Starting phenix.real_space_refine on Thu Mar 14 19:51:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eiq_28161/03_2024/8eiq_28161_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eiq_28161/03_2024/8eiq_28161.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eiq_28161/03_2024/8eiq_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_28161/03_2024/8eiq_28161_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eiq_28161/03_2024/8eiq_28161_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eiq_28161/03_2024/8eiq_28161.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eiq_28161/03_2024/8eiq_28161.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eiq_28161/03_2024/8eiq_28161_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eiq_28161/03_2024/8eiq_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-dev-5265/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: 5.63, per 1000 atoms: 0.59 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: 3.87 Conformation dependent library (CDL) restraints added in 1.5 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: 2.71 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: 3.07 Time building geometry restraints manager: 4.19 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: 5763 33.65 - 67.30: 133 67.30 - 100.95: 7 100.95 - 134.60: 0 134.60 - 168.25: 1 Dihedral angle restraints: 5904 sinusoidal: 2479 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 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 dihedral pdb=" N LEU A 233 " pdb=" CA LEU A 233 " pdb=" CB LEU A 233 " pdb=" CG LEU A 233 " ideal model delta sinusoidal sigma weight residual -180.00 -121.94 -58.06 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 5901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 778 0.026 - 0.053: 504 0.053 - 0.079: 154 0.079 - 0.106: 47 0.106 - 0.132: 36 Chirality restraints: 1519 Sorted by residual: 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 chirality pdb=" CA HIS A 139 " pdb=" N HIS A 139 " pdb=" C HIS A 139 " pdb=" CB HIS A 139 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.21e-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: 3.410 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: 18.110 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 29.500 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: 0.000 Load rotamer database and sin/cos tables:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.150 ------------------------------------------------------------------------------- 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= 0.396 Angle : 1.026 40.386 13275 Z= 0.395 Chirality : 0.040 0.132 1519 Planarity : 0.005 0.126 1604 Dihedral : 13.069 168.247 3688 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 : 1.287 Fit side-chains REVERT: A 3 ARG cc_start: 0.7146 (mmm160) cc_final: 0.6817 (mmm160) REVERT: A 29 ARG cc_start: 0.8326 (mtm180) cc_final: 0.7867 (mtt90) REVERT: A 54 GLU cc_start: 0.7816 (tp30) cc_final: 0.7509 (tp30) REVERT: A 115 GLU cc_start: 0.7315 (tp30) cc_final: 0.6685 (mp0) REVERT: A 442 LYS cc_start: 0.7853 (ptpt) cc_final: 0.6772 (pttt) REVERT: A 443 ASP cc_start: 0.8168 (m-30) cc_final: 0.7592 (p0) REVERT: A 447 LYS cc_start: 0.7784 (ttmt) cc_final: 0.7145 (ttpp) REVERT: A 501 THR cc_start: 0.8306 (m) cc_final: 0.7833 (p) REVERT: A 588 GLU cc_start: 0.7740 (pt0) cc_final: 0.7355 (pt0) REVERT: A 606 LYS cc_start: 0.7645 (mmtt) cc_final: 0.7218 (mtpt) REVERT: A 612 LYS cc_start: 0.7455 (mttt) cc_final: 0.7048 (tppt) REVERT: A 624 SER cc_start: 0.8841 (p) cc_final: 0.8506 (p) REVERT: A 903 TYR cc_start: 0.6882 (m-80) cc_final: 0.6279 (m-80) REVERT: A 1046 GLU cc_start: 0.7683 (tp30) cc_final: 0.7482 (mm-30) REVERT: A 1065 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8050 (mp) REVERT: A 1325 ARG cc_start: 0.7043 (ttm-80) cc_final: 0.6763 (tpp-160) REVERT: A 1341 ASP cc_start: 0.8312 (t0) cc_final: 0.7796 (t0) REVERT: A 1448 LYS cc_start: 0.7469 (ptpp) cc_final: 0.7033 (ptpt) outliers start: 18 outliers