Starting phenix.real_space_refine on Sat Dec 9 01:09:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eiq_28161/12_2023/8eiq_28161_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eiq_28161/12_2023/8eiq_28161.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eiq_28161/12_2023/8eiq_28161_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eiq_28161/12_2023/8eiq_28161_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eiq_28161/12_2023/8eiq_28161_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eiq_28161/12_2023/8eiq_28161.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eiq_28161/12_2023/8eiq_28161.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eiq_28161/12_2023/8eiq_28161_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eiq_28161/12_2023/8eiq_28161_updated.pdb" } resolution = 3.0 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 48 5.16 5 C 6251 2.51 5 N 1582 2.21 5 O 1683 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1424": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9578 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1162, 9287 Classifications: {'peptide': 1162} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 31, 'TRANS': 1130} 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 Chain: "B" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 211 Unusual residues: {' MG': 2, 'ATP': 2, 'CLR': 1, 'CV6': 1, 'D12': 1, 'VX7': 1, 'WJX': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Time building chain proxies: 5.81, per 1000 atoms: 0.61 Number of scatterers: 9578 At special positions: 0 Unit cell: (75.036, 82.472, 145.34, 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 48 16.00 P 6 15.00 Mg 2 11.99 F 6 9.00 O 1683 8.00 N 1582 7.00 C 6251 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: 3.92 Conformation dependent library (CDL) restraints added in 1.8 seconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2216 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 5 sheets defined 62.7% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'A' and resid 5 through 8 removed outlier: 3.691A pdb=" N LYS A 8 " --> pdb=" O PRO A 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 5 through 8' Processing helix chain 'A' and resid 11 through 16 Processing helix chain 'A' and resid 18 through 27 Proline residue: A 22 - end of helix removed outlier: 3.868A pdb=" N ARG A 25 " --> pdb=" O PRO A 22 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY A 27 " --> pdb=" O LEU A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 46 through 63 removed outlier: 3.606A pdb=" N GLU A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG A 59 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 96 removed outlier: 3.612A pdb=" N CYS A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N TRP A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ARG A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 removed outlier: 4.335A pdb=" N ARG A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 108 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TYR A 109 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 118 removed outlier: 3.562A pdb=" N SER A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 114 through 118' Processing helix chain 'A' and resid 120 through 166 removed outlier: 3.992A pdb=" N HIS A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix removed outlier: 3.920A pdb=" N LYS A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 185 Processing helix chain 'A' and resid 187 through 196 removed outlier: 3.760A pdb=" N PHE A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ASP A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU A 193 " --> pdb=" O ASN A 189 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ALA A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 218 removed outlier: 3.522A pdb=" N VAL A 201 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A 203 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ALA A 204 " --> pdb=" O VAL A 201 " (cutoff:3.500A) Proline residue: A 205 - end of helix removed outlier: 3.676A pdb=" N MET A 212 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 215 " --> pdb=" O MET A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 267 removed outlier: 3.935A pdb=" N GLY A 228 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 229 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 231 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS A 246 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN A 250 " --> pdb=" O TYR A 247 