Starting phenix.real_space_refine on Mon Mar 18 21:06:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jy4_36719/03_2024/8jy4_36719.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jy4_36719/03_2024/8jy4_36719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jy4_36719/03_2024/8jy4_36719.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jy4_36719/03_2024/8jy4_36719.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jy4_36719/03_2024/8jy4_36719.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jy4_36719/03_2024/8jy4_36719.pdb" } resolution = 3.58 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= 0.007 sd= 0.053 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: 5 Type Number sf(0) Gaussians S 57 5.16 5 C 7139 2.51 5 N 1820 2.21 5 O 1978 1.98 5 H 11252 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 3": "OE1" <-> "OE2" Residue "A ASP 22": "OD1" <-> "OD2" Residue "A TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A ASP 210": "OD1" <-> "OD2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 496": "OD1" <-> "OD2" Residue "A GLU 504": "OE1" <-> "OE2" Residue "A GLU 518": "OE1" <-> "OE2" Residue "A PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 620": "OD1" <-> "OD2" Residue "A ASP 630": "OD1" <-> "OD2" Residue "A ASP 634": "OD1" <-> "OD2" Residue "A GLU 651": "OE1" <-> "OE2" Residue "A ASP 656": "OD1" <-> "OD2" Residue "A TYR 703": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 735": "OE1" <-> "OE2" Residue "A ASP 750": "OD1" <-> "OD2" Residue "A PHE 824": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 829": "OD1" <-> "OD2" Residue "A GLU 830": "OE1" <-> "OE2" Residue "A TYR 845": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1006": "OD1" <-> "OD2" Residue "A PHE 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1039": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1093": "OD1" <-> "OD2" Residue "A TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1275": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1279": "OE1" <-> "OE2" Residue "A TYR 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1352": "OE1" <-> "OE2" Residue "A GLU 1375": "OE1" <-> "OE2" Residue "A ASP 1383": "OD1" <-> "OD2" Residue "A TYR 1401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1404": "OE1" <-> "OE2" Residue "A GLU 1470": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22246 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 22246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1383, 22246 Classifications: {'peptide': 1383} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 1339} Chain breaks: 3 Time building chain proxies: 9.12, per 1000 atoms: 0.41 Number of scatterers: 22246 At special positions: 0 Unit cell: (104.86, 128.4, 146.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 O 1978 8.00 N 1820 7.00 C 7139 6.00 H 11252 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 26 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.94 Conformation dependent library (CDL) restraints added in 2.2 seconds 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2618 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 6 sheets defined 70.4% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 12 through 17 removed outlier: 3.606A pdb=" N ASP A 17 " --> pdb=" O SER A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 31 Processing helix chain 'A' and resid 33 through 44 Processing helix chain 'A' and resid 45 through 54 removed outlier: 4.583A pdb=" N VAL A 51 " --> pdb=" O GLN A 47 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER A 54 " --> pdb=" O HIS A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 88 removed outlier: 3.609A pdb=" N LEU A 66 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 121 removed outlier: 3.690A pdb=" N TYR A 101 " --> pdb=" O PRO A 97 " (cutoff:3.500A) Proline residue: A 104 - end of helix Processing helix chain 'A' and resid 129 through 157 removed outlier: 3.549A pdb=" N ILE A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLN A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 184 removed outlier: 3.651A pdb=" N LEU A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.831A pdb=" N THR A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 222 through 226 removed outlier: 3.514A pdb=" N VAL A 226 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 266 removed outlier: 3.609A pdb=" N HIS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 334 removed outlier: 7.335A pdb=" N MET A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A 321 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER A 325 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU A 328 " --> pdb=" O LYS A 324 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 351 removed outlier: 3.823A pdb=" N GLN A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 405 removed outlier: 3.875A pdb=" N GLY A 360 " --> pdb=" O TYR A 356 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR A 381 " --> pdb=" O CYS A 377 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A 384 " --> pdb=" O CYS A 380 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY A 389 " --> pdb=" O CYS A 385 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 395 " --> pdb=" O LYS A 391 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR A 401 " --> pdb=" O MET A 397 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 416 through 423 removed outlier: 3.674A pdb=" N ASN A 422 " --> pdb=" O GLY A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 437 removed outlier: 3.567A pdb=" N ASP A 433 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 441 Processing helix chain 'A' and resid 442 through 460 removed outlier: 3.584A pdb=" N GLU A 458 " --> pdb=" O PHE A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 508 removed outlier: 3.873A pdb=" N GLY A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) Proline residue: A 475 - end of helix removed outlier: 4.060A pdb=" N LYS A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASN A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER A 507 " --> pdb=" O ASN A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 515 removed outlier: 3.555A pdb=" N PHE A 515 " --> pdb=" O ILE A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 552 removed outlier: 3.699A pdb=" N PHE A 521 " --> pdb=" O TRP A 517 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN A 535 " --> pdb=" O LYS A 531 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA A 538 " --> pdb=" O LYS A 534 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 569 removed outlier: 3.668A pdb=" N SER A 558 " --> pdb=" O PRO A 554 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 559 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL A 566 " --> pdb=" O PHE A 562 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASP A 569 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 581 Processing helix chain 'A' and resid 582 through 618 removed outlier: 3.733A pdb=" N ASN A 587 " --> pdb=" O ILE A 583 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE A 591 " --> pdb=" O ASN A 587 " (cutoff:3.500A) Proline residue: A 592 - end of helix Proline residue: A 597 - end of helix removed outlier: 3.812A pdb=" N SER A 601 " --> pdb=" O PRO A 597 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER A 602 " --> pdb=" O MET A 598 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER A 607 " --> pdb=" O MET A 603 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL A 608 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 613 " --> pdb=" O SER A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 686 Processing helix chain 'A' and resid 714 through 721 Processing helix chain 'A' and resid 726 through 737 Processing helix chain 'A' and resid 738 through 746 removed outlier: 3.774A pdb=" N ASP A 742 " --> pdb=" O ALA A 738 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU A 744 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET A 745 " --> pdb=" O PRO A 741 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU A 746 " --> pdb=" O ASP A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 778 removed outlier: 3.673A pdb=" N ASN A 778 " --> pdb=" O ALA A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 803 Processing helix chain 'A' and resid 824 through 828 Processing helix chain 'A' and resid 848 through 852 removed outlier: 3.626A pdb=" N LYS A 851 " --> pdb=" O LEU A 848 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS A 852 " --> pdb=" O LEU A 849 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 848 through 852' Processing helix chain 'A' and resid 964 through 975 Processing helix chain 'A' and resid 975 through 1005 removed outlier: 3.619A pdb=" N PHE A 981 " --> pdb=" O PHE A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1009 Processing helix chain 'A' and resid 1016 through 1065 removed outlier: 3.800A pdb=" N GLN A1034 " --> pdb=" O LEU A1030 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY A1035 " --> pdb=" O GLY A1031 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA A1041 " --> pdb=" O PHE A1037 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TRP A1044 " --> pdb=" O ILE A1040 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS A1057 " --> pdb=" O SER A1053 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS A1058 " --> pdb=" O ASN A1054 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A1061 " --> pdb=" O HIS A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1075 removed outlier: 3.841A pdb=" N PHE A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1084 removed outlier: 3.966A pdb=" N ILE A1080 " --> pdb=" O PRO A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1094 removed outlier: 4.008A pdb=" N ASP A1092 " --> pdb=" O ILE A1088 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A1094 " --> pdb=" O THR A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1118 removed outlier: 4.102A pdb=" N SER A1101 " --> pdb=" O GLN A1097 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A1108 " --> pdb=" O THR A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1168 removed outlier: 4.021A pdb=" N ILE A1126 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE A1128 " --> pdb=" O THR A1124 " (cutoff:3.500A) Proline residue: A1129 - end of helix removed outlier: 3.748A pdb=" N PHE A1140 " --> pdb=" O SER A1136 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER A1143 " --> pdb=" O MET A1139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A1146 " --> pdb=" O VAL A1142 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLN A1147 " --> pdb=" O SER A1143 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A1157 " --> pdb=" O SER A1153 " (cutoff:3.500A) Proline residue: A1158 - end of helix Processing helix chain 'A' and resid 1169 through 1177 removed outlier: 3.667A pdb=" N ILE A1173 " --> pdb=" O GLY A1169 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A1175 " --> pdb=" O PRO A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1213 removed outlier: 3.732A pdb=" N VAL A1188 " --> pdb=" O LYS A1184 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG A1189 " --> pdb=" O HIS A1185 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR A1192 " --> pdb=" O VAL A1188 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN A1193 " --> pdb=" O ARG A1189 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N CYS A1196 " --> pdb=" O THR A1192 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER A1199 " --> pdb=" O LYS A1195 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A1203 " --> pdb=" O SER A1199 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A1207 " --> pdb=" O SER A1203 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA A1208 " --> pdb=" O ASN A1204 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG A1210 " --> pdb=" O TRP A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1229 removed outlier: 3.973A pdb=" N VAL A1219 " --> pdb=" O GLY A1215 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A1222 " --> pdb=" O THR A1218 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1246 removed outlier: 3.961A pdb=" N PHE A1240 " --> pdb=" O ASP A1236 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A1241 " --> pdb=" O THR A1237 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A1245 " --> pdb=" O VAL A1241 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A1246 " --> pdb=" O LEU A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1266 removed outlier: 3.976A pdb=" N ASN A1253 " --> pdb=" O THR A1249 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP A1254 " --> pdb=" O GLN A1250 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A1256 " --> pdb=" O LEU A1252 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A1259 " --> pdb=" O LEU A1255 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A1261 " --> pdb=" O ARG A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1277 removed outlier: 3.682A pdb=" N TYR A1275 " --> pdb=" O ARG A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1348 removed outlier: 3.590A pdb=" N THR A1344 " --> pdb=" O LYS A1340 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A1348 " --> pdb=" O THR A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1368 No H-bonds generated for 'chain 'A' and resid 1366 through 1368' Processing helix chain 'A' and resid 1369 through 1375 Processing helix chain 'A' and resid 1391 through 1396 Processing helix chain 'A' and resid 1402 through 1413 Processing helix chain 'A' and resid 1415 through 1422 Processing helix chain 'A' and resid 1424 through 1427 Processing helix chain 'A' and resid 1431 through 1435 Processing helix chain 'A' and resid 1438 through 1454 Processing helix chain 'A' and resid 1468 through 1483 Processing helix chain 'A' and resid 1494 through 1498 Processing helix chain 'A' and resid 1517 through 1524 Processing helix chain 'A' and resid 1526 through 1533 Processing sheet with id=AA1, first strand: chain 