final: 6 residues processed: 170 average time/residue: 1.4811 time to fit residues: 266.5150 Evaluate side-chains 101 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1272 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 0.0070 chunk 47 optimal weight: 5.9990 chunk 91 optimal weight: 0.0370 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- 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: 0.8283 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9786 Z= 0.136 Angle : 0.498 9.559 13275 Z= 0.257 Chirality : 0.039 0.153 1519 Planarity : 0.004 0.029 1604 Dihedral : 8.922 166.837 1490 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.30 % Favored : 98.61 % Rotamer: Outliers : 3.06 % Allowed : 10.67 % Favored : 86.26 % 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: 0.22 (0.24), residues: 1152 helix: 0.66 (0.19), residues: 721 sheet: -0.25 (0.59), residues: 81 loop : -0.61 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 865 HIS 0.004 0.001 HIS A 147 PHE 0.019 0.001 PHE A 630 TYR 0.010 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 142 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 111 time to evaluate : 1.154 Fit side-chains REVERT: A 3 ARG cc_start: 0.7163 (mmm160) cc_final: 0.6807 (mmm160) REVERT: A 29 ARG cc_start: 0.8328 (mtm180) cc_final: 0.7881 (mtt90) REVERT: A 54 GLU cc_start: 0.7596 (tp30) cc_final: 0.7322 (tp30) REVERT: A 58 ASP cc_start: 0.7850 (m-30) cc_final: 0.7570 (m-30) REVERT: A 115 GLU cc_start: 0.7275 (tp30) cc_final: 0.6689 (mp0) REVERT: A 175 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7377 (mp) REVERT: A 442 LYS cc_start: 0.7875 (ptpt) cc_final: 0.6817 (pttt) REVERT: A 443 ASP cc_start: 0.8189 (m-30) cc_final: 0.7649 (p0) REVERT: A 447 LYS cc_start: 0.7820 (ttmt) cc_final: 0.7521 (ttpp) REVERT: A 606 LYS cc_start: 0.7727 (mmtt) cc_final: 0.7305 (mtpt) REVERT: A 612 LYS cc_start: 0.7492 (mttt) cc_final: 0.7074 (tppt) REVERT: A 903 TYR cc_start: 0.6828 (m-80) cc_final: 0.6203 (m-80) REVERT: A 1046 GLU cc_start: 0.7656 (tp30) cc_final: 0.6989 (mp0) REVERT: A 1065 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7834 (mp) REVERT: A 1157 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8517 (mmm) REVERT: A 1288 VAL cc_start: 0.8903 (t) cc_final: 0.8649 (m) REVERT: A 1341 ASP cc_start: 0.8304 (t0) cc_final: 0.7751 (t0) REVERT: A 1390 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.6866 (mt0) REVERT: A 1448 LYS cc_start: 0.7425 (ptpp) cc_final: 0.6930 (ptpt) outliers start: 31 outliers final: 9 residues processed: 133 average time/residue: 1.2390 time to fit residues: 176.7660 Evaluate side-chains 107 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 932 PHE Chi-restraints excluded: chain A residue 1012 GLN Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1157 MET Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1171 THR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1273 SER Chi-restraints excluded: chain A residue 1390 GLN 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: 0.5980 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 114 optimal weight: 0.0040 chunk 94 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A1054 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9786 Z= 0.173 Angle : 0.476 9.122 13275 Z= 0.243 Chirality : 0.039 0.147 1519 Planarity : 0.003 0.040 1604 Dihedral : 8.593 163.536 1483 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.48 % Favored : 98.44 % Rotamer: Outliers : 3.26 % Allowed : 12.85 % Favored : 83.89 % 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: 0.62 (0.25), residues: 1152 helix: 1.06 (0.20), residues: 722 sheet: -0.30 (0.57), residues: 86 loop : -0.64 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 127 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 94 time to evaluate : 1.102 Fit side-chains REVERT: A 3 ARG cc_start: 0.7205 (mmm160) cc_final: 0.6838 (mmm160) REVERT: A 29 ARG cc_start: 0.8326 (mtm180) cc_final: 0.7872 (mtt90) REVERT: A 54 GLU cc_start: 0.7612 (tp30) cc_final: 