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 252 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY A 253 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER A 256 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 259 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL A 260 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 262 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET A 265 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 266 " --> pdb=" O SER A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 275 Processing helix chain 'A' and resid 278 through 307 removed outlier: 3.662A pdb=" N THR A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 305 " --> pdb=" O TYR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 removed outlier: 3.526A pdb=" N LEU A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Proline residue: A 324 - end of helix removed outlier: 3.625A pdb=" N ILE A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 351 removed outlier: 3.826A pdb=" N VAL A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 376 removed outlier: 3.530A pdb=" N GLN A 376 " --> pdb=" O GLN A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 472 removed outlier: 3.596A pdb=" N LEU A 468 " --> pdb=" O LYS A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 514 through 523 removed outlier: 3.551A pdb=" N LYS A 522 " --> pdb=" O ARG A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 532 removed outlier: 3.902A pdb=" N LYS A 532 " --> pdb=" O GLU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 563 removed outlier: 3.782A pdb=" N ALA A 554 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 589 Processing helix chain 'A' and resid 630 through 633 No H-bonds generated for 'chain 'A' and resid 630 through 633' Processing helix chain 'A' and resid 847 through 853 Processing helix chain 'A' and resid 857 through 884 removed outlier: 3.912A pdb=" N PHE A 861 " --> pdb=" O LYS A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 926 removed outlier: 3.597A pdb=" N VAL A 920 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 923 " --> pdb=" O VAL A 920 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ASP A 924 " --> pdb=" O GLY A 921 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 926 " --> pdb=" O ALA A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 957 removed outlier: 3.565A pdb=" N LEU A 935 " --> pdb=" O PHE A 931 " (cutoff:3.500A) Proline residue: A 936 - end of helix removed outlier: 3.532A pdb=" N ILE A 942 " --> pdb=" O VAL A 938 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 943 " --> pdb=" O HIS A 939 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 957 " --> pdb=" O LEU A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 966 removed outlier: 4.021A pdb=" N THR A 966 " --> pdb=" O SER A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 1011 removed outlier: 3.630A pdb=" N ARG A 975 " --> pdb=" O GLY A 971 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE A 980 " --> pdb=" O PHE A 976 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LEU A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) Proline residue: A 988 - end of helix removed outlier: 3.523A pdb=" N PHE A 992 " --> pdb=" O PRO A 988 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL A1010 " --> pdb=" O ALA A1006 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A1011 " --> pdb=" O VAL A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1060 Proline residue: A1021 - end of helix removed outlier: 3.669A pdb=" N GLN A1035 " --> pdb=" O ALA A1031 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N THR A1036 " --> pdb=" O TYR A1032 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN A1039 " --> pdb=" O GLN A1035 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG A1048 " --> pdb=" O GLU A1044 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N SER A1049 " --> pdb=" O SER A1045 " (cutoff:3.500A) Proline residue: A1050 - end of helix removed outlier: 3.721A pdb=" N LEU A1059 " --> pdb=" O LEU A1055 " (cutoff:3.500A) removed outlier: 3.524A 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: 3.725A pdb=" N ALA A1081 " --> pdb=" O LEU A1077 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN A1088 " --> pdb=" O LEU A1084 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU A1104 " --> pdb=" O GLN A1100 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE A1107 " --> pdb=" O ILE A1103 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A1110 " --> pdb=" O ILE A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1167 