Starting phenix.real_space_refine on Mon Mar 18 15:30:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we8_37474/03_2024/8we8_37474_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we8_37474/03_2024/8we8_37474.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we8_37474/03_2024/8we8_37474_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we8_37474/03_2024/8we8_37474_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we8_37474/03_2024/8we8_37474_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we8_37474/03_2024/8we8_37474.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we8_37474/03_2024/8we8_37474.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we8_37474/03_2024/8we8_37474_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we8_37474/03_2024/8we8_37474_updated.pdb" } resolution = 2.9 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= -0.002 sd= 0.133 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 Ca 2 9.91 5 P 4 5.49 5 S 114 5.16 5 Cl 1 4.86 5 C 13768 2.51 5 N 3505 2.21 5 O 3915 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 199": "OD1" <-> "OD2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 288": "OE1" <-> "OE2" Residue "A ASP 306": "OD1" <-> "OD2" Residue "A ASP 312": "OD1" <-> "OD2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "A GLU 681": "OE1" <-> "OE2" Residue "A PHE 909": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 957": "OD1" <-> "OD2" Residue "A GLU 1088": "OE1" <-> "OE2" Residue "A ASP 1301": "OD1" <-> "OD2" Residue "A PHE 1376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1482": "OE1" <-> "OE2" Residue "A ASP 1525": "OD1" <-> "OD2" Residue "D TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 116": "OD1" <-> "OD2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "D GLU 278": "OE1" <-> "OE2" Residue "D GLU 281": "OE1" <-> "OE2" Residue "D ASP 379": "OD1" <-> "OD2" Residue "D GLU 425": "OE1" <-> "OE2" Residue "D ASP 452": "OD1" <-> "OD2" Residue "D ASP 491": "OD1" <-> "OD2" Residue "D ASP 563": "OD1" <-> "OD2" Residue "D PHE 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 665": "OD1" <-> "OD2" Residue "D ASP 771": "OD1" <-> "OD2" Residue "D ASP 849": "OD1" <-> "OD2" Residue "D ASP 865": "OD1" <-> "OD2" Residue "D PHE 875": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1068": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C ASP 270": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21309 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 10183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1261, 10183 Classifications: {'peptide': 1261} Link IDs: {'PTRANS': 39, 'TRANS': 1221} Chain breaks: 7 Chain: "D" Number of atoms: 7570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7570 Classifications: {'peptide': 948} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 907} Chain breaks: 5 Chain: "C" Number of atoms: 2575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2575 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 304} Chain: "B" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 486 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 56} Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 256 Unusual residues: {' CA': 1, '3PE': 1, '6UB': 1, 'CLR': 4, 'NAG': 1, 'PT5': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PT5:plan-6': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.51, per 1000 atoms: 0.59 Number of scatterers: 21309 At special positions: 0 Unit cell: (170.442, 174.898, 187.152, 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) Ca 2 19.99 Cl 1 17.00 S 114 16.00 P 4 15.00 O 3915 8.00 N 3505 7.00 C 13768 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 316 " - pdb=" SG CYS A 332 " distance=2.03 Simple disulfide: pdb=" SG CYS A1078 " - pdb=" SG CYS A1089 " distance=2.03 Simple disulfide: pdb=" SG CYS A1479 " - pdb=" SG CYS A1495 " distance=2.03 Simple disulfide: pdb=" SG CYS D 303 " - pdb=" SG CYS D1044 " distance=2.03 Simple disulfide: pdb=" SG CYS D 404 " - pdb=" SG CYS D1071 " distance=2.03 Simple disulfide: pdb=" SG CYS D 667 " - pdb=" SG CYS D 697 " distance=2.03 Simple disulfide: pdb=" SG CYS D 904 " - pdb=" SG CYS D 974 " distance=2.03 Simple disulfide: pdb=" SG CYS D 996 " - pdb=" SG CYS D1026 " distance=2.03 Simple disulfide: pdb=" SG CYS D 999 " - pdb=" SG CYS D1024 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 22 " distance=2.03 Simple disulfide: pdb=" SG CYS B 17 " - pdb=" SG CYS B 39 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 52 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 58 " 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " NAG E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " NAG G 3 " " NAG G 3 " - " NAG G 4 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A2306 " - " ASN A1436 " " NAG D1202 " - " ASN D 92 " " NAG D1203 " - " ASN D 781 " " NAG E 1 " - " ASN D 184 " " NAG F 1 " - " ASN D 348 " " NAG G 1 " - " ASN D 468 " " NAG H 1 " - " ASN D 613 " " NAG I 1 " - " ASN D 895 " Time building additional restraints: 8.24 Conformation dependent library (CDL) restraints added in 3.8 seconds 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4912 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 95 helices and 17 sheets defined 46.7% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.90 Creating SS restraints... Processing helix chain 'A' and resid 125 through 137 removed outlier: 4.111A pdb=" N ILE A 130 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 154 through 169 removed outlier: 3.999A pdb=" N ARG A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 178 No H-bonds generated for 'chain 'A' and resid 175 through 178' Processing helix chain 'A' and resid 194 through 215 Processing helix chain 'A' and resid 234 through 247 removed outlier: 3.905A pdb=" N ALA A 238 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE A 239 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 243 " --> pdb=" O ARG A 240 " (cutoff:3.500A) Proline residue: A 244 - end of helix Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.903A pdb=" N VAL A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 289 removed outlier: 4.108A pdb=" N HIS A 270 " --> pdb=" O PRO A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 360 Processing helix chain 'A' and resid 365 through 375 Processing helix chain 'A' and resid 382 through 415 removed outlier: 3.760A pdb=" N THR A 387 " --> pdb=" O ILE A 383 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 394 " --> pdb=" O ILE A 390 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 446 removed outlier: 3.592A pdb=" N LEU A 424 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TRP A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP A 446 " --> pdb=" O THR A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 521 removed outlier: 4.396A pdb=" N ARG A 515 " --> pdb=" O ARG A 511 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N CYS A 517 " --> pdb=" O CYS A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 542 Processing helix chain 'A' and resid 550 through 577 removed outlier: 3.755A pdb=" N GLU A 554 " --> pdb=" O ASN A 550 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP A 557 " --> pdb=" O THR A 553 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN A 560 " --> pdb=" O GLN A 556 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR A 576 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 585 removed outlier: 3.604A pdb=" N PHE A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 603 removed outlier: 3.578A pdb=" N PHE A 591 " --> pdb=" O LEU A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 614 No H-bonds generated for 'chain 'A' and resid 612 through 614' Processing helix chain 'A' and resid 616 through 630 removed outlier: 3.612A pdb=" N ILE A 630 " --> pdb=" O ILE A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 646 removed outlier: 3.968A pdb=" N ASN A 639 " --> pdb=" O ASN A 635 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A 640 " --> pdb=" O SER A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 673 Processing helix chain 'A' and resid 692 through 704 Processing helix chain 'A' and resid 708 through 719 removed outlier: 3.631A pdb=" N TYR A 719 " --> pdb=" O GLY A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 781 removed outlier: 3.540A pdb=" N VAL A 729 " --> pdb=" O GLY A 726 