0.7386 (tp30) REVERT: A 115 GLU cc_start: 0.7315 (tp30) cc_final: 0.6778 (mp0) REVERT: A 265 MET cc_start: 0.8469 (ptp) cc_final: 0.8251 (ttm) REVERT: A 442 LYS cc_start: 0.7907 (ptpt) cc_final: 0.6849 (pttt) REVERT: A 443 ASP cc_start: 0.8261 (m-30) cc_final: 0.7652 (p0) REVERT: A 447 LYS cc_start: 0.8005 (ttmt) cc_final: 0.7523 (ttpp) REVERT: A 535 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6650 (pm20) REVERT: A 606 LYS cc_start: 0.7787 (mmtt) cc_final: 0.7375 (mtpt) REVERT: A 612 LYS cc_start: 0.7506 (mttt) cc_final: 0.7094 (tppt) REVERT: A 903 TYR cc_start: 0.6894 (m-80) cc_final: 0.6246 (m-80) REVERT: A 1065 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7904 (mp) REVERT: A 1288 VAL cc_start: 0.8924 (t) cc_final: 0.8668 (m) REVERT: A 1341 ASP cc_start: 0.8360 (t0) cc_final: 0.7777 (t0) REVERT: A 1420 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6724 (mppt) REVERT: A 1448 LYS cc_start: 0.7435 (ptpp) cc_final: 0.6921 (ptpt) outliers start: 33 outliers final: 13 residues processed: 120 average time/residue: 1.2219 time to fit residues: 157.7343 Evaluate side-chains 105 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 932 PHE Chi-restraints excluded: chain A residue 955 SER Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1420 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 0.2980 chunk 55 optimal weight: 0.0370 chunk 11 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A 609 HIS A1054 HIS A1428 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2325 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= 0.159 Angle : 0.460 9.483 13275 Z= 0.235 Chirality : 0.038 0.143 1519 Planarity : 0.003 0.042 1604 Dihedral : 8.432 163.317 1483 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.65 % Favored : 98.26 % Rotamer: Outliers : 2.77 % Allowed : 14.13 % Favored : 83.10 % 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 (0.25), residues: 1152 helix: 1.21 (0.20), residues: 719 sheet: -0.23 (0.57), residues: 86 loop : -0.66 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 865 HIS 0.003 0.000 HIS A 147 PHE 0.010 0.001 PHE A 81 TYR 0.009 0.001 TYR A 304 ARG 0.007 0.000 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 125 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 97 time to evaluate : 1.017 Fit side-chains REVERT: A 3 ARG cc_start: 0.7238 (mmm160) cc_final: 0.6871 (mmm160) REVERT: A 29 ARG cc_start: 0.8337 (mtm180) cc_final: 0.7875 (mtt90) REVERT: A 54 GLU cc_start: 0.7641 (tp30) cc_final: 0.7399 (tp30) REVERT: A 115 GLU cc_start: 0.7324 (tp30) cc_final: 0.6789 (mp0) REVERT: A 265 MET cc_start: 0.8470 (ptp) cc_final: 0.8237 (ttm) REVERT: A 301 TYR cc_start: 0.8211 (m-10) cc_final: 0.7045 (m-10) REVERT: A 442 LYS cc_start: 0.7885 (ptpt) cc_final: 0.6825 (pttt) REVERT: A 443 ASP cc_start: 0.8299 (m-30) cc_final: 0.7645 (p0) REVERT: A 447 LYS cc_start: 0.8025 (ttmt) cc_final: 0.7473 (ttpp) REVERT: A 535 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6679 (pm20) REVERT: A 606 LYS cc_start: 0.7809 (mmtt) cc_final: 0.7391 (mtpt) REVERT: A 612 LYS cc_start: 0.7576 (mttt) cc_final: 0.7100 (tppt) REVERT: A 903 TYR cc_start: 0.6934 (m-80) cc_final: 0.6294 (m-80) REVERT: A 1046 GLU cc_start: 0.7746 (tp30) cc_final: 0.7281 (mp0) REVERT: A 1065 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7929 (mp) REVERT: A 1203 ILE cc_start: 0.6058 (OUTLIER) cc_final: 0.5799 (pp) REVERT: A 1288 VAL cc_start: 0.8941 (t) cc_final: 0.8683 (m) REVERT: A 1341 ASP cc_start: 0.8347 (t0) cc_final: 0.7749 (t0) REVERT: A 1390 GLN cc_start: 0.7073 (OUTLIER) cc_final: 0.6840 (mt0) REVERT: A 1429 LYS cc_start: 0.8166 (tptp) cc_final: 0.7949 (tmtm) REVERT: A 1448 LYS cc_start: 0.7519 (ptpp) cc_final: 0.6992 (ptpt) outliers start: 28 outliers final: 12 residues processed: 118 average time/residue: 1.2023 time to fit residues: 152.2067 Evaluate side-chains 105 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 932 PHE Chi-restraints excluded: chain A residue 955 SER Chi-restraints excluded: chain A residue 