removed outlier: 3.613A pdb=" N SER A1141 " --> pdb=" O MET A1137 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR A1142 " --> pdb=" O ASN A1138 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TRP A1145 " --> pdb=" O SER A1141 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP A1152 " --> pdb=" O ASN A1148 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A1158 " --> pdb=" O ASP A1154 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N SER A1159 " --> pdb=" O SER A1155 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A1160 " --> pdb=" O LEU A1156 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE A1166 " --> pdb=" O ARG A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1257 Processing helix chain 'A' and resid 1283 through 1285 No H-bonds generated for 'chain 'A' and resid 1283 through 1285' Processing helix chain 'A' and resid 1300 through 1304 Processing helix chain 'A' and resid 1312 through 1321 removed outlier: 3.675A pdb=" N GLU A1321 " --> pdb=" O LYS A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1325 through 1329 Processing helix chain 'A' and resid 1348 through 1361 removed outlier: 3.677A pdb=" N GLN A1352 " --> pdb=" O HIS A1348 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A1353 " --> pdb=" O GLY A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1390 removed outlier: 3.953A pdb=" N GLN A1382 " --> pdb=" O PRO A1378 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE A1383 " --> pdb=" O VAL A1379 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE A1384 " --> pdb=" O THR A1380 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A1389 " --> pdb=" O ARG A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1405 through 1409 removed outlier: 3.653A pdb=" N LEU A1408 " --> pdb=" O GLU A1405 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU A1409 " --> pdb=" O ALA A1406 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1405 through 1409' Processing helix chain 'A' and resid 1427 through 1433 removed outlier: 3.788A pdb=" N GLU A1433 " --> pdb=" O LYS A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1439 No H-bonds generated for 'chain 'A' and resid 1436 through 1439' Processing helix chain 'A' and resid 1443 through 1449 removed outlier: 3.575A pdb=" N VAL A1447 " --> pdb=" O PRO A1443 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LYS A1448 " --> pdb=" O SER A1444 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 14 Processing sheet with id= A, first strand: chain 'A' and resid 446 through 448 removed outlier: 3.538A pdb=" N PHE A 446 " --> pdb=" O MET A 394 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU A 395 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A 481 " --> pdb=" O GLU A 395 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 623 through 628 removed outlier: 6.493A pdb=" N ILE A 618 " --> pdb=" O TYR A 625 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TYR A 627 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE A 616 " --> pdb=" O TYR A 627 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARG A 600 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL A 456 " --> pdb=" O ARG A 600 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU A 602 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N GLY A 458 " --> pdb=" O LEU A 602 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR A 569 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL A 603 " --> pdb=" O TYR A 569 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LEU A 571 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N SER A 489 " --> pdb=" O LEU A 570 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1232 through 1234 Processing sheet with id= D, first strand: chain 'A' and resid 1240 through 1244 removed outlier: 6.916A pdb=" N GLN A1412 " --> pdb=" O GLY A1241 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N LEU A1243 " --> pdb=" O GLN A1412 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A1414 " --> pdb=" O LEU A1243 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1286 through 1289 removed outlier: 6.790A pdb=" N ILE A1366 " --> pdb=" O GLY A1287 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N ILE A1289 " --> pdb=" O ILE A1366 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU A1368 " --> pdb=" O ILE A1289 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR A1396 " --> pdb=" O LEU A1367 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEU A1369 " --> pdb=" O THR A1396 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE A1398 " --> pdb=" O LEU A1369 " (cutoff:3.500A) No H-bonds generated for sheet with id= E 449 hydrogen bonds defined for protein. 