'A' and resid 627 through 629 removed outlier: 6.189A pdb=" N ARG A 628 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 654 through 657 removed outlier: 5.440A pdb=" N ALA A 642 " --> pdb=" O ASP A 656 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N SER A 643 " --> pdb=" O VAL A 691 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU A 689 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.176A pdb=" N ALA A 702 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU A 830 " --> pdb=" O LEU A 666 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1317 through 1324 removed outlier: 7.256A pdb=" N ARG A1318 " --> pdb=" O GLN A1306 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLN A1306 " --> pdb=" O ARG A1318 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE A1320 " --> pdb=" O ASN A1304 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N PHE A1302 " --> pdb=" O ILE A1359 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE A1359 " --> pdb=" O PHE A1302 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ASN A1304 " --> pdb=" O GLN A1357 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLN A1357 " --> pdb=" O ASN A1304 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1377 through 1380 removed outlier: 6.471A pdb=" N LYS A1329 " --> pdb=" O LYS A1503 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N MET A1505 " --> pdb=" O LYS A1329 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLY A1331 " --> pdb=" O MET A1505 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N LEU A1507 " --> pdb=" O GLY A1331 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL A1333 " --> pdb=" O LEU A1507 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU A1514 " --> pdb=" O VAL A1506 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASP A1508 " --> pdb=" O ILE A1512 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ILE A1512 " --> pdb=" O ASP A1508 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1389 through 1390 638 hydrogen bonds defined for protein. 1860 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: 8.38 Time building geometry restraints manager: 18.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11234 1.03 - 1.23: 19 1.23 - 1.42: 4631 1.42 - 1.62: 6502 1.62 - 1.81: 94 Bond restraints: 22480 Sorted by residual: bond pdb=" CA PHE A1084 " pdb=" CB PHE A1084 " ideal model delta sigma weight residual 1.528 1.545 -0.017 1.35e-02 5.49e+03 1.61e+00 bond pdb=" CA ASP A 786 " pdb=" CB ASP A 786 " ideal model delta sigma weight residual 1.522 1.530 -0.007 7.00e-03 2.04e+04 1.10e+00 bond pdb=" CA CYS A 142 " pdb=" C CYS A 142 " ideal model delta sigma weight residual 1.523 1.508 0.014 1.41e-02 5.03e+03 1.05e+00 bond pdb=" CA ASP A 786 " pdb=" C ASP A 786 " ideal model delta sigma weight residual 1.531 1.524 0.008 7.40e-03 1.83e+04 1.03e+00 bond pdb=" CB TRP A 46 " pdb=" CG TRP A 46 " ideal model delta sigma weight residual 1.498 1.528 -0.030 3.10e-02 1.04e+03 9.39e-01 ... (remaining 22475 not shown) Histogram of bond angle deviations from ideal: 100.48 - 107.22: 552 107.22 - 113.96: 27050 113.96 - 120.71: 7957 120.71 - 127.45: 5044 127.45 - 134.19: 117 Bond angle restraints: 40720 Sorted by residual: angle pdb=" N VAL A 840 " pdb=" CA VAL A 840 " pdb=" C VAL A 840 " ideal model delta sigma weight residual 111.62 109.07 2.55 7.90e-01 1.60e+00 1.05e+01 angle pdb=" N LYS A 757 " pdb=" CA LYS A 757 " pdb=" CB LYS A 757 " ideal model delta sigma weight residual 114.17 110.52 3.65 1.14e+00 7.69e-01 1.03e+01 angle pdb=" N ILE A1040 " pdb=" CA ILE A1040 " pdb=" C ILE A1040 " ideal model delta sigma weight residual 112.98 109.39 3.59 1.25e+00 6.40e-01 8.26e+00 angle pdb=" N PHE A1084 " pdb=" CA PHE A1084 " pdb=" C PHE A1084 " ideal model delta sigma weight residual 112.26 108.78 3.48 1.32e+00 5.74e-01 6.93e+00 angle pdb=" N PHE A1084 " pdb=" CA PHE A1084 " pdb=" CB PHE A1084 " ideal model delta sigma weight residual 111.17 106.88 4.29 1.64e+00 3.72e-01 6.84e+00 ... (remaining 40715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 9302 17.84 - 35.67: 902 35.67 - 53.51: 231 53.51 - 71.35: 60 71.35 - 89.19: 9 Dihedral angle restraints: 10504 sinusoidal: 5686 harmonic: 4818 Sorted by residual: dihedral pdb=" CB GLU A 647 " pdb=" CG GLU A 647 " pdb=" CD GLU A 647 " pdb=" OE1 GLU A 647 " ideal model delta sinusoidal sigma weight residual 0.00 -89.19 89.19 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU A 614 " pdb=" CG GLU A 614 " pdb=" CD GLU A 614 " pdb=" OE1 GLU A 614 " ideal model delta sinusoidal sigma weight residual 0.00 88.77 -88.77 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CA HIS A 823 " pdb=" C HIS A 823 " pdb=" N PHE A 824 " pdb=" CA PHE A 824 " ideal model delta harmonic sigma weight residual -180.00 -164.55 -15.45 0 5.00e+00 4.00e-02 9.55e+00 ... (remaining 10501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1142 0.028 - 0.055: 423 0.055 - 0.083: 135 0.083 - 0.111: 65 0.111 - 0.139: 19 Chirality restraints: 1784 Sorted by residual: chirality pdb=" CB ILE A 479 " pdb=" CA ILE A 479 " pdb=" CG1 ILE A 479 " pdb=" CG2 ILE A 479 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE A1524 " pdb=" N ILE A1524 " pdb=" C ILE A1524 " pdb=" CB ILE A1524 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE A 759 " pdb=" N ILE A 759 " pdb=" C ILE A 759 " pdb=" CB ILE A 759 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 1781 not shown) Planarity restraints: 3220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 746 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO A 747 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 747 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 747 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A1084 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C PHE A1084 " 0.033 2.00e-02 2.50e+03 pdb=" O PHE A1084 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA A1085 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A1157 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO A1158 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A1158 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1158 " -0.021 5.00e-02 4.00e+02 ... (remaining 3217 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1097 2.18 - 2.78: 45268 2.78 - 3.39: 62741 3.39 - 3.99: 77298 3.99 - 4.60: 121616 Nonbonded interactions: 308020 Sorted by model distance: nonbonded pdb=" O PHE A 800 " pdb=" H GLY A 805 " model vdw 1.573 1.850 nonbonded pdb=" OE1 GLN A 707 " pdb=" H GLN A 707 " model vdw 1.581 1.850 nonbonded pdb="HD21 ASN A 712 " pdb=" OE1 GLU A1165 " model vdw 1.590 1.850 nonbonded pdb=" O LEU A1211 " pdb=" H GLY A1215 " model vdw 1.610 1.850 nonbonded pdb=" O ALA A1002 " pdb="HH21 ARG A1023 " model vdw 1.649 1.850 ... (remaining 308015 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 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: 0.330 Extract box with map and model: 3.560 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 68.110 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 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 : 0.003 0.036 11228 Z= 0.186 Angle : 0.551 5.557 15225 Z= 0.320 Chirality : 0.037 0.139 1784 Planarity : 0.003 0.050 1887 Dihedral : 15.961 89.185 4073 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.98 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 20.77 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.52 (0.23), residues: 1375 helix: -0.21 (0.18), residues: 864 sheet: 0.29 (0.57), residues: 90 loop : -0.41 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 358 HIS 0.002 0.001 HIS A 692 PHE 0.009 0.001 PHE A1240 TYR 0.010 0.001 TYR A 206 ARG 0.004 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8348 (mm-30) REVERT: A 362 LEU cc_start: 0.9336 (tp) cc_final: 0.9121 (tt) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.4412 time to fit residues: 159.9845 Evaluate side-chains 178 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 55 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 80 optimal weight: 20.0000 chunk 125 optimal weight: 20.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 GLN ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1162 HIS ** A1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11228 Z= 0.330 Angle : 0.676 5.918 15225 Z= 0.380 Chirality : 0.040 0.135 1784 Planarity : 0.004 0.047 1887 Dihedral : 3.912 15.964 1474 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.64 % Favored : 96.29 % Rotamer: Outliers : 2.69 % Allowed : 21.82 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.50 (0.22), residues: 1375 helix: -0.18 (0.17), residues: 873 sheet: 0.31 (0.60), residues: 80 loop : -0.44 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 41 HIS 0.002 0.001 HIS A 694 PHE 0.014 0.001 PHE A1043 TYR 0.011 0.001 TYR A 101 ARG 0.004 0.000 ARG A1174 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 169 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 SER cc_start: 0.9271 (OUTLIER) cc_final: 0.9063 (p) REVERT: A 362 LEU cc_start: 0.9504 (tp) cc_final: 0.9225 (tt) outliers start: 33 outliers final: 24 residues processed: 188 average time/residue: 0.4387 time to fit residues: 125.7361 Evaluate side-chains 183 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 158 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 