1042 GLN Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1390 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 0.0070 chunk 1 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1054 HIS A1428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9786 Z= 0.173 Angle : 0.464 9.345 13275 Z= 0.238 Chirality : 0.038 0.143 1519 Planarity : 0.003 0.045 1604 Dihedral : 8.386 162.538 1483 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.36 % Allowed : 13.64 % Favored : 83.00 % 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 (0.25), residues: 1152 helix: 1.23 (0.20), residues: 720 sheet: -0.26 (0.56), residues: 86 loop : -0.69 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 865 HIS 0.003 0.001 HIS A 147 PHE 0.011 0.001 PHE A 81 TYR 0.009 0.001 TYR A 304 ARG 0.011 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 126 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 92 time to evaluate : 1.038 Fit side-chains REVERT: A 3 ARG cc_start: 0.7227 (mmm160) cc_final: 0.6853 (mmm160) REVERT: A 29 ARG cc_start: 0.8320 (mtm180) cc_final: 0.7893 (mtt90) REVERT: A 54 GLU cc_start: 0.7645 (tp30) cc_final: 0.7394 (tp30) REVERT: A 115 GLU cc_start: 0.7354 (tp30) cc_final: 0.6821 (mp0) REVERT: A 195 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8943 (mp) REVERT: A 242 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7520 (mtp-110) REVERT: A 301 TYR cc_start: 0.8245 (m-10) cc_final: 0.7069 (m-10) REVERT: A 375 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8176 (mp) REVERT: A 442 LYS cc_start: 0.7915 (ptpt) cc_final: 0.6841 (pttt) REVERT: A 443 ASP cc_start: 0.8365 (m-30) cc_final: 0.7650 (p0) REVERT: A 447 LYS cc_start: 0.8104 (ttmt) cc_final: 0.7488 (ttpp) REVERT: A 494 PHE cc_start: 0.7328 (t80) cc_final: 0.7000 (t80) REVERT: A 501 THR cc_start: 0.7765 (OUTLIER) cc_final: 0.7207 (p) REVERT: A 535 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6691 (pm20) REVERT: A 606 LYS cc_start: 0.7834 (mmtt) cc_final: 0.7393 (mtpt) REVERT: A 612 LYS cc_start: 0.7591 (mttt) cc_final: 0.7098 (tppt) REVERT: A 903 TYR cc_start: 0.6964 (m-80) cc_final: 0.6336 (m-80) REVERT: A 1046 GLU cc_start: 0.7725 (tp30) cc_final: 0.7220 (mp0) REVERT: A 1065 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7954 (mp) REVERT: A 1203 ILE cc_start: 0.5774 (OUTLIER) cc_final: 0.5466 (pp) REVERT: A 1288 VAL cc_start: 0.8950 (t) cc_final: 0.8680 (m) REVERT: A 1341 ASP cc_start: 0.8351 (t0) cc_final: 0.7751 (t0) REVERT: A 1390 GLN cc_start: 0.7129 (OUTLIER) cc_final: 0.6893 (mt0) REVERT: A 1448 LYS cc_start: 0.7533 (ptpp) cc_final: 0.7005 (ptpt) outliers start: 34 outliers final: 16 residues processed: 119 average time/residue: 1.3410 time to fit residues: 170.5808 Evaluate side-chains 113 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 89 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 932 PHE Chi-restraints excluded: chain A residue 955 SER Chi-restraints excluded: chain A residue 1042 GLN Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1171 THR Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1390 GLN 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: 2.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 0.0970 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9786 Z= 0.223 Angle : 0.495 9.306 13275 Z= 0.254 Chirality : 0.040 0.143 1519 Planarity : 0.003 0.048 1604 Dihedral : 8.550 159.724 1483 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.66 % Allowed : 13.83 % Favored : 82.51 % 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: 0.61 (0.25), residues: 1152 helix: 1.11 (0.20), residues: 720 sheet: -0.35 (0.55), residues: 86 loop : -0.77 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1274 HIS 0.004 0.001 HIS A 147 PHE 0.011 0.001 PHE A 81 TYR 0.010 0.001 TYR A 304 ARG 0.008 0.000 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 128 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 91 time to evaluate : 1.226 Fit side-chains REVERT: A 3 ARG cc_start: 0.7211 (mmm160) cc_final: 0.6859 (mmm160) REVERT: A 29 ARG cc_start: 0.8347 (mtm180) cc_final: 0.7916 (mtt90) REVERT: A 54 GLU cc_start: 0.7636 (tp30) cc_final: 0.7375 (tp30) REVERT: A 115 GLU cc_start: 0.7369 (tp30) cc_final: 0.6837 (mp0) REVERT: A 195 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8973 (mp) REVERT: A 242 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7590 (mtp-110) REVERT: A 265 MET cc_start: 0.8484 (ptp) cc_final: 0.8255 (ttm) REVERT: A 375 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8222 (mp) REVERT: A 402 GLU cc_start: 0.4181 (pt0) cc_final: 0.3930 (pt0) REVERT: A 442 LYS cc_start: 0.7933 (ptpt) cc_final: 0.6865 (pttt) REVERT: A 443 ASP cc_start: 0.8368 (m-30) cc_final: 0.7580 (p0) REVERT: A 447 LYS cc_start: 0.8095 (ttmt) cc_final: 0.7444 (ttpp) REVERT: A 494 PHE cc_start: 0.7351 (t80) cc_final: 0.6969 (t80) REVERT: A 501 THR cc_start: 0.7877 (OUTLIER) cc_final: 0.7298 (p) REVERT: A 535 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6707 (pm20) REVERT: A 606 LYS cc_start: 0.7846 (mmtt) cc_final: 0.7396 (mtpt) REVERT: A 612 LYS cc_start: 0.7583 (mttt) cc_final: 0.7103 (tppt) REVERT: A 903 TYR cc_start: 0.6985 (m-80) cc_final: 0.6351 (m-80) REVERT: A 1046 GLU cc_start: 0.7733 (tp30) cc_final: 0.7253 (mp0) REVERT: A 1065 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7986 (mp) REVERT: A 1203 ILE cc_start: 0.5884 (OUTLIER) cc_final: 0.5598 (pp) REVERT: A 1288 VAL cc_start: 0.8957 (t) cc_final: 0.8680 (m) REVERT: A 1341 ASP cc_start: 0.8332 (t0) cc_final: 0.7715 (t0) REVERT: A 1390 GLN cc_start: 0.7197 (OUTLIER) cc_final: 0.6908 (mt0) REVERT: A 1428 GLN cc_start: 0.7144 (pm20) cc_final: 0.6755 (mp10) REVERT: A 1429 LYS cc_start: 0.7996 (tptp) cc_final: 0.7724 (tptp) REVERT: A 1448 LYS cc_start: 0.7552 (ptpp) cc_final: 0.7020 (ptpt) outliers start: 37 outliers final: 18 residues processed: 120 average time/residue: 1.6249 time to fit residues: 208.7575 Evaluate side-chains 114 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 88 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 932 PHE Chi-restraints excluded: chain A residue 955 SER Chi-restraints excluded: chain A residue 1042 GLN Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1171 THR Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1390 GLN 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: 5.9990 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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: 0.8369 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9786 Z= 0.238 Angle : 0.503 9.283 13275 Z= 0.257 Chirality : 0.040 0.143 1519 Planarity : 0.003 0.048 1604 Dihedral : 8.555 156.493 1483 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.82 % Favored : 98.09 % Rotamer: Outliers : 3.85 % Allowed : 14.23 % Favored : 81.92 % 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: 1.07 (0.20), residues: 717 sheet: -0.37 (0.55), residues: 86 loop : -0.85 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 865 HIS 0.004 0.001 HIS A 147 PHE 0.011 0.001 PHE A 81 TYR 0.010 0.001 TYR A 304 ARG 0.009 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 128 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 89 time to evaluate : 1.028 Fit side-chains REVERT: A 3 ARG cc_start: 0.7244 (mmm160) cc_final: 0.6893 (mmm160) REVERT: A 29 ARG cc_start: 0.8355 (mtm180) cc_final: 0.7943 (mtt90) REVERT: A 54 GLU cc_start: 0.7650 (tp30) cc_final: 0.7385 (tp30) REVERT: A 115 GLU cc_start: 0.7370 (tp30) cc_final: 0.6826 (mp0) REVERT: A 195 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8974 (mp) REVERT: A 242 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7577 (mtp-110) REVERT: A 265 MET cc_start: 0.8498 (ptp) cc_final: 0.8228 (ttm) REVERT: A 375 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8233 (mp) REVERT: A 402 GLU cc_start: 0.4183 (pt0) cc_final: 0.3872 (pt0) REVERT: A 442 LYS cc_start: 0.7931 (ptpt) cc_final: 0.6868 (pttt) REVERT: A 443 ASP cc_start: 0.8385 (m-30) cc_final: 0.7577 (p0) REVERT: A 447 LYS cc_start: 0.8117 (ttmt) cc_final: 0.7471 (ttpp) REVERT: A 494 PHE cc_start: 0.7348 (t80) cc_final: 0.6977 (t80) REVERT: A 501 THR cc_start: 0.7933 (OUTLIER) cc_final: 0.7364 (p) REVERT: A 535 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6738 (pm20) REVERT: A 606 LYS cc_start: 0.7840 (mmtt) cc_final: 0.7409 (mtpt) REVERT: A 612 LYS cc_start: 0.7586 (mttt) cc_final: 0.7106 (tppt) REVERT: A 903 TYR cc_start: 0.6937 (m-80) cc_final: 0.6309 (m-80) REVERT: A 1046 GLU cc_start: 0.7718 (tp30) cc_final: 0.7246 (mp0) REVERT: A 1065 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8016 (mp) REVERT: A 1203 ILE cc_start: 0.6113 (OUTLIER) cc_final: 0.5782 (pp) REVERT: A 1341 ASP cc_start: 0.8331 (t0) cc_final: 0.7701 (t0) REVERT: A 1390 GLN cc_start: 0.7255 (OUTLIER) cc_final: 0.6913 (mt0) REVERT: A 1428 GLN cc_start: 0.7199 (pm20) cc_final: 0.6748 (mp10) REVERT: A 1429 LYS cc_start: 0.8043 (tptp) cc_final: 0.7779 (tptp) REVERT: A 1448 LYS cc_start: 0.7559 (ptpp) cc_final: 0.7033 (ptpt) outliers start: 39 outliers final: 21 residues processed: 118 average time/residue: 1.4121 time to fit residues: 177.6448 Evaluate side-chains 118 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 89 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 932 PHE Chi-restraints excluded: chain A residue 955 SER Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 1012 GLN Chi-restraints excluded: chain A residue 1042 GLN Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1171 THR Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1390 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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: 0.8349 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9786 Z= 0.192 Angle : 0.478 9.353 13275 Z= 0.245 Chirality : 0.039 0.138 1519 Planarity : 0.003 0.048 1604 Dihedral : 8.418 156.727 1483 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.16 % Allowed : 15.12 % 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: 0.63 (0.25), residues: 1152 helix: 1.14 (0.20), residues: 719 sheet: -0.31 (0.55), residues: 86 loop : -0.81 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 865 HIS 0.003 0.001 HIS A 147 PHE 0.010 0.001 PHE A 81 TYR 0.009 0.001 TYR A 304 ARG 0.009 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 119 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 87 time to evaluate : 1.213 Fit side-chains REVERT: A 3 ARG cc_start: 0.7275 (mmm160) cc_final: 0.6891 (mmm160) REVERT: A 29 ARG cc_start: 0.8354 (mtm180) cc_final: 0.7958 (mtt90) REVERT: A 54 GLU cc_start: 0.7630 (tp30) cc_final: 0.7378 (tp30) REVERT: A 115 GLU cc_start: 0.7340 (tp30) cc_final: 0.6818 (mp0) REVERT: A 170 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7500 (mtt90) REVERT: A 195 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8972 (mp) REVERT: A 242 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7559 (mtp-110) REVERT: A 265 MET cc_start: 0.8471 (ptp) cc_final: 0.8194 (ttm) REVERT: A 301 TYR cc_start: 0.8266 (m-10) cc_final: 0.7033 (m-10) REVERT: A 375 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8150 (mp) REVERT: A 402 GLU cc_start: 0.4420 (pt0) cc_final: 0.4168 (pt0) REVERT: A 442 LYS cc_start: 0.7925 (ptpt) cc_final: 0.6866 (pttt) REVERT: A 443 ASP cc_start: 0.8385 (m-30) cc_final: 0.7589 (p0) REVERT: A 447 LYS cc_start: 0.8111 (ttmt) cc_final: 0.7443 (ttpp) REVERT: A 494 PHE cc_start: 0.7337 (t80) cc_final: 0.6966 (t80) REVERT: A 501 THR cc_start: 0.7839 (OUTLIER) cc_final: 0.7261 (p) REVERT: A 535 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6732 (pm20) REVERT: A 606 LYS cc_start: 0.7844 (mmtt) cc_final: 0.7416 (mtpt) REVERT: A 612 LYS cc_start: 0.7574 (mttt) cc_final: 0.7081 (tppt) REVERT: A 903 TYR cc_start: 0.6925 (m-80) cc_final: 0.6303 (m-80) REVERT: A 1046 GLU cc_start: 0.7691 (tp30) cc_final: 0.7188 (mp0) REVERT: A 1203 ILE cc_start: 0.5945 (OUTLIER) cc_final: 0.5619 (pp) REVERT: A 1420 LYS cc_start: 0.7295 (OUTLIER) cc_final: 0.6585 (mppt) REVERT: A 1428 GLN cc_start: 0.7239 (pm20) cc_final: 0.6780 (mp10) REVERT: A 1448 