1176 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: 2.91 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2936 1.34 - 1.46: 1404 1.46 - 1.57: 5355 1.57 - 1.69: 12 1.69 - 1.81: 79 Bond restraints: 9786 Sorted by residual: bond pdb=" C19 WJX A1508 " pdb=" S WJX A1508 " ideal model delta sigma weight residual 1.832 1.620 0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C1 WJX A1508 " pdb=" C2 WJX A1508 " ideal model delta sigma weight residual 1.343 1.538 -0.195 2.00e-02 2.50e+03 9.47e+01 bond pdb=" N WJX A1508 " pdb=" C5 WJX A1508 " ideal model delta sigma weight residual 1.514 1.366 0.148 2.00e-02 2.50e+03 5.48e+01 bond pdb=" N WJX A1508 " pdb=" C3 WJX A1508 " ideal model delta sigma weight residual 1.359 1.490 -0.131 2.00e-02 2.50e+03 4.28e+01 bond pdb=" C2 WJX A1508 " pdb=" C3 WJX A1508 " ideal model delta sigma weight residual 1.660 1.535 0.125 2.00e-02 2.50e+03 3.93e+01 ... (remaining 9781 not shown) Histogram of bond angle deviations from ideal: 58.57 - 74.08: 6 74.08 - 89.58: 1 89.58 - 105.09: 143 105.09 - 120.60: 9767 120.60 - 136.11: 3358 Bond angle restraints: 13275 Sorted by residual: angle pdb=" O1A ATP A1504 " pdb=" PA ATP A1504 " pdb=" O2A ATP A1504 " ideal model delta sigma weight residual 114.42 74.03 40.39 3.53e+00 8.04e-02 1.31e+02 angle pdb=" O1A ATP A1504 " pdb=" PA ATP A1504 " pdb=" O5' ATP A1504 " ideal model delta sigma weight residual 110.65 71.06 39.59 3.49e+00 8.21e-02 1.29e+02 angle pdb=" O1A ATP A1503 " pdb=" PA ATP A1503 " pdb=" O2A ATP A1503 " ideal model delta sigma weight residual 114.42 74.52 39.90 3.53e+00 8.04e-02 1.28e+02 angle pdb=" O1A ATP A1503 " pdb=" PA ATP A1503 " pdb=" O5' ATP A1503 " ideal model delta sigma weight residual 110.65 71.35 39.30 3.49e+00 8.21e-02 1.27e+02 angle pdb=" PB ATP A1504 " pdb=" O3B ATP A1504 " pdb=" PG ATP A1504 " ideal model delta sigma weight residual 139.87 132.06 7.81 1.00e+00 1.00e+00 6.10e+01 ... (remaining 13270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.65: 5736 33.65 - 67.30: 131 67.30 - 100.95: 8 100.95 - 134.60: 1 134.60 - 168.25: 1 Dihedral angle restraints: 5877 sinusoidal: 2452 harmonic: 3425 Sorted by residual: dihedral pdb=" C18 WJX A1508 " pdb=" N4 WJX A1508 " pdb=" S WJX A1508 " pdb=" C19 WJX A1508 " ideal model delta sinusoidal sigma weight residual 203.67 35.42 168.25 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" N CV6 A1509 " pdb=" C12 CV6 A1509 " pdb=" C13 CV6 A1509 " pdb=" C14 CV6 A1509 " ideal model delta sinusoidal sigma weight residual -179.02 -50.06 -128.96 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" N LEU A1065 " pdb=" CA LEU A1065 " pdb=" CB LEU A1065 " pdb=" CG LEU A1065 " ideal model delta sinusoidal sigma weight residual -180.00 -121.41 -58.59 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 5874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.185: 1518 0.185 - 0.369: 0 0.369 - 0.554: 0 0.554 - 0.739: 0 0.739 - 0.923: 1 Chirality restraints: 1519 Sorted by residual: chirality pdb=" C16 CV6 A1509 " pdb=" C15 CV6 A1509 " pdb=" C17 CV6 A1509 " pdb=" C19 CV6 A1509 " both_signs ideal model delta sigma weight residual True 2.52 1.60 0.92 2.00e-01 2.50e+01 2.13e+01 chirality pdb=" CA ILE A 601 " pdb=" N ILE A 601 " pdb=" C ILE A 601 " pdb=" CB ILE A 601 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA ILE A 482 " pdb=" N ILE A 482 " pdb=" C ILE A 482 " pdb=" CB ILE A 482 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 1516 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C16 CV6 A1509 " 0.091 2.00e-02 2.50e+03 1.26e-01 3.55e+02 pdb=" C19 CV6 A1509 " 0.026 2.00e-02 2.50e+03 pdb=" C20 CV6 A1509 " -0.103 2.00e-02 2.50e+03 pdb=" C21 CV6 A1509 " -0.199 2.00e-02 2.50e+03 pdb=" C22 CV6 A1509 " -0.167 2.00e-02 2.50e+03 pdb=" C23 CV6 A1509 " -0.030 2.00e-02 2.50e+03 pdb=" C24 CV6 A1509 " 0.065 2.00e-02 2.50e+03 pdb=" O4 CV6 A1509 " 0.152 2.00e-02 2.50e+03 pdb=" O5 CV6 A1509 " 0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 WJX A1508 " -0.137 2.00e-02 2.50e+03 7.98e-02 7.97e+01 pdb=" C6 WJX A1508 " 0.084 2.00e-02 2.50e+03 pdb=" N4 WJX A1508 " -0.038 2.00e-02 2.50e+03 pdb=" O1 WJX A1508 " 0.035 2.00e-02 2.50e+03 pdb=" S WJX A1508 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N WJX A1508 " -0.039 2.00e-02 2.50e+03 5.13e-02 5.92e+01 pdb=" C18 WJX A1508 " 0.099 2.00e-02 2.50e+03 pdb=" C5 WJX A1508 " -0.015 2.00e-02 2.50e+03 pdb=" C6 WJX A1508 " -0.013 2.00e-02 2.50e+03 pdb=" C7 WJX A1508 " -0.046 2.00e-02 2.50e+03 