518 GLU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1157 SER Chi-restraints excluded: chain A residue 1222 SER Chi-restraints excluded: chain A residue 1327 MET Chi-restraints excluded: chain A residue 1445 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 125 optimal weight: 10.0000 chunk 135 optimal weight: 30.0000 chunk 111 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A1097 GLN A1162 HIS A1247 ASN ** A1382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11228 Z= 0.214 Angle : 0.597 8.409 15225 Z= 0.318 Chirality : 0.038 0.186 1784 Planarity : 0.004 0.042 1887 Dihedral : 3.836 15.570 1474 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.56 % Favored : 96.36 % Rotamer: Outliers : 2.52 % Allowed : 22.48 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.25 (0.22), residues: 1375 helix: 0.12 (0.17), residues: 877 sheet: 0.19 (0.59), residues: 80 loop : -0.57 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 41 HIS 0.002 0.001 HIS A1496 PHE 0.012 0.001 PHE A1043 TYR 0.011 0.001 TYR A 101 ARG 0.003 0.000 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 170 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.8874 (OUTLIER) cc_final: 0.8485 (m-10) REVERT: A 387 LYS cc_start: 0.9135 (mtpt) cc_final: 0.8874 (mtpp) outliers start: 31 outliers final: 20 residues processed: 193 average time/residue: 0.4019 time to fit residues: 120.8330 Evaluate side-chains 183 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 162 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1222 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 35 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1162 HIS ** A1382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11228 Z= 0.266 Angle : 0.601 6.430 15225 Z= 0.326 Chirality : 0.038 0.137 1784 Planarity : 0.004 0.042 1887 Dihedral : 3.820 16.290 1474 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.22 % Favored : 95.71 % Rotamer: Outliers : 3.09 % Allowed : 22.80 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.23 (0.22), residues: 1375 helix: 0.15 (0.17), residues: 886 sheet: 0.00 (0.58), residues: 80 loop : -0.57 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 41 HIS 0.002 0.001 HIS A1057 PHE 0.009 0.001 PHE A1043 TYR 0.012 0.001 TYR A 101 ARG 0.003 0.000 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 162 time to evaluate : 2.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.8903 (OUTLIER) cc_final: 0.8543 (m-10) REVERT: A 387 LYS cc_start: 0.9200 (mtpt) cc_final: 0.8949 (mtpp) outliers start: 38 outliers final: 29 residues processed: 185 average time/residue: 0.4158 time to fit residues: 120.3695 Evaluate side-chains 188 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 158 time to evaluate : 2.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 518 GLU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1092 ASP Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1222 SER Chi-restraints excluded: chain A residue 1270 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 119 optimal weight: 20.0000 chunk 33 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 HIS A 638 GLN A1162 HIS ** A1382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11228 Z= 0.284 Angle : 0.611 6.717 15225 Z= 0.331 Chirality : 0.038 0.141 1784 Planarity : 0.004 0.045 1887 Dihedral : 3.811 17.182 1474 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.44 % Favored : 95.49 % Rotamer: Outliers : 3.34 % Allowed : 21.66 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.14 (0.22), residues: 1375 helix: 0.27 (0.16), residues: 886 sheet: -0.10 (0.62), residues: 75 loop : -0.63 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 709 HIS 0.002 0.001 HIS A1414 PHE 0.010 0.001 PHE A 580 TYR 0.011 0.001 TYR A 101 ARG 0.005 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 158 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.8924 (OUTLIER) cc_final: 0.8617 (m-10) REVERT: A 387 LYS cc_start: 0.9284 (mtpt) cc_final: 0.9020 (mtpp) REVERT: A 595 MET cc_start: 0.8125 (ppp) cc_final: 0.7864 (ppp) outliers start: 41 outliers final: 35 residues processed: 181 average time/residue: 0.4089 time to fit residues: 115.6876 Evaluate side-chains 185 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 149 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 518 GLU Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1092 ASP Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1134 TYR Chi-restraints excluded: chain A residue 1222 SER Chi-restraints excluded: chain A residue 1270 GLU Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1445 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 133 