LYS cc_start: 0.7543 (ptpp) cc_final: 0.7014 (ptpt) outliers start: 32 outliers final: 19 residues processed: 113 average time/residue: 1.3855 time to fit residues: 166.9758 Evaluate side-chains 113 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 86 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 932 PHE Chi-restraints excluded: chain A residue 955 SER Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 1042 GLN Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1420 LYS 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: 5.9990 chunk 108 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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: 0.8325 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9786 Z= 0.158 Angle : 0.460 9.474 13275 Z= 0.235 Chirality : 0.038 0.136 1519 Planarity : 0.003 0.044 1604 Dihedral : 8.223 157.884 1483 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.77 % Allowed : 15.71 % Favored : 81.52 % 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: 0.80 (0.25), residues: 1152 helix: 1.30 (0.20), residues: 717 sheet: -0.20 (0.56), residues: 86 loop : -0.80 (0.31), residues: 349 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 0.009 0.001 PHE A 81 TYR 0.009 0.001 TYR A 304 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 117 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 89 time to evaluate : 1.143 Fit side-chains REVERT: A 3 ARG cc_start: 0.7277 (mmm160) cc_final: 0.6896 (mmm160) REVERT: A 29 ARG cc_start: 0.8332 (mtm180) cc_final: 0.7951 (mtt90) REVERT: A 54 GLU cc_start: 0.7623 (tp30) cc_final: 0.7374 (tp30) REVERT: A 115 GLU cc_start: 0.7296 (tp30) cc_final: 0.6793 (mp0) REVERT: A 170 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7443 (mtt90) REVERT: A 242 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7507 (mtp-110) REVERT: A 265 MET cc_start: 0.8435 (ptp) cc_final: 0.8199 (ttm) REVERT: A 301 TYR cc_start: 0.8197 (m-10) cc_final: 0.6975 (m-10) REVERT: A 375 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8095 (mp) REVERT: A 442 LYS cc_start: 0.7905 (ptpt) cc_final: 0.6851 (pttt) REVERT: A 443 ASP cc_start: 0.8373 (m-30) cc_final: 0.7584 (p0) REVERT: A 447 LYS cc_start: 0.8114 (ttmt) cc_final: 0.7492 (ttpp) REVERT: A 494 PHE cc_start: 0.7342 (t80) cc_final: 0.6981 (t80) REVERT: A 501 THR cc_start: 0.7784 (OUTLIER) cc_final: 0.7193 (p) REVERT: A 535 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6704 (pm20) REVERT: A 606 LYS cc_start: 0.7838 (mmtt) cc_final: 0.7406 (mtpt) REVERT: A 612 LYS cc_start: 0.7584 (mttt) cc_final: 0.7085 (tppt) REVERT: A 903 TYR cc_start: 0.6969 (m-80) cc_final: 0.6338 (m-80) REVERT: A 1046 GLU cc_start: 0.7658 (tp30) cc_final: 0.7107 (mp0) REVERT: A 1203 ILE cc_start: 0.5794 (OUTLIER) cc_final: 0.5446 (pp) REVERT: A 1288 VAL cc_start: 0.8984 (t) cc_final: 0.8720 (m) REVERT: A 1420 LYS cc_start: 0.7282 (OUTLIER) cc_final: 0.6647 (mppt) REVERT: A 1428 GLN cc_start: 0.7261 (pm20) cc_final: 0.6758 (mp10) REVERT: A 1429 LYS cc_start: 0.8100 (tptp) cc_final: 0.7861 (tptp) REVERT: A 1448 LYS cc_start: 0.7530 (ptpp) cc_final: 0.6992 (ptpt) outliers start: 28 outliers final: 17 residues processed: 111 average time/residue: 1.4102 time to fit residues: 166.9851 Evaluate side-chains 112 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 88 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 932 PHE Chi-restraints excluded: chain A residue 955 SER Chi-restraints excluded: chain A residue 1012 GLN Chi-restraints excluded: chain A residue 1042 GLN Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1420 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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: 0.8399 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9786 Z= 0.331 Angle : 0.561 9.075 13275 Z= 0.286 Chirality : 0.042 0.149 1519 Planarity : 0.004 0.055 1604 Dihedral : 8.706 147.662 1483 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.96 % Allowed : 15.51 % Favored : 81.52 % 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: 