pdb=" C8 WJX A1508 " -0.047 2.00e-02 2.50e+03 pdb=" C9 WJX A1508 " -0.014 2.00e-02 2.50e+03 pdb=" N1 WJX A1508 " -0.010 2.00e-02 2.50e+03 pdb=" N2 WJX A1508 " 0.085 2.00e-02 2.50e+03 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 23 2.53 - 3.12: 6903 3.12 - 3.71: 13603 3.71 - 4.31: 19957 4.31 - 4.90: 33658 Nonbonded interactions: 74144 Sorted by model distance: nonbonded pdb=" OG1 THR A 465 " pdb="MG MG A1501 " model vdw 1.936 2.170 nonbonded pdb=" OE1 GLN A 493 " pdb="MG MG A1501 " model vdw 1.939 2.170 nonbonded pdb="MG MG A1501 " pdb=" O3G ATP A1503 " model vdw 2.018 2.170 nonbonded pdb="MG MG A1502 " pdb=" O3G ATP A1504 " model vdw 2.031 2.170 nonbonded pdb=" OH TYR A 512 " pdb=" OE1 GLU A 514 " model vdw 2.041 2.440 ... (remaining 74139 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.180 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: 18.200 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 30.140 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:13.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 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 0.212 9786 Z= 0.420 Angle : 1.106 40.386 13275 Z= 0.418 Chirality : 0.046 0.923 1519 Planarity : 0.005 0.126 1604 Dihedral : 13.249 168.247 3661 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.78 % Allowed : 5.24 % Favored : 92.98 % 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: -1.39 (0.22), residues: 1152 helix: -0.85 (0.17), residues: 717 sheet: -0.58 (0.55), residues: 87 loop : -0.74 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 865 HIS 0.003 0.001 HIS A 139 PHE 0.012 0.001 PHE A 81 TYR 0.009 0.001 TYR A 304 ARG 0.004 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 1.193 Fit side-chains outliers start: 18 outliers final: 6 residues processed: 170 average time/residue: 1.5139 time to fit residues: 272.5853 Evaluate side-chains 93 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 1.114 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 1.4984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.0070 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 0.0070 chunk 47 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 71 ASN A 98 GLN A 287 ASN A 353 GLN A 452 GLN A 597 ASN A1100 GLN A1238 GLN A1309 GLN A1352 GLN A1375 HIS A1428 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9786 Z= 0.152 Angle : 0.506 9.180 13275 Z= 0.265 Chirality : 0.039 0.152 1519 Planarity : 0.004 0.027 1604 Dihedral : 9.601 167.963 1451 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.13 % Favored : 98.78 % Rotamer: Outliers : 3.26 % Allowed : 11.56 % Favored : 85.18 % 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: 0.24 (0.24), residues: 1152 helix: 0.69 (0.19), residues: 721 sheet: -0.27 (0.59), residues: 81 loop : -0.65 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 865 HIS 0.004 0.001 HIS A 147 PHE 0.019 0.001 PHE A 630 TYR 0.009 0.001 TYR A 362 ARG 0.005 0.000 ARG A1239 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 103 time to evaluate : 1.072 Fit side-chains outliers start: 33 outliers final: 10 residues processed: 127 average time/residue: 1.2438 time to fit residues: 170.0780 Evaluate side-chains 100 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 1.142 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.1451 time to fit residues: 2.2226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 8.9990 chunk 32 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A1054 HIS A1428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9786 Z= 0.191 Angle : 0.491 9.067 13275 Z= 0.252 Chirality : 0.039 0.149 1519 Planarity : 0.003 0.036 1604 Dihedral : 9.333 163.659 1451 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.74 % Favored : 98.18 % Rotamer: Outliers : 3.46 % Allowed : 13.24 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1152 helix: 1.01 (0.20), residues: 722 sheet: -0.44 (0.55), residues: 86 loop : -0.71 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 865 HIS 0.003 0.001 HIS A 147 PHE 0.013 0.001 PHE A 81 TYR 0.009 0.001 TYR A 304 ARG 0.006 0.000 ARG A1239 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 89 time to evaluate : 1.235 Fit side-chains outliers start: 35 outliers final: 16 residues processed: 116 average time/residue: 1.4339 time to fit residues: 178.1535 Evaluate side-chains 101 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 1.164 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 5 average time/residue: 0.7487 time to fit residues: 5.7025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1054 