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS A 739 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU A 749 " --> pdb=" O ASN A 746 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE A 751 " --> pdb=" O PHE A 748 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP A 754 " --> pdb=" O ILE A 751 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN A 755 " --> pdb=" O ALA A 752 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS A 777 " --> pdb=" O GLU A 774 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 780 " --> pdb=" O LYS A 777 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR A 781 " --> pdb=" O LEU A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 918 removed outlier: 3.544A pdb=" N LEU A 917 " --> pdb=" O SER A 913 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 918 " --> pdb=" O SER A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 972 removed outlier: 4.116A pdb=" N TYR A 958 " --> pdb=" O GLY A 954 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1003 removed outlier: 3.657A pdb=" N VAL A 999 " --> pdb=" O LEU A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1017 No H-bonds generated for 'chain 'A' and resid 1014 through 1017' Processing helix chain 'A' and resid 1019 through 1022 Processing helix chain 'A' and resid 1025 through 1028 Processing helix chain 'A' and resid 1035 through 1070 removed outlier: 5.214A pdb=" N ASN A1051 " --> pdb=" O ARG A1047 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ILE A1052 " --> pdb=" O THR A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1099 No H-bonds generated for 'chain 'A' and resid 1097 through 1099' Processing helix chain 'A' and resid 1121 through 1132 removed outlier: 3.696A pdb=" N MET A1126 " --> pdb=" O LEU A1122 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A1127 " --> pdb=" O ALA A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1146 removed outlier: 3.663A pdb=" N ASP A1146 " --> pdb=" O TYR A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1172 removed outlier: 3.533A pdb=" N ILE A1164 " --> pdb=" O GLU A1161 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A1172 " --> pdb=" O TYR A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1190 Processing helix chain 'A' and resid 1194 through 1196 No H-bonds generated for 'chain 'A' and resid 1194 through 1196' Processing helix chain 'A' and resid 1206 through 1214 Processing helix chain 'A' and resid 1229 through 1236 Processing helix chain 'A' and resid 1239 through 1258 removed outlier: 3.572A pdb=" N MET A1258 " --> pdb=" O ILE A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1291 Processing helix chain 'A' and resid 1294 through 1300 removed outlier: 4.200A pdb=" N PHE A1299 " --> pdb=" O PRO A1295 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A1300 " --> pdb=" O LYS A1296 " (cutoff:3.500A) Processing helix chain 'A' and resid 1302 through 1321 removed outlier: 3.518A pdb=" N ILE A1316 " --> pdb=" O ILE A1312 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP A1317 " --> pdb=" O GLY A1313 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A1319 " --> pdb=" O ILE A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1376 through 1390 removed outlier: 4.017A pdb=" N PHE A1379 " --> pdb=" O PHE A1376 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG A1380 " --> pdb=" O ARG A1377 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A1381 " --> pdb=" O LEU A1378 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A1385 " --> pdb=" O MET A1382 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG A1390 " --> pdb=" O LEU A1387 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1407 removed outlier: 3.620A pdb=" N THR A1396 " --> pdb=" O GLU A1392 " (cutoff:3.500A) Processing helix chain 'A' and resid 1409 through 1430 removed outlier: 3.921A pdb=" N ILE A1415 " --> pdb=" O VAL A1411 " (cutoff:3.500A) Processing helix chain 'A' and resid 1450 through 1462 Processing helix chain 'A' and resid 1466 through 1473 Processing helix chain 'A' and resid 1498 through 1525 removed outlier: 3.839A pdb=" N VAL A1501 " --> pdb=" O SER A1498 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A1506 " --> pdb=" O TYR A1503 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE A1507 " --> pdb=" O PHE A1504 " (cutoff:3.500A) Processing helix chain 'A' and resid 1527 through 1530 No H-bonds generated for 'chain 'A' and resid 1527 through 1530' Processing helix chain 'A' and resid 1539 through 1552 removed outlier: 4.519A pdb=" N GLU A1551 " --> pdb=" O ARG A1547 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N TYR A1552 " --> pdb=" O ILE A1548 " (cutoff:3.500A) Processing helix chain 'A' and resid 1562 through 1571 removed outlier: 3.560A pdb=" N VAL A1565 " --> pdb=" O HIS A1562 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A1569 " --> pdb=" O VAL A1566 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A1571 " --> pdb=" O LEU A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1586 through 1593 Processing helix chain 'A' and resid 1606 through 1617 Processing helix chain 'A' and resid 1626 through 1633 Processing helix chain 'D' and resid 30 through 52 removed outlier: 3.548A pdb=" N MET D 40 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR D 46 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU D 47 " --> pdb=" O ASP D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 63 removed outlier: 3.673A pdb=" N VAL D 58 " --> pdb=" O VAL D 54 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASP D 59 " --> pdb=" O ASN D 55 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE D 60 " --> pdb=" O GLN D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 67 No H-bonds generated for 'chain 'D' and resid 65 through 67' Processing helix chain 'D' and resid 75 through 110 removed outlier: 3.615A pdb=" N ARG D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER D 94 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 187 removed outlier: 4.517A pdb=" N SER D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 199 removed outlier: 3.811A pdb=" N LYS D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 240 No H-bonds generated for 'chain 'D' and resid 238 through 240' Processing helix chain 'D' and resid 242 through 248 removed outlier: 3.655A pdb=" N GLY D 247 " --> pdb=" O TRP D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'D' and resid 267 through 282 removed outlier: 3.547A pdb=" N GLU D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR D 282 " --> pdb=" O GLU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 removed outlier: 3.803A pdb=" N ASN D 324 " --> pdb=" O ASP D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 343 Processing helix chain 'D' and resid 370 through 376 Processing helix chain 'D' and resid 397 through 405 removed outlier: 3.741A pdb=" N ALA D 403 " --> pdb=" O ILE D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 removed outlier: 3.593A pdb=" N ILE D 419 " --> pdb=" O ILE D 416 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG D 420 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE D 421 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN D 422 " --> pdb=" O ILE D 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 422' Processing helix chain 'D' and resid 425 through 430 removed outlier: 3.537A pdb=" N LEU D 430 " --> pdb=" O LEU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 435 No H-bonds generated for 'chain 'D' and resid 432 through 435' Processing helix chain 'D' and resid 439 through 441 No H-bonds generated for 'chain 'D' and resid 439 through 441' Processing helix chain 'D' and resid 494 through 500 removed outlier: 3.647A pdb=" N LEU D 500 " --> pdb=" O ASP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 580 Processing helix chain 'D' and resid 639 through 648 removed outlier: 3.748A pdb=" N GLU D 646 " --> pdb=" O ALA D 642 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR D 647 " --> pdb=" O ARG D 643 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU D 648 " --> pdb=" O TYR D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 656 removed outlier: 4.327A pdb=" N GLU D 654 " --> pdb=" O ASP D 651 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER D 656 " --> pdb=" O PHE D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 676 through 687 removed outlier: 3.625A pdb=" N GLU D 685 " --> pdb=" O LEU D 681 