cc_final: 0.7202 (mmp) outliers start: 22 outliers final: 15 residues processed: 119 average time/residue: 0.2361 time to fit residues: 38.8070 Evaluate side-chains 120 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 846 TRP Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1420 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9451 Z= 0.180 Angle : 0.520 10.934 12813 Z= 0.259 Chirality : 0.039 0.123 1476 Planarity : 0.003 0.028 1553 Dihedral : 8.489 174.952 1386 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.63 % Favored : 96.29 % Rotamer: Outliers : 2.82 % Allowed : 15.91 % Favored : 81.27 % 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: 0.88 (0.26), residues: 1132 helix: 1.83 (0.21), residues: 678 sheet: -0.04 (0.71), residues: 60 loop : -1.61 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1274 HIS 0.003 0.001 HIS A 484 PHE 0.019 0.001 PHE A 236 TYR 0.012 0.001 TYR A 380 ARG 0.003 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 100 time to evaluate : 0.987 Fit side-chains REVERT: A 74 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.5391 (mmt-90) REVERT: A 242 ARG cc_start: 0.7964 (mmt90) cc_final: 0.6958 (ttt-90) REVERT: A 332 ILE cc_start: 0.7233 (OUTLIER) cc_final: 0.6780 (pp) REVERT: A 488 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.7772 (mt) REVERT: A 611 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7366 (ttmm) REVERT: A 1126 GLU cc_start: 0.7305 (mm-30) cc_final: 0.6898 (mt-10) outliers start: 28 outliers final: 19 residues processed: 121 average time/residue: 0.2249 time to fit residues: 37.9779 Evaluate side-chains 122 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 99 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 846 TRP Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1420 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 108 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 GLN A 270 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9451 Z= 0.144 Angle : 0.499 10.111 12813 Z= 0.246 Chirality : 0.038 0.123 1476 Planarity : 0.003 0.028 1553 Dihedral : 8.400 174.927 1386 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.54 % Favored : 96.37 % Rotamer: Outliers : 2.52 % Allowed : 16.11 % Favored : 81.37 % 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: 0.89 (0.26), residues: 1132 helix: 1.78 (0.21), residues: 685 sheet: 0.01 (0.71), residues: 60 loop : -1.56 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1274 HIS 0.002 0.001 HIS A 147 PHE 0.017 0.001 PHE A 236 TYR 0.010 0.001 TYR A 380 ARG 0.002 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 106 time to evaluate : 1.145 Fit side-chains REVERT: A 74 ARG cc_start: 0.6842 (OUTLIER) cc_final: 0.5291 (mmt-90) REVERT: A 242 ARG cc_start: 0.7935 (mmt90) cc_final: 0.6937 (ttt-90) REVERT: A 332 ILE cc_start: 0.7240 (OUTLIER) cc_final: 0.6806 (pp) REVERT: A 488 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.7723 (mt) REVERT: A 611 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7342 (ttmm) REVERT: A 1126 GLU cc_start: 0.7291 (mm-30) cc_final: 0.6894 (mt-10) outliers start: 25 outliers final: 19 residues processed: 126 average time/residue: 0.2231 time to fit residues: 39.1772 Evaluate side-chains 127 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 104 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 846 TRP Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1420 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 104 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 9 optimal weight: 0.0040 chunk 69 optimal weight: 0.6980 chunk 55 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9451 Z= 0.147 Angle : 0.510 10.115 12813 Z= 0.252 Chirality : 0.038 0.121 1476 Planarity : 0.003 0.028 1553 Dihedral : 8.365 174.781 1386 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.27 % Favored : 96.64 % Rotamer: Outliers : 2.42 % Allowed : 15.91 % Favored : 81.67 % 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: 0.91 (0.26), residues: 1132 helix: 1.78 (0.21), residues: 688 sheet: 0.03 (0.71), residues: 60 loop : -1.55 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1274 HIS 0.002 0.001 HIS A 147 PHE 0.017 0.001 PHE A 236 TYR 0.013 0.001 TYR A1424 ARG 0.002 0.000 ARG A 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 1.121 Fit side-chains REVERT: A 74 ARG cc_start: 0.6813 (OUTLIER) cc_final: 0.5263 (mmt-90) REVERT: A 242 ARG cc_start: 0.7930 (mmt90) cc_final: 0.6955 (ttt-90) REVERT: A 332 ILE cc_start: 0.7234 (OUTLIER) cc_final: 0.6800 (pp) REVERT: A 488 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.7700 (mt) REVERT: A 611 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7345 (ttmm) REVERT: A 1126 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6863 (mt-10) outliers start: 24 outliers final: 20 residues processed: 121 average time/residue: 0.2371 time to fit residues: 39.9538 Evaluate side-chains 126 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 102 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 846 TRP Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1354 MET Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1420 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.129657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.111680 restraints weight = 25900.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.115548 restraints weight = 11552.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.117615 restraints weight = 6451.628| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9451 Z= 0.163 Angle : 0.521 10.165 12813 Z= 0.258 Chirality : 0.039 0.119 1476 Planarity : 0.003 0.028 1553 Dihedral : 8.430 176.122 1386 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.71 % Favored : 96.20 % Rotamer: Outliers : 2.62 % Allowed : 15.71 % Favored : 81.67 % 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: 0.87 (0.26), residues: 1132 helix: 1.75 (0.21), residues: 687 sheet: 0.08 (0.70), residues: 60 loop : -1.56 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1274 HIS 0.003 0.001 HIS A 484 PHE 0.018 0.001 PHE A 236 TYR 0.011 0.001 TYR A 380 ARG 0.002 0.000 ARG A 600 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2200.40 seconds wall clock time: 40 minutes 20.68 seconds (2420.68 seconds total)