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9786 Z= 0.340 Angle : 0.568 9.168 13275 Z= 0.292 Chirality : 0.043 0.154 1519 Planarity : 0.004 0.051 1604 Dihedral : 9.520 155.366 1451 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.00 % Favored : 97.92 % Rotamer: Outliers : 4.64 % Allowed : 13.34 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.24), residues: 1152 helix: 0.79 (0.20), residues: 718 sheet: -0.60 (0.54), residues: 86 loop : -0.98 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1274 HIS 0.005 0.001 HIS A 147 PHE 0.015 0.002 PHE A 81 TYR 0.010 0.002 TYR A 304 ARG 0.008 0.001 ARG A1239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 84 time to evaluate : 1.141 Fit side-chains outliers start: 47 outliers final: 23 residues processed: 119 average time/residue: 1.4372 time to fit residues: 183.3607 Evaluate side-chains 105 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 82 time to evaluate : 1.078 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 17 residues processed: 6 average time/residue: 0.1760 time to fit residues: 3.0934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 10.0000 chunk 1 optimal weight: 0.6980 chunk 84 optimal weight: 0.4980 chunk 46 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A1054 HIS A1428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9786 Z= 0.155 Angle : 0.469 9.465 13275 Z= 0.242 Chirality : 0.038 0.143 1519 Planarity : 0.003 0.039 1604 Dihedral : 9.087 158.976 1451 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.66 % Allowed : 14.03 % Favored : 82.31 % 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: 0.55 (0.25), residues: 1152 helix: 1.08 (0.20), residues: 719 sheet: -0.42 (0.56), residues: 86 loop : -0.83 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 865 HIS 0.003 0.000 HIS A 147 PHE 0.009 0.001 PHE A 81 TYR 0.009 0.001 TYR A 304 ARG 0.008 0.000 ARG A1239 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 85 time to evaluate : 1.287 Fit side-chains outliers start: 37 outliers final: 19 residues processed: 115 average time/residue: 1.3461 time to fit residues: 166.6125 Evaluate side-chains 103 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 84 time to evaluate : 0.956 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 16 residues processed: 3 average time/residue: 1.0821 time to fit residues: 4.7609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN A 965 ASN A1054 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9786 Z= 0.383 Angle : 0.591 9.061 13275 Z= 0.302 Chirality : 0.044 0.151 1519 Planarity : 0.004 0.054 1604 Dihedral : 9.538 145.960 1451 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.60 % Favored : 97.31 % Rotamer: Outliers : 3.75 % Allowed : 14.53 % Favored : 81.72 % 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: 0.02 (0.24), residues: 1152 helix: 0.72 (0.20), residues: 717 sheet: -0.67 (0.55), residues: 86 loop : -1.14 (0.29), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 865 HIS 0.006 0.001 HIS A 147 PHE 0.014 0.002 PHE A 81 TYR 0.021 0.002 TYR A 301 ARG 0.008 0.001 ARG A1239 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 85 time to evaluate : 1.180 Fit side-chains outliers start: 38 outliers final: 22 residues processed: 116 average time/residue: 1.5311 time to fit residues: 189.8373 Evaluate side-chains 102 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 80 time to evaluate : 1.141 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 20 residues processed: 2 average time/residue: 0.1849 time to fit residues: 2.9913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.9980 chunk 64 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1054 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9786 Z= 0.158 Angle : 0.477 9.327 13275 Z= 0.246 Chirality : 0.038 0.142 1519 Planarity : 0.003 0.041 1604 Dihedral : 9.117 154.315 1451 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.16 % Allowed : 15.91 % Favored : 80.93 % 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: 0.42 (0.25), residues: 1152 helix: 1.02 (0.20), residues: 718 sheet: -0.39 (0.55), residues: 86 loop : -0.98 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 865 HIS 0.003 0.001 HIS A 147 PHE 0.010 0.001 PHE A 494 TYR 0.012 0.001 TYR A 512 ARG 0.008 0.000 ARG A1239 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 83 time to evaluate : 1.112 Fit side-chains outliers start: 32 outliers final: 19 residues processed: 110 average time/residue: 1.3384 time to fit residues: 158.0075 Evaluate side-chains 101 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 