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE D 687 " --> pdb=" O PHE D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 718 removed outlier: 3.608A pdb=" N ASN D 713 " --> pdb=" O ALA D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 751 Processing helix chain 'D' and resid 758 through 760 No H-bonds generated for 'chain 'D' and resid 758 through 760' Processing helix chain 'D' and resid 762 through 769 removed outlier: 3.637A pdb=" N ASP D 769 " --> pdb=" O LYS D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 826 removed outlier: 3.648A pdb=" N GLU D 823 " --> pdb=" O ASN D 819 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASN D 824 " --> pdb=" O SER D 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 870 No H-bonds generated for 'chain 'D' and resid 868 through 870' Processing helix chain 'D' and resid 875 through 877 No H-bonds generated for 'chain 'D' and resid 875 through 877' Processing helix chain 'D' and resid 880 through 888 Processing helix chain 'D' and resid 1021 through 1023 No H-bonds generated for 'chain 'D' and resid 1021 through 1023' Processing helix chain 'D' and resid 1043 through 1046 No H-bonds generated for 'chain 'D' and resid 1043 through 1046' Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.644A pdb=" N SER C 46 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA C 48 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLN C 49 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 134 removed outlier: 3.639A pdb=" N LYS C 130 " --> pdb=" O SER C 126 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN C 133 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS C 134 " --> pdb=" O LYS C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 207 removed outlier: 3.787A pdb=" N ALA C 199 " --> pdb=" O MET C 195 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 200 " --> pdb=" O MET C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 263 removed outlier: 3.542A pdb=" N ARG C 256 " --> pdb=" O SER C 252 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER C 263 " --> pdb=" O GLU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 removed outlier: 3.656A pdb=" N ARG C 302 " --> pdb=" O LYS C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 327 removed outlier: 3.626A pdb=" N TYR C 322 " --> pdb=" O GLN C 318 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASP C 323 " --> pdb=" O MET C 319 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU C 325 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL C 326 " --> pdb=" O TYR C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 359 removed outlier: 3.512A pdb=" N ALA C 359 " --> pdb=" O VAL C 355 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 296 through 298 removed outlier: 3.722A pdb=" N THR A 297 " --> pdb=" O LYS A 333 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1076 through 1078 Processing sheet with id= C, first strand: chain 'A' and resid 1092 through 1096 Processing sheet with id= D, first strand: chain 'D' and resid 68 through 72 Processing sheet with id= E, first strand: chain 'D' and resid 122 through 124 Processing sheet with id= F, first strand: chain 'D' and resid 165 through 167 removed outlier: 6.748A pdb=" N VAL D 466 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N VAL D 487 " --> pdb=" O LEU D 464 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU D 464 " --> pdb=" O VAL D 487 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 298 through 300 removed outlier: 6.204A pdb=" N ILE D 256 " --> pdb=" O ALA D 292 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N PHE D 294 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL D 258 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG D 383 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LEU D 360 " --> pdb=" O ARG D 383 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE D 385 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N THR D 362 " --> pdb=" O PHE D 385 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N PHE D 387 " --> pdb=" O THR D 362 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TYR D 409 " --> pdb=" O THR D 386 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N SER D 388 " --> pdb=" O TYR D 409 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N TYR D 411 " --> pdb=" O SER D 388 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 459 through 461 Processing sheet with id= I, first strand: chain 'D' and resid 511 through 515 Processing sheet with id= J, first strand: chain 'D' and resid 732 through 736 removed outlier: 3.898A pdb=" N MET D 793 " --> pdb=" O THR D 776 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 852 through 854 Processing sheet with id= L, first strand: chain 'D' and resid 892 through 899 removed outlier: 3.522A pdb=" N GLN D 980 " --> pdb=" O ASN D 895 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE D 975 " --> pdb=" O SER D1038 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 902 through 904 removed outlier: 3.831A pdb=" N SER D 902 " --> pdb=" O CYS D 974 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 171 through 174 removed outlier: 3.741A pdb=" N ALA C 63 " --> pdb=" O VAL C 174 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 116 through 119 removed outlier: 3.779A pdb=" N ALA C 116 " --> pdb=" O GLY C 106 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY C 106 " --> pdb=" O ALA C 116 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE C 105 " --> pdb=" O GLU C 97 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU C 97 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ARG C 107 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ILE C 95 " --> pdb=" O ARG C 107 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 180 through 183 removed outlier: 5.673A pdb=" N ILE C 288 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL C 183 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL C 290 " --> pdb=" O VAL C 183 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'B' and resid 48 through 52 removed outlier: 3.515A pdb=" N TYR B 23 " --> pdb=" O GLY B 38 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY B 38 " --> pdb=" O TYR B 23 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE B 27 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILE B 34 " --> pdb=" O ILE B 27 " (cutoff:3.500A) 839 hydrogen bonds defined for protein. 2067 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.45 Time building geometry restraints manager: 8.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3435 1.30 - 1.43: 5623 1.43 - 1.56: 12532 1.56 - 1.69: 7 1.69 - 1.82: 173 Bond restraints: 21770 Sorted by residual: bond pdb=" CA PHE A 909 " pdb=" C PHE A 909 " ideal model delta sigma weight residual 1.524 1.453 0.071 1.29e-02 6.01e+03 3.00e+01 bond pdb=" CA ASN A 137 " pdb=" C ASN A 137 " ideal model delta sigma weight residual 1.525 1.457 0.067 1.35e-02 5.49e+03 2.48e+01 bond pdb=" CA LEU A 907 " pdb=" C LEU A 907 " ideal model delta sigma weight residual 1.522 1.455 0.067 1.37e-02 5.33e+03 2.43e+01 bond pdb=" CA ALA A 140 " pdb=" C ALA A 140 " ideal model delta sigma weight residual 1.522 1.463 0.059 1.25e-02 6.40e+03 2.24e+01 bond pdb=" CA ILE A1223 " pdb=" C ILE A1223 " ideal model delta sigma weight residual 1.525 1.488 0.037 8.10e-03 1.52e+04 2.10e+01 ... (remaining 21765 not shown) Histogram of bond angle deviations from ideal: 97.51 - 104.83: 357 104.83 - 112.16: 10791 112.16 - 119.49: 7500 119.49 - 126.82: 10594 126.82 - 134.15: 260 Bond angle restraints: 29502 Sorted by residual: angle pdb=" N LEU A1290 " pdb=" CA LEU A1290 " pdb=" C LEU A1290 " ideal model delta sigma weight residual 113.43 97.51 15.92 1.26e+00 6.30e-01 1.60e+02 angle pdb=" C18 PT5 A2307 " pdb=" C19 PT5 A2307 " pdb=" C20 PT5 A2307 " ideal model delta sigma weight residual 85.86 121.23 -35.37 3.00e+00 1.11e-01 1.39e+02 angle pdb=" C15 PT5 A2307 " pdb=" C16 PT5 A2307 " pdb=" C17 PT5 A2307 " ideal model delta sigma weight residual 152.67 119.21 33.46 3.00e+00 1.11e-01 1.24e+02 angle pdb=" C21 PT5 A2307 " pdb=" C22 PT5 A2307 " pdb=" C23 PT5 A2307 " ideal model delta sigma weight residual 152.70 119.94 32.76 3.00e+00 1.11e-01 1.19e+02 angle pdb=" N ALA A 174 " pdb=" CA ALA A 174 " pdb=" C ALA A 174 " ideal model delta sigma weight residual 113.88 100.67 13.21 1.23e+00 6.61e-01 1.15e+02 ... (remaining 