0.35 (0.24), residues: 1152 helix: 0.97 (0.20), residues: 711 sheet: -0.42 (0.54), residues: 86 loop : -0.98 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 865 HIS 0.005 0.001 HIS A 147 PHE 0.011 0.002 PHE A 446 TYR 0.010 0.002 TYR A 304 ARG 0.010 0.001 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 118 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 88 time to evaluate : 1.153 Fit side-chains REVERT: A 3 ARG cc_start: 0.7303 (mmm160) cc_final: 0.6938 (mmm160) REVERT: A 29 ARG cc_start: 0.8341 (mtm180) cc_final: 0.7962 (mtt90) REVERT: A 54 GLU cc_start: 0.7663 (tp30) cc_final: 0.7424 (tp30) REVERT: A 115 GLU cc_start: 0.7369 (tp30) cc_final: 0.6812 (mp0) REVERT: A 170 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7528 (mtt90) REVERT: A 195 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8969 (mp) REVERT: A 242 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7619 (mtp-110) REVERT: A 265 MET cc_start: 0.8523 (ptp) cc_final: 0.8237 (ttm) REVERT: A 375 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8261 (mp) REVERT: A 442 LYS cc_start: 0.7944 (ptpt) cc_final: 0.6898 (pttt) REVERT: A 443 ASP cc_start: 0.8437 (m-30) cc_final: 0.7534 (p0) REVERT: A 447 LYS cc_start: 0.8078 (ttmt) cc_final: 0.7459 (ttpp) REVERT: A 494 PHE cc_start: 0.7362 (t80) cc_final: 0.7000 (t80) REVERT: A 501 THR cc_start: 0.8116 (OUTLIER) cc_final: 0.7524 (p) REVERT: A 535 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6792 (pm20) REVERT: A 606 LYS cc_start: 0.7820 (mmtt) cc_final: 0.7402 (mtpt) REVERT: A 612 LYS cc_start: 0.7586 (mttt) cc_final: 0.7104 (tppt) REVERT: A 903 TYR cc_start: 0.6929 (m-80) cc_final: 0.6331 (m-80) REVERT: A 1019 THR cc_start: 0.8589 (t) cc_final: 0.8271 (t) REVERT: A 1046 GLU cc_start: 0.7709 (tp30) cc_final: 0.7265 (mp0) REVERT: A 1065 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8063 (mp) REVERT: A 1203 ILE cc_start: 0.5911 (OUTLIER) cc_final: 0.5599 (pp) REVERT: A 1341 ASP cc_start: 0.8350 (t0) cc_final: 0.7699 (t0) REVERT: A 1420 LYS cc_start: 0.7409 (OUTLIER) cc_final: 0.6697 (mppt) REVERT: A 1428 GLN cc_start: 0.7243 (pm20) cc_final: 0.6743 (mp10) REVERT: A 1429 LYS cc_start: 0.8088 (tptp) cc_final: 0.7823 (tptp) REVERT: A 1448 LYS cc_start: 0.7529 (ptpp) cc_final: 0.7012 (ptpt) outliers start: 30 outliers final: 19 residues processed: 112 average time/residue: 1.4124 time to fit residues: 168.6131 Evaluate side-chains 115 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 87 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 932 PHE Chi-restraints excluded: chain A residue 955 SER Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 1042 GLN Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1171 THR Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1420 LYS Chi-restraints excluded: chain A residue 1425 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 25 optimal weight: 0.0970 chunk 92 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 95 optimal weight: 0.0970 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.120470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.096610 restraints weight = 12640.574| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.94 r_work: 0.2945 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2847 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= 0.120 Angle : 0.442 9.683 13275 Z= 0.227 Chirality : 0.037 0.130 1519 Planarity : 0.003 0.041 1604 Dihedral : 8.178 156.472 1483 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.17 % Allowed : 16.50 % Favored : 81.32 % 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 (0.25), residues: 1152 helix: 1.38 (0.20), residues: 715 sheet: -0.11 (0.56), residues: 86 loop : -0.84 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 865 HIS 0.002 0.000 HIS A 199 PHE 0.007 0.001 PHE A1107 TYR 0.012 0.001 TYR A 512 ARG 0.010 0.000 ARG A1239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3604.01 seconds wall clock time: 64 minutes 28.02 seconds (3868.02 seconds total)