optimal weight: 30.0000 chunk 110 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 128 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11228 Z= 0.248 Angle : 0.588 7.281 15225 Z= 0.315 Chirality : 0.038 0.137 1784 Planarity : 0.003 0.045 1887 Dihedral : 3.753 17.063 1474 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.22 % Favored : 95.71 % Rotamer: Outliers : 3.34 % Allowed : 21.82 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.10 (0.22), residues: 1375 helix: 0.49 (0.17), residues: 892 sheet: -0.12 (0.55), residues: 90 loop : -0.63 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 709 HIS 0.003 0.001 HIS A1185 PHE 0.010 0.001 PHE A 337 TYR 0.011 0.001 TYR A 101 ARG 0.003 0.000 ARG A1083 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 157 time to evaluate : 2.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.8957 (OUTLIER) cc_final: 0.8588 (m-10) REVERT: A 387 LYS cc_start: 0.9296 (mtpt) cc_final: 0.9029 (mtpp) REVERT: A 502 MET cc_start: 0.9084 (ttp) cc_final: 0.7894 (ttp) REVERT: A 1118 MET cc_start: 0.7095 (tpp) cc_final: 0.6654 (tpp) REVERT: A 1210 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8321 (mmm160) outliers start: 41 outliers final: 37 residues processed: 180 average time/residue: 0.4399 time to fit residues: 122.5412 Evaluate side-chains 188 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 149 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1092 ASP Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1134 TYR Chi-restraints excluded: chain A residue 1210 ARG Chi-restraints excluded: chain A residue 1222 SER Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1445 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 97 optimal weight: 0.0370 chunk 75 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 133 optimal weight: 30.0000 chunk 83 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 GLN ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11228 Z= 0.168 Angle : 0.572 7.898 15225 Z= 0.290 Chirality : 0.038 0.153 1784 Planarity : 0.003 0.048 1887 Dihedral : 3.685 16.021 1474 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.27 % Favored : 96.65 % Rotamer: Outliers : 2.69 % Allowed : 22.56 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 (0.23), residues: 1375 helix: 0.98 (0.17), residues: 894 sheet: 0.02 (0.55), residues: 90 loop : -0.41 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 709 HIS 0.002 0.001 HIS A1057 PHE 0.027 0.001 PHE A1084 TYR 0.010 0.001 TYR A 101 ARG 0.004 0.000 ARG A 498 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 164 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 LYS cc_start: 0.9265 (mtpt) cc_final: 0.8984 (mtpp) REVERT: A 1118 MET cc_start: 0.6989 (tpp) cc_final: 0.6613 (tpp) REVERT: A 1210 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8270 (mmm160) outliers start: 33 outliers final: 26 residues processed: 181 average time/residue: 0.3982 time to fit residues: 111.6958 Evaluate side-chains 178 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 151 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 526 GLN Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1092 ASP Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1210 ARG Chi-restraints excluded: chain A residue 1347 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 120 optimal weight: 20.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 GLN ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11228 Z= 0.207 Angle : 0.578 7.794 15225 Z= 0.302 Chirality : 0.038 0.137 1784 Planarity : 0.003 0.048 1887 Dihedral : 3.627 16.429 1474 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.49 % Favored : 96.44 % Rotamer: Outliers : 3.09 % Allowed : 22.64 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.72 (0.23), residues: 1375 helix: 1.00 (0.17), residues: 894 sheet: 0.02 (0.55), residues: 90 loop : -0.44 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 709 HIS 0.003 0.001 HIS A1057 PHE 0.011 0.001 PHE A 580 TYR 0.011 0.001 TYR A 101 ARG 0.003 0.000 ARG A1257 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 149 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.8890 (OUTLIER) cc_final: 0.8567 (m-10) REVERT: A 387 LYS cc_start: 0.9301 (mtpt) cc_final: 0.9032 (mtpp) REVERT: A 1118 MET cc_start: 0.7012 (tpp) cc_final: 0.6726 (tpp) REVERT: A 1210 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8285 (mmm160) outliers start: 38 outliers final: 30 residues processed: 170 average time/residue: 0.4087 time to fit residues: 107.5790 Evaluate side-chains 179 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 147 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1092 