29497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.98: 12556 31.98 - 63.96: 897 63.96 - 95.94: 71 95.94 - 127.92: 24 127.92 - 159.90: 3 Dihedral angle restraints: 13551 sinusoidal: 5962 harmonic: 7589 Sorted by residual: dihedral pdb=" CB CYS D 904 " pdb=" SG CYS D 904 " pdb=" SG CYS D 974 " pdb=" CB CYS D 974 " ideal model delta sinusoidal sigma weight residual 93.00 178.92 -85.92 1 1.00e+01 1.00e-02 8.92e+01 dihedral pdb=" CB CYS A1479 " pdb=" SG CYS A1479 " pdb=" SG CYS A1495 " pdb=" CB CYS A1495 " ideal model delta sinusoidal sigma weight residual -86.00 -161.43 75.43 1 1.00e+01 1.00e-02 7.18e+01 dihedral pdb=" CB CYS B 17 " pdb=" SG CYS B 17 " pdb=" SG CYS B 39 " pdb=" CB CYS B 39 " ideal model delta sinusoidal sigma weight residual 93.00 158.36 -65.36 1 1.00e+01 1.00e-02 5.60e+01 ... (remaining 13548 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2587 0.045 - 0.090: 623 0.090 - 0.135: 142 0.135 - 0.180: 13 0.180 - 0.225: 8 Chirality restraints: 3373 Sorted by residual: chirality pdb=" C1 NAG D1202 " pdb=" ND2 ASN D 92 " pdb=" C2 NAG D1202 " pdb=" O5 NAG D1202 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CG LEU D 853 " pdb=" CB LEU D 853 " pdb=" CD1 LEU D 853 " pdb=" CD2 LEU D 853 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA LYS A1289 " pdb=" N LYS A1289 " pdb=" C LYS A1289 " pdb=" CB LYS A1289 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 3370 not shown) Planarity restraints: 3700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A1538 " -0.057 5.00e-02 4.00e+02 8.70e-02 1.21e+01 pdb=" N PRO A1539 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO A1539 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A1539 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 380 " -0.051 5.00e-02 4.00e+02 7.60e-02 9.24e+00 pdb=" N PRO A 381 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 381 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 381 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1288 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C LEU A1288 " -0.044 2.00e-02 2.50e+03 pdb=" O LEU A1288 " 0.016 2.00e-02 2.50e+03 pdb=" N LYS A1289 " 0.015 2.00e-02 2.50e+03 ... (remaining 3697 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1573 2.74 - 3.28: 21319 3.28 - 3.82: 34643 3.82 - 4.36: 41241 4.36 - 4.90: 70281 Nonbonded interactions: 169057 Sorted by model distance: nonbonded pdb=" OH TYR A 546 " pdb=" OD1 ASP A1151 " model vdw 2.197 2.440 nonbonded pdb=" O4 NAG F 2 " pdb=" O7 NAG F 2 " model vdw 2.199 2.440 nonbonded pdb=" N GLU A 681 " pdb=" OE1 GLU A 681 " model vdw 2.202 2.520 nonbonded pdb=" OE1 GLN A1060 " pdb=" OH TYR A1169 " model vdw 2.214 2.440 nonbonded pdb=" O GLU D 182 " pdb=" OG1 THR D 186 " model vdw 2.219 2.440 ... (remaining 169052 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' } 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: 1.750 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: 0.030 Extract box with map and model: 6.170 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 55.400 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.100 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:11.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 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 : 0.004 0.083 21770 Z= 0.291 Angle : 0.759 35.366 29502 Z= 0.381 Chirality : 0.041 0.225 3373 Planarity : 0.004 0.087 3692 Dihedral : 20.186 159.901 8597 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.97 % Favored : 93.60 % Rotamer: Outliers : 5.44 % Allowed : 30.14 % Favored : 64.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % 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: -1.07 (0.17), residues: 2561 helix: 0.22 (0.15), residues: 1213 sheet: -0.99 (0.37), residues: 222 loop : -1.66 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1549 HIS 0.003 0.001 HIS B 6 PHE 0.023 0.001 PHE A 909 TYR 0.017 0.001 TYR D 68 ARG 0.015 0.000 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 282 time to evaluate : 2.209 Fit side-chains REVERT: A 620 ARG cc_start: 0.7726 (ttp-110) cc_final: 0.7412 (ttm110) REVERT: A 1225 LYS cc_start: 0.6192 (OUTLIER) cc_final: 0.5499 (mptt) REVERT: A 1383 ARG cc_start: 0.8195 (ttp-170) cc_final: 0.7625 (ptp-170) outliers start: 125 outliers final: 110 residues processed: 395 average time/residue: 0.9458 time to fit residues: 442.9242 Evaluate side-chains 382 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 271 time to evaluate : 2.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 898 ASN Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1200 CYS Chi-restraints excluded: chain A residue 1225 LYS Chi-restraints excluded: chain A residue 1275 ASN Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1389 SER Chi-restraints excluded: chain A residue 1394 ILE Chi-restraints excluded: chain A residue 1418 LEU Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1483 SER Chi-restraints excluded: chain A residue 1515 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 553 SER Chi-restraints excluded: chain D residue 555 GLU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 682 ASN Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 770 ASN Chi-restraints excluded: chain D residue 783 SER Chi-restraints excluded: chain D residue 788 TYR Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 805 LYS Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 816 ILE Chi-restraints excluded: chain D residue 850 CYS Chi-restraints excluded: chain D residue 852 ILE Chi-restraints excluded: chain D residue 881 SER Chi-restraints excluded: chain D residue 897 SER Chi-restraints excluded: chain D residue 973 SER Chi-restraints excluded: chain D residue 979 THR Chi-restraints excluded: chain D residue 1037 THR Chi-restraints excluded: chain D residue 1045 ASP Chi-restraints excluded: chain D residue 1071 CYS Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 39 CYS Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 59 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 217 optimal weight: 2.9990 chunk 195 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 202 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 234 optimal weight: 8.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 ASN A 904 ASN A1526 ASN D 65 GLN D 290 ASN ** D 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 901 GLN D1036 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 21770 Z= 0.331 Angle : 0.659 9.414 29502 Z= 0.329 Chirality : 0.045 0.251 3373 Planarity : 0.005 0.081 3692 Dihedral : 13.995 134.949 3747 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.68 % Favored : 93.13 % Rotamer: Outliers : 7.80 % Allowed : 27.40 % Favored : 64.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % 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: -1.31 (0.16), residues: 2561 helix: -0.01 (0.15), residues: 1212 sheet: -1.09 (0.34), residues: 240 loop : -1.76 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1549 HIS 0.005 0.001 HIS A 931 PHE 0.015 0.002 PHE C 92 TYR 0.016 0.002 TYR D 512 ARG 0.005 0.000 ARG A1383 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 289 time to evaluate : 2.