1.131 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 2 average time/residue: 0.9384 time to fit residues: 3.5464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 0.0570 chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9786 Z= 0.146 Angle : 0.460 9.476 13275 Z= 0.236 Chirality : 0.038 0.140 1519 Planarity : 0.003 0.037 1604 Dihedral : 8.834 157.665 1451 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.87 % Allowed : 16.11 % Favored : 81.03 % 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: 0.71 (0.25), residues: 1152 helix: 1.27 (0.20), residues: 715 sheet: -0.24 (0.56), residues: 86 loop : -0.91 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 865 HIS 0.003 0.000 HIS A 147 PHE 0.010 0.001 PHE A 494 TYR 0.026 0.001 TYR A 512 ARG 0.008 0.000 ARG A1239 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 85 time to evaluate : 1.191 Fit side-chains outliers start: 29 outliers final: 18 residues processed: 109 average time/residue: 1.3961 time to fit residues: 163.0494 Evaluate side-chains 95 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 1.205 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 17 residues processed: 1 average time/residue: 0.1444 time to fit residues: 1.8082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 108 optimal weight: 0.4980 chunk 63 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 104 optimal weight: 0.0050 chunk 69 optimal weight: 0.8980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9786 Z= 0.133 Angle : 0.455 9.548 13275 Z= 0.232 Chirality : 0.037 0.141 1519 Planarity : 0.003 0.040 1604 Dihedral : 8.718 158.124 1451 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.27 % Allowed : 17.49 % Favored : 80.24 % 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: 0.86 (0.25), residues: 1152 helix: 1.39 (0.20), residues: 712 sheet: -0.19 (0.57), residues: 86 loop : -0.84 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 865 HIS 0.002 0.000 HIS A 147 PHE 0.010 0.001 PHE A 494 TYR 0.024 0.001 TYR A 512 ARG 0.009 0.000 ARG A1239 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 85 time to evaluate : 1.169 Fit side-chains outliers start: 23 outliers final: 19 residues processed: 103 average time/residue: 1.3523 time to fit residues: 149.5661 Evaluate side-chains 101 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 1.134 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 16 residues processed: 3 average time/residue: 0.6431 time to fit residues: 3.7129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 73 optimal weight: 0.2980 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9786 Z= 0.287 Angle : 0.550 9.283 13275 Z= 0.281 Chirality : 0.041 0.151 1519 Planarity : 0.004 0.048 1604 Dihedral : 9.184 149.324 1451 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.08 % Allowed : 18.08 % Favored : 79.84 % 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: 0.39 (0.25), residues: 1152 helix: 1.00 (0.20), residues: 717 sheet: -0.46 (0.56), residues: 86 loop : -1.00 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1274 HIS 0.004 0.001 HIS A 147 PHE 0.012 0.001 PHE A 494 TYR 0.016 0.002 TYR A 301 ARG 0.009 0.000 ARG A1239 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 81 time to evaluate : 1.114 Fit side-chains outliers start: 21 outliers final: 17 residues processed: 100 average time/residue: 1.4087 time to fit residues: 150.9913 Evaluate side-chains 95 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 1 average time/residue: 0.2641 time to fit residues: 1.9507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.0040 chunk 28 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.119326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.095367 restraints weight = 12570.208| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.88 r_work: 0.2957 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9786 Z= 0.146 Angle : 0.469 9.398 13275 Z= 0.241 Chirality : 0.038 0.146 1519 Planarity : 0.003 0.039 1604 Dihedral : 8.855 155.448 1451 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.08 % Allowed : 18.18 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.25), residues: 1152 helix: 1.24 (0.20), residues: 715 sheet: -0.28 (0.57), residues: 86 loop : -0.87 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 865 HIS 0.003 0.000 HIS A 147 PHE 0.011 0.001 PHE A 494 TYR 0.020 0.001 TYR A 512 ARG 0.008 0.000 ARG A1239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3624.90 seconds wall clock time: 65 minutes 45.15 seconds (3945.15 seconds total)