ASP Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1210 ARG Chi-restraints excluded: chain A residue 1222 SER Chi-restraints excluded: chain A residue 1347 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 74 optimal weight: 0.0770 chunk 53 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 117 optimal weight: 20.0000 chunk 81 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 GLN ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11228 Z= 0.169 Angle : 0.583 8.448 15225 Z= 0.291 Chirality : 0.038 0.145 1784 Planarity : 0.003 0.049 1887 Dihedral : 3.574 15.872 1474 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.27 % Favored : 96.65 % Rotamer: Outliers : 2.20 % Allowed : 23.86 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.95 (0.23), residues: 1375 helix: 1.20 (0.17), residues: 896 sheet: 0.08 (0.57), residues: 85 loop : -0.39 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 709 HIS 0.002 0.000 HIS A1057 PHE 0.010 0.001 PHE A 337 TYR 0.010 0.001 TYR A 401 ARG 0.003 0.000 ARG A1083 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 159 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.8858 (OUTLIER) cc_final: 0.8488 (m-10) REVERT: A 387 LYS cc_start: 0.9301 (mtpt) cc_final: 0.9024 (mtpp) REVERT: A 1210 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8361 (mmm160) outliers start: 27 outliers final: 23 residues processed: 174 average time/residue: 0.4182 time to fit residues: 112.2835 Evaluate side-chains 180 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 155 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 526 GLN Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1092 ASP Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1210 ARG Chi-restraints excluded: chain A residue 1347 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 91 optimal weight: 8.9990 chunk 137 optimal weight: 20.0000 chunk 126 optimal weight: 8.9990 chunk 109 optimal weight: 0.0670 chunk 11 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 overall best weight: 4.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 GLN ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11228 Z= 0.240 Angle : 0.603 10.045 15225 Z= 0.315 Chirality : 0.038 0.136 1784 Planarity : 0.003 0.047 1887 Dihedral : 3.575 16.407 1474 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.71 % Favored : 96.22 % Rotamer: Outliers : 2.44 % Allowed : 24.27 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.83 (0.23), residues: 1375 helix: 1.10 (0.17), residues: 896 sheet: 0.07 (0.56), residues: 85 loop : -0.47 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 709 HIS 0.002 0.001 HIS A1057 PHE 0.013 0.001 PHE A 580 TYR 0.010 0.001 TYR A 101 ARG 0.003 0.000 ARG A1083 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 148 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.8901 (OUTLIER) cc_final: 0.8534 (m-10) REVERT: A 387 LYS cc_start: 0.9324 (mtpt) cc_final: 0.9067 (mtpp) REVERT: A 1210 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8361 (mmm160) outliers start: 30 outliers final: 27 residues processed: 165 average time/residue: 0.4202 time to fit residues: 106.9475 Evaluate side-chains 176 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 147 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 526 GLN Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1092 ASP Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1210 ARG Chi-restraints excluded: chain A residue 1222 SER Chi-restraints excluded: chain A residue 1347 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 GLN ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.054555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.040418 restraints weight = 190374.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.042336 restraints weight = 78647.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.043598 restraints weight = 44422.782| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11228 Z= 0.179 Angle : 0.594 9.540 15225 Z= 0.299 Chirality : 0.038 0.144 1784 Planarity : 0.003 0.048 1887 Dihedral : 3.581 16.023 1474 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.64 % Favored : 96.29 % Rotamer: Outliers : 2.12 % Allowed : 24.35 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.23), residues: 1375 helix: 1.26 (0.17), residues: 896 sheet: 0.08 (0.56), residues: 85 loop : -0.41 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 456 HIS 0.002 0.000 HIS A1057 PHE 0.012 0.001 PHE A1163 TYR 0.009 0.001 TYR A 101 ARG 0.003 0.000 ARG A1083 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4198.19 seconds wall clock time: 75 minutes 13.23 seconds (4513.23 seconds total)