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 ASP cc_start: 0.7363 (p0) cc_final: 0.7138 (p0) REVERT: A 426 GLU cc_start: 0.6770 (mp0) cc_final: 0.6463 (mm-30) REVERT: A 620 ARG cc_start: 0.7701 (ttp-110) cc_final: 0.7295 (ttm110) REVERT: A 686 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8063 (mmt180) REVERT: A 972 MET cc_start: 0.5711 (ttp) cc_final: 0.5322 (ttt) REVERT: A 1159 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8138 (ptt180) REVERT: A 1221 ARG cc_start: 0.6601 (OUTLIER) cc_final: 0.5310 (mmp80) REVERT: A 1225 LYS cc_start: 0.5888 (OUTLIER) cc_final: 0.4965 (mptt) REVERT: A 1277 LEU cc_start: 0.8404 (tt) cc_final: 0.8143 (tp) REVERT: A 1390 ARG cc_start: 0.6959 (OUTLIER) cc_final: 0.6553 (mmt180) REVERT: A 1406 GLN cc_start: 0.8206 (tm-30) cc_final: 0.7954 (tm-30) REVERT: D 177 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8583 (m) REVERT: D 191 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7871 (pt0) REVERT: D 379 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8430 (p0) REVERT: D 675 ASN cc_start: 0.6627 (t0) cc_final: 0.6365 (t0) REVERT: D 708 ASP cc_start: 0.8164 (m-30) cc_final: 0.7962 (m-30) REVERT: D 757 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7732 (tp30) REVERT: D 848 MET cc_start: 0.4901 (OUTLIER) cc_final: 0.4627 (pmm) REVERT: C 203 PHE cc_start: 0.4417 (OUTLIER) cc_final: 0.3234 (p90) outliers start: 179 outliers final: 95 residues processed: 423 average time/residue: 1.0331 time to fit residues: 514.2873 Evaluate side-chains 377 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 271 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 414 LYS Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 686 ARG Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 898 ASN Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1159 ARG Chi-restraints excluded: chain A residue 1188 THR Chi-restraints excluded: chain A residue 1221 ARG Chi-restraints excluded: chain A residue 1225 LYS Chi-restraints excluded: chain A residue 1236 VAL Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1390 ARG Chi-restraints excluded: chain A residue 1394 ILE Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1567 THR Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 455 GLU Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 507 CYS Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 555 GLU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 615 THR Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 757 GLU Chi-restraints excluded: chain D residue 770 ASN Chi-restraints excluded: chain D residue 788 TYR Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 805 LYS Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 816 ILE Chi-restraints excluded: chain D residue 848 MET Chi-restraints excluded: chain D residue 850 CYS Chi-restraints excluded: chain D residue 871 ILE Chi-restraints excluded: chain D residue 897 SER Chi-restraints excluded: chain D residue 973 SER Chi-restraints excluded: chain D residue 1037 THR Chi-restraints excluded: chain D residue 1045 ASP Chi-restraints excluded: chain D residue 1057 ASP Chi-restraints excluded: chain D residue 1064 VAL Chi-restraints excluded: chain D residue 1071 CYS Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 203 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 312 MET Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 39 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 130 optimal weight: 8.9990 chunk 72 optimal weight: 0.7980 chunk 194 optimal weight: 9.9990 chunk 159 optimal weight: 0.9990 chunk 64 optimal weight: 0.0980 chunk 234 optimal weight: 7.9990 chunk 253 optimal weight: 0.0870 chunk 209 optimal weight: 1.9990 chunk 232 optimal weight: 0.2980 chunk 80 optimal weight: 0.5980 chunk 188 optimal weight: 6.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN A 428 GLN ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 ASN ** D 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21770 Z= 0.148 Angle : 0.564 9.898 29502 Z= 0.278 Chirality : 0.041 0.252 3373 Planarity : 0.005 0.080 3692 Dihedral : 12.026 133.189 3672 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.74 % Favored : 94.06 % Rotamer: Outliers : 5.36 % Allowed : 29.22 % Favored : 65.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % 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: -1.10 (0.16), residues: 2561 helix: 0.17 (0.15), residues: 1225 sheet: -0.96 (0.34), residues: 240 loop : -1.68 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 185 HIS 0.003 0.001 HIS A 931 PHE 0.011 0.001 PHE A1308 TYR 0.010 0.001 TYR A1552 ARG 0.008 0.000 ARG A1018 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 291 time to evaluate : 2.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 GLU cc_start: 0.7129 (mp0) cc_final: 0.6867 (mm-30) REVERT: A 614 LEU cc_start: 0.5813 (OUTLIER) cc_final: 0.5511 (tt) REVERT: A 620 ARG cc_start: 0.7740 (ttp-110) cc_final: 0.7421 (ttm110) REVERT: A 972 MET cc_start: 0.5664 (ttp) cc_final: 0.5345 (ttt) REVERT: A 1159 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8289 (ptm160) REVERT: A 1277 LEU cc_start: 0.8419 (tt) cc_final: 0.8119 (tp) REVERT: A 1390 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.6413 (mmt180) REVERT: A 1406 GLN cc_start: 0.8335 (tm-30) cc_final: 0.8036 (tm-30) REVERT: A 1467 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.7497 (pp30) REVERT: A 1526 ASN cc_start: 0.7927 (OUTLIER) cc_final: 0.7713 (t0) REVERT: A 1551 GLU cc_start: 0.4149 (OUTLIER) cc_final: 0.3363 (tm-30) REVERT: D 848 MET cc_start: 0.4806 (OUTLIER) cc_final: 0.4506 (pmm) REVERT: D 897 SER cc_start: 0.8775 (OUTLIER) cc_final: 0.8520 (m) outliers start: 123 outliers final: 57 residues processed: 386 average time/residue: 1.0112 time to fit residues: 458.6342 Evaluate side-chains 340 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 275 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1159 ARG Chi-restraints excluded: chain A residue 1236 VAL Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1390 ARG Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1526 ASN Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain A residue 1618 LEU Chi-restraints excluded: chain A residue 1637 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 455 GLU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 615 THR Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 788 TYR Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 805 LYS Chi-restraints excluded: chain D residue 848 MET Chi-restraints excluded: chain D residue 850 CYS Chi-restraints excluded: chain D residue 852 ILE Chi-restraints excluded: chain D residue 866 ASP Chi-restraints excluded: chain D residue 897 SER Chi-restraints excluded: chain D residue 1071 CYS Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 39 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 231 optimal weight: 0.7980 chunk 176 optimal weight: 0.9990 chunk 121 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 235 optimal weight: 5.9990 chunk 249 optimal weight: 0.2980 chunk 123 optimal weight: 5.9990 chunk 223 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21770 Z= 0.196 Angle : 0.575 11.056 29502 Z= 0.282 Chirality : 0.042 0.248 3373 Planarity : 0.004 0.077 3692 Dihedral : 11.275 131.750 3628 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.29 % Favored : 93.52 % Rotamer: Outliers : 6.10 % Allowed : 28.27 % Favored : 65.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % 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: -1.10 (0.16), residues: 2561 helix: 0.17 (0.15), residues: 1234 sheet: -1.01 (0.33), residues: 238 loop : -1.68 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1549 HIS 0.003 0.001 HIS C 94 PHE 0.012 0.001 PHE D 686 TYR 0.012 0.001 TYR D 512 ARG 0.006 0.000 ARG A1018 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 277 time to evaluate : 2.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6798 (mt-10) REVERT: A 426 GLU cc_start: 0.7067 (mp0) cc_final: 0.6806 (mm-30) REVERT: A 614 LEU cc_start: 0.5844 (OUTLIER) cc_final: 0.5567 (tt) REVERT: A 620 ARG cc_start: 0.7769 (ttp-110) cc_final: 0.7428 (ttm110) REVERT: A 686 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8679 (mmt90) REVERT: A 773 LYS cc_start: 0.6426 (OUTLIER) cc_final: 0.6194 (mtpp) REVERT: A 972 MET cc_start: 0.6071 (ttp) cc_final: 0.5688 (ttt) REVERT: A 1159 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8412 (ptm160) REVERT: A 1242 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.5751 (tm-30) REVERT: A 1277 LEU cc_start: 0.8368 (tt) cc_final: 0.8097 (tp) REVERT: A 1390 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.6135 (mmt180) REVERT: A 1406 GLN cc_start: 0.8414 (tm-30) cc_final: 0.8060 (tm-30) REVERT: A 1467 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.7498 (pp30) REVERT: A 1551 GLU cc_start: 0.3736 (OUTLIER) cc_final: 0.3249 (tm-30) REVERT: D 379 ASP cc_start: 0.8724 (OUTLIER) cc_final: 0.8476 (p0) REVERT: D 679 PHE cc_start: 0.7846 (t80) cc_final: 0.7568 (t80) REVERT: D 848 MET cc_start: 0.4829 (OUTLIER) cc_final: 0.4526 (pmm) REVERT: C 107 ARG cc_start: 0.2292 (OUTLIER) cc_final: 0.1956 (ppp80) REVERT: C 311 GLN cc_start: 0.6533 (OUTLIER) cc_final: 0.6279 (tp40) outliers start: 140 outliers final: 72 residues processed: 380 average time/residue: 1.0811 time to fit residues: 480.9236 Evaluate side-chains 349 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 265 time to evaluate : 2.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 414 LYS Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 686 ARG Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 898 ASN Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1126 MET Chi-restraints excluded: chain A residue 1159 ARG Chi-restraints excluded: chain A residue 1236 VAL Chi-restraints excluded: chain A residue 1242 GLU Chi-restraints excluded: chain A residue 1275 ASN Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1390 ARG Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain A residue 1567 THR Chi-restraints excluded: chain A residue 1618 LEU Chi-restraints excluded: chain A residue 1637 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 455 GLU Chi-restraints excluded: chain D residue 507 CYS Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 615 THR Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 788 TYR Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 848 MET Chi-restraints excluded: chain D residue 850 CYS Chi-restraints excluded: chain D residue 852 ILE Chi-restraints excluded: chain D residue 1057 ASP Chi-restraints excluded: chain D residue 1064 VAL Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 312 MET Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 39 CYS Chi-restraints excluded: chain B residue 41 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 207 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 3 optimal weight: 0.0970 chunk 185 optimal weight: 5.9990 chunk 102 optimal weight: 0.0370 chunk 212 optimal weight: 6.9990 chunk 172 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 223 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 overall best weight: 2.1660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21770 Z= 0.287 Angle : 0.609 11.728 29502 Z= 0.300 Chirality : 0.043 0.242 3373 Planarity : 0.005 0.083 3692 Dihedral : 11.131 130.806 3618 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.72 % Favored : 93.05 % Rotamer: Outliers : 6.27 % Allowed : 28.35 % Favored : 65.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % 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: -1.19 (0.16), residues: 2561 helix: 0.11 (0.15), residues: 1229 sheet: -1.00 (0.33), residues: 238 loop : -1.75 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1549 HIS 0.004 0.001 HIS C 94 PHE 0.025 0.002 PHE A 208 TYR 0.015 0.001 TYR D 512 ARG 0.004 0.000 ARG A1018 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 271 time to evaluate : 2.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6933 (mt-10) REVERT: A 614 LEU cc_start: 0.5828 (OUTLIER) cc_final: 0.5547 (tt) REVERT: A 686 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8193 (mmt180) REVERT: A 773 LYS cc_start: 0.6448 (OUTLIER) cc_final: 0.6174 (mtpp) REVERT: A 972 MET cc_start: 0.6240 (ttp) cc_final: 0.5779 (ttt) REVERT: A 1159 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8293 (ptm160) REVERT: A 1277 LEU cc_start: 0.8383 (tt) cc_final: 0.8129 (tp) REVERT: A 1390 ARG cc_start: 0.6875 (OUTLIER) cc_final: 0.6423 (mmt180) REVERT: A 1406 GLN cc_start: 0.8544 (tm-30) cc_final: 0.8193 (tm-30) REVERT: A 1467 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.7793 (pp30) REVERT: A 1526 ASN cc_start: 0.8178 (OUTLIER) cc_final: 0.7875 (t0) REVERT: A 1549 TRP cc_start: 0.5579 (OUTLIER) cc_final: 0.4926 (t-100) REVERT: A 1551 GLU cc_start: 0.3745 (OUTLIER) cc_final: 0.3298 (tm-30) REVERT: D 177 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8535 (m) REVERT: D 440 LYS cc_start: 0.8534 (mtpp) cc_final: 0.8271 (mtpp) REVERT: D 679 PHE cc_start: 0.7863 (t80) cc_final: 0.7513 (t80) REVERT: D 805 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.7652 (mmtp) REVERT: D 848 MET cc_start: 0.4792 (OUTLIER) cc_final: 0.4517 (pmm) REVERT: D 1016 ILE cc_start: 0.5058 (OUTLIER) cc_final: 0.4600 (pp) REVERT: C 107 ARG cc_start: 0.2303 (OUTLIER) cc_final: 0.1961 (ppp80) REVERT: C 204 LEU cc_start: 0.6026 (mt) cc_final: 0.5796 (tt) REVERT: C 320 MET cc_start: 0.6920 (OUTLIER) cc_final: 0.6551 (pp-130) outliers start: 144 outliers final: 90 residues processed: 381 average time/residue: 1.0513 time to fit residues: 470.1261 Evaluate side-chains 369 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 264 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 414 LYS Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 686 ARG Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 898 ASN Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1126 MET Chi-restraints excluded: chain A residue 1159 ARG Chi-restraints excluded: chain A residue 1236 VAL Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1275 ASN Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1390 ARG Chi-restraints excluded: chain A residue 1392 GLU Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1498 SER Chi-restraints excluded: chain A residue 1526 ASN Chi-restraints excluded: chain A residue 1549 TRP Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain A residue 1567 THR Chi-restraints excluded: chain A residue 1616 THR Chi-restraints excluded: chain A residue 1618 LEU Chi-restraints excluded: chain A residue 1637 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 455 GLU Chi-restraints excluded: chain D residue 507 CYS Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 615 THR Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 688 ASP Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 788 TYR Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 805 LYS Chi-restraints excluded: chain D residue 848 MET Chi-restraints excluded: chain D residue 850 CYS Chi-restraints excluded: chain D residue 852 ILE Chi-restraints excluded: chain D residue 1016 ILE Chi-restraints excluded: chain D residue 1057 ASP Chi-restraints excluded: chain D residue 1064 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 312 MET Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 39 CYS Chi-restraints excluded: chain B residue 41 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 83 optimal weight: 0.6980 chunk 224 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 249 optimal weight: 0.9990 chunk 207 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN A 429 GLN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 ASN ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21770 Z= 0.167 Angle : 0.578 12.957 29502 Z= 0.281 Chirality : 0.042 0.460 3373 Planarity : 0.004 0.081 3692 Dihedral : 10.647 133.459 3617 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.05 % Favored : 93.71 % Rotamer: Outliers : 5.18 % Allowed : 29.62 % Favored : 65.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % 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: -1.00 (0.17), residues: 2561 helix: 0.29 (0.15), residues: 1226 sheet: -0.91 (0.34), residues: 238 loop : -1.69 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 185 HIS 0.002 0.001 HIS C 94 PHE 0.019 0.001 PHE D 733 TYR 0.011 0.001 TYR D 512 ARG 0.008 0.000 ARG A 412 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 279 time to evaluate : 3.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7433 (tp30) REVERT: A 310 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6800 (mt-10) REVERT: A 515 ARG cc_start: 0.5424 (ppt170) cc_final: 0.4736 (tmt-80) REVERT: A 614 LEU cc_start: 0.5783 (OUTLIER) cc_final: 0.5512 (tt) REVERT: A 972 MET cc_start: 0.6322 (ttp) cc_final: 0.5881 (ttt) REVERT: A 1159 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8380 (ptm160) REVERT: A 1221 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.6407 (mtp85) REVERT: A 1242 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6695 (tm-30) REVERT: A 1277 LEU cc_start: 0.8398 (tt) cc_final: 0.8092 (tp) REVERT: A 1390 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6356 (mmt180) REVERT: A 1406 GLN cc_start: 0.8575 (tm-30) cc_final: 0.8237 (tm-30) REVERT: A 1467 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.7518 (pp30) REVERT: A 1526 ASN cc_start: 0.8027 (t0) cc_final: 0.7815 (t0) REVERT: A 1528 ASP cc_start: 0.7673 (t0) cc_final: 0.7001 (m-30) REVERT: A 1549 TRP cc_start: 0.5671 (OUTLIER) cc_final: 0.4908 (t-100) REVERT: A 1551 GLU cc_start: 0.3706 (OUTLIER) cc_final: 0.3118 (tm-30) REVERT: D 36 TRP cc_start: 0.6043 (OUTLIER) cc_final: 0.4500 (t60) REVERT: D 177 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8476 (m) REVERT: D 379 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8410 (p0) REVERT: D 675 ASN cc_start: 0.6881 (t0) cc_final: 0.6637 (t0) REVERT: D 679 PHE cc_start: 0.7839 (t80) cc_final: 0.7512 (t80) REVERT: D 788 TYR cc_start: 0.6122 (OUTLIER) cc_final: 0.5537 (m-80) REVERT: D 805 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.7594 (mmtp) REVERT: D 848 MET cc_start: 0.4926 (OUTLIER) cc_final: 0.4629 (pmm) REVERT: C 107 ARG cc_start: 0.2225 (OUTLIER) cc_final: 0.1912 (ppp80) REVERT: C 204 LEU cc_start: 0.6273 (mt) cc_final: 0.5981 (tt) outliers start: 119 outliers final: 69 residues processed: 377 average time/residue: 1.0818 time to fit residues: 479.2485 Evaluate side-chains 348 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 263 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 429 GLN Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1159 ARG Chi-restraints excluded: chain A residue 1221 ARG Chi-restraints excluded: chain A residue 1236 VAL Chi-restraints excluded: chain A residue 1242 GLU Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1390 ARG Chi-restraints excluded: chain A residue 1392 GLU Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1498 SER Chi-restraints excluded: chain A residue 1549 TRP Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain A residue 1618 LEU Chi-restraints excluded: chain A residue 1637 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 36 TRP Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 455 GLU Chi-restraints excluded: chain D residue 507 CYS Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 615 THR Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 688 ASP Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 788 TYR Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 805 LYS Chi-restraints excluded: chain D residue 848 MET Chi-restraints excluded: chain D residue 850 CYS Chi-restraints excluded: chain D residue 852 ILE Chi-restraints excluded: chain D residue 1045 ASP Chi-restraints excluded: chain D residue 1057 ASP Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 39 CYS Chi-restraints excluded: chain B residue 41 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 240 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 142 optimal weight: 0.5980 chunk 182 optimal weight: 1.9990 chunk 141 optimal weight: 0.3980 chunk 210 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21770 Z= 0.195 Angle : 0.585 13.137 29502 Z= 0.284 Chirality : 0.042 0.350 3373 Planarity : 0.004 0.080 3692 Dihedral : 10.376 132.535 3616 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.09 % Favored : 93.64 % Rotamer: Outliers : 5.31 % Allowed : 30.36 % Favored : 64.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % 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: -1.00 (0.17), residues: 2561 helix: 0.28 (0.15), residues: 1225 sheet: -0.92 (0.34), residues: 238 loop : -1.66 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 46 HIS 0.005 0.001 HIS C 94 PHE 0.017 0.001 PHE D 733 TYR 0.014 0.001 TYR D 68 ARG 0.006 0.000 ARG A 412 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 269 time to evaluate : 2.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7458 (tp30) REVERT: A 306 ASP cc_start: 0.7223 (p0) cc_final: 0.7016 (p0) REVERT: A 310 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6806 (mt-10) REVERT: A 515 ARG cc_start: 0.5458 (ppt170) cc_final: 0.4737 (tmt-80) REVERT: A 614 LEU cc_start: 0.5782 (OUTLIER) cc_final: 0.5516 (tt) REVERT: A 686 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8167 (mmt180) REVERT: A 916 SER cc_start: 0.8224 (OUTLIER) cc_final: 0.7494 (m) REVERT: A 972 MET cc_start: 0.6332 (ttp) cc_final: 0.5904 (ttt) REVERT: A 1159 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8404 (ptm160) REVERT: A 1221 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.6385 (mtp85) REVERT: A 1277 LEU cc_start: 0.8378 (tt) cc_final: 0.8052 (tp) REVERT: A 1390 ARG cc_start: 0.6965 (OUTLIER) cc_final: 0.6438 (mmt180) REVERT: A 1406 GLN cc_start: 0.8617 (tm-30) cc_final: 0.8267 (tm-30) REVERT: A 1467 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.7523 (pp30) REVERT: A 1478 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7997 (ptmm) REVERT: A 1526 ASN cc_start: 0.8122 (OUTLIER) cc_final: 0.7896 (t0) REVERT: A 1528 ASP cc_start: 0.7716 (t0) cc_final: 0.7057 (m-30) REVERT: A 1549 TRP cc_start: 0.5743 (OUTLIER) cc_final: 0.4899 (t-100) REVERT: A 1551 GLU cc_start: 0.3707 (OUTLIER) cc_final: 0.3131 (tm-30) REVERT: D 36 TRP cc_start: 0.6040 (OUTLIER) cc_final: 0.4457 (t60) REVERT: D 177 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8488 (m) REVERT: D 379 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8415 (p0) REVERT: D 675 ASN cc_start: 0.6883 (t0) cc_final: 0.6623 (t0) REVERT: D 679 PHE cc_start: 0.7790 (t80) cc_final: 0.7461 (t80) REVERT: D 788 TYR cc_start: 0.6138 (OUTLIER) cc_final: 0.5648 (m-80) REVERT: D 805 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.7613 (mmtp) REVERT: D 848 MET cc_start: 0.4556 (OUTLIER) cc_final: 0.4322 (pmm) REVERT: D 1016 ILE cc_start: 0.4924 (OUTLIER) cc_final: 0.4505 (pp) REVERT: C 107 ARG cc_start: 0.2249 (OUTLIER) cc_final: 0.1927 (ppp80) REVERT: C 204 LEU cc_start: 0.6315 (mt) cc_final: 0.6023 (tt) REVERT: C 320 MET cc_start: 0.6824 (OUTLIER) cc_final: 0.6333 (pp-130) REVERT: C 325 LEU cc_start: 0.3753 (pt) cc_final: 0.3426 (mt) outliers start: 122 outliers final: 76 residues processed: 364 average time/residue: 1.0480 time to fit residues: 446.3115 Evaluate side-chains 354 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 257 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 686 ARG Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 898 ASN Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1159 ARG Chi-restraints excluded: chain A residue 1221 ARG Chi-restraints excluded: chain A residue 1236 VAL Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1268 LYS Chi-restraints excluded: chain A residue 1275 ASN Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1390 ARG Chi-restraints excluded: chain A residue 1392 GLU Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1478 LYS Chi-restraints excluded: chain A residue 1498 SER Chi-restraints excluded: chain A residue 1526 ASN Chi-restraints excluded: chain A residue 1549 TRP Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain A residue 1618 LEU Chi-restraints excluded: chain A residue 1637 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 36 TRP Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 455 GLU Chi-restraints excluded: chain D residue 507 CYS Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 615 THR Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 688 ASP Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 788 TYR Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 805 LYS Chi-restraints excluded: chain D residue 848 MET Chi-restraints excluded: chain D residue 850 CYS Chi-restraints excluded: chain D residue 852 ILE Chi-restraints excluded: chain D residue 1016 ILE Chi-restraints excluded: chain D residue 1045 ASP Chi-restraints excluded: chain D residue 1057 ASP Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 312 MET Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 39 CYS Chi-restraints excluded: chain B residue 41 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 153 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 148 optimal weight: 0.0470 chunk 74 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 158 optimal weight: 0.4980 chunk 169 optimal weight: 0.0670 chunk 122 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 226 optimal weight: 7.9990 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 ASN D 475 ASN ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21770 Z= 0.139 Angle : 0.563 13.567 29502 Z= 0.272 Chirality : 0.041 0.281 3373 Planarity : 0.004 0.082 3692 Dihedral : 9.720 134.044 3614 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.47 % Favored : 94.26 % Rotamer: Outliers : 4.49 % Allowed : 31.32 % Favored : 64.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % 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: -0.79 (0.17), residues: 2561 helix: 0.44 (0.15), residues: 1227 sheet: -0.74 (0.34), residues: 236 loop : -1.58 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 185 HIS 0.003 0.001 HIS D 306 PHE 0.019 0.001 PHE D 686 TYR 0.014 0.001 TYR D 64 ARG 0.006 0.000 ARG A 412 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 291 time to evaluate : 2.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7342 (tp30) REVERT: A 310 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6748 (mt-10) REVERT: A 515 ARG cc_start: 0.5377 (ppt170) cc_final: 0.4749 (tmt-80) REVERT: A 614 LEU cc_start: 0.5635 (OUTLIER) cc_final: 0.5376 (tt) REVERT: A 911 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.6870 (mm) REVERT: A 916 SER cc_start: 0.8186 (OUTLIER) cc_final: 0.7493 (m) REVERT: A 921 ASP cc_start: 0.8441 (t0) cc_final: 0.8109 (t0) REVERT: A 972 MET cc_start: 0.6302 (ttp) cc_final: 0.5837 (ptt) REVERT: A 1026 LEU cc_start: 0.8647 (mt) cc_final: 0.8436 (mt) REVERT: A 1159 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8353 (ptm160) REVERT: A 1242 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.5237 (tm-30) REVERT: A 1277 LEU cc_start: 0.8348 (tt) cc_final: 0.7999 (tp) REVERT: A 1390 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.5896 (mmt180) REVERT: A 1406 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8315 (tm-30) REVERT: A 1478 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7946 (ptmm) REVERT: A 1526 ASN cc_start: 0.7863 (OUTLIER) cc_final: 0.7663 (t0) REVERT: A 1528 ASP cc_start: 0.7662 (t0) cc_final: 0.7039 (m-30) REVERT: A 1551 GLU cc_start: 0.3527 (OUTLIER) cc_final: 0.3185 (tm-30) REVERT: D 177 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8373 (m) REVERT: D 675 ASN cc_start: 0.6854 (t0) cc_final: 0.6571 (t0) REVERT: D 679 PHE cc_start: 0.7718 (t80) cc_final: 0.7495 (t80) REVERT: D 788 TYR cc_start: 0.6234 (OUTLIER) cc_final: 0.5877 (m-80) REVERT: D 805 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.7441 (mmtp) REVERT: D 848 MET cc_start: 0.4500 (OUTLIER) cc_final: 0.4238 (pmm) REVERT: D 884 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6517 (mtt-85) REVERT: D 1016 ILE cc_start: 0.4648 (OUTLIER) cc_final: 0.4277 (pp) REVERT: C 107 ARG cc_start: 0.2338 (OUTLIER) cc_final: 0.2063 (ppp80) REVERT: C 204 LEU cc_start: 0.6512 (mt) cc_final: 0.6190 (tt) REVERT: C 325 LEU cc_start: 0.3634 (pt) cc_final: 0.3408 (mt) REVERT: C 339 GLU cc_start: 0.6868 (tp30) cc_final: 0.6467 (tm-30) outliers start: 103 outliers final: 56 residues processed: 373 average time/residue: 1.0613 time to fit residues: 464.5916 Evaluate side-chains 348 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 275 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1159 ARG Chi-restraints excluded: chain A residue 1236 VAL Chi-restraints excluded: chain A residue 1242 GLU Chi-restraints excluded: chain A residue 1271 MET Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1390 ARG Chi-restraints excluded: chain A residue 1392 GLU Chi-restraints excluded: chain A residue 1478 LYS Chi-restraints excluded: chain A residue 1526 ASN Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain A residue 1637 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 455 GLU Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 615 THR Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 788 TYR Chi-restraints excluded: chain D residue 805 LYS Chi-restraints excluded: chain D residue 848 MET Chi-restraints excluded: chain D residue 850 CYS Chi-restraints excluded: chain D residue 852 ILE Chi-restraints excluded: chain D residue 884 ARG Chi-restraints excluded: chain D residue 1016 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 312 MET Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 361 HIS Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 39 CYS Chi-restraints excluded: chain B residue 41 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 238 optimal weight: 3.9990 chunk 217 optimal weight: 1.9990 chunk 231 optimal weight: 0.0070 chunk 139 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 181 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 209 optimal weight: 6.9990 chunk 219 optimal weight: 4.9990 chunk 230 optimal weight: 0.0870 chunk 152 optimal weight: 0.7980 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21770 Z= 0.147 Angle : 0.578 14.296 29502 Z= 0.278 Chirality : 0.041 0.278 3373 Planarity : 0.004 0.073 3692 Dihedral : 9.316 133.027 3606 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.78 % Favored : 93.95 % Rotamer: Outliers : 3.79 % Allowed : 32.10 % Favored : 64.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % 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: -0.66 (0.17), residues: 2561 helix: 0.55 (0.16), residues: 1206 sheet: -0.69 (0.35), residues: 226 loop : -1.45 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 185 HIS 0.003 0.001 HIS B 6 PHE 0.014 0.001 PHE A 588 TYR 0.011 0.001 TYR D1068 ARG 0.008 0.000 ARG A 412 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 276 time to evaluate : 2.268 Fit side-chains revert: symmetry clash REVERT: A 310 GLU cc_start: 0.6967 (mt-10) cc_final: 0.6629 (mt-10) REVERT: A 515 ARG cc_start: 0.5409 (ppt170) cc_final: 0.4936 (tmt-80) REVERT: A 614 LEU cc_start: 0.5807 (OUTLIER) cc_final: 0.5564 (tt) REVERT: A 911 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.6848 (mm) REVERT: A 916 SER cc_start: 0.8179 (OUTLIER) cc_final: 0.7488 (m) REVERT: A 921 ASP cc_start: 0.8480 (t0) cc_final: 0.8124 (t0) REVERT: A 972 MET cc_start: 0.6213 (ttp) cc_final: 0.5859 (ptt) REVERT: A 1159 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8300 (ptm160) REVERT: A 1390 ARG cc_start: 0.6871 (OUTLIER) cc_final: 0.6217 (mmt180) REVERT: A 1406 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8316 (tm-30) REVERT: A 1478 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7927 (ptmm) REVERT: A 1528 ASP cc_start: 0.7649 (t0) cc_final: 0.7050 (m-30) REVERT: A 1551 GLU cc_start: 0.3658 (OUTLIER) cc_final: 0.3110 (tm-30) REVERT: D 36 TRP cc_start: 0.6006 (OUTLIER) cc_final: 0.4656 (t60) REVERT: D 177 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8386 (m) REVERT: D 788 TYR cc_start: 0.6250 (OUTLIER) cc_final: 0.5920 (m-80) REVERT: D 805 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.7391 (mmtp) REVERT: D 848 MET cc_start: 0.4430 (OUTLIER) cc_final: 0.4207 (pmm) REVERT: D 884 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.6472 (mtt-85) REVERT: D 1016 ILE cc_start: 0.4384 (OUTLIER) cc_final: 0.4029 (pp) REVERT: C 204 LEU cc_start: 0.6441 (mt) cc_final: 0.6112 (tt) REVERT: C 339 GLU cc_start: 0.6885 (tp30) cc_final: 0.6472 (tm-30) REVERT: C 351 GLU cc_start: 0.5836 (mt-10) cc_final: 0.5285 (pt0) outliers start: 87 outliers final: 50 residues processed: 340 average time/residue: 1.0404 time to fit residues: 414.1173 Evaluate side-chains 328 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 264 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 898 ASN Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1159 ARG Chi-restraints excluded: chain A residue 1236 VAL Chi-restraints excluded: chain A residue 1271 MET Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain A residue 1390 ARG Chi-restraints excluded: chain A residue 1392 GLU Chi-restraints excluded: chain A residue 1478 LYS Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain A residue 1637 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 36 TRP Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 455 GLU Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 615 THR Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 788 TYR Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 805 LYS Chi-restraints excluded: chain D residue 848 MET Chi-restraints excluded: chain D residue 850 CYS Chi-restraints excluded: chain D residue 852 ILE Chi-restraints excluded: chain D residue 884 ARG Chi-restraints excluded: chain D residue 1016 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 39 CYS Chi-restraints excluded: chain B residue 41 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 245 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 257 optimal weight: 6.9990 chunk 236 optimal weight: 6.9990 chunk 204 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 125 optimal weight: 0.3980 chunk 162 optimal weight: 2.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN A1526 ASN ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21770 Z= 0.283 Angle : 0.631 14.375 29502 Z= 0.307 Chirality : 0.044 0.272 3373 Planarity : 0.005 0.082 3692 Dihedral : 9.340 130.168 3597 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.36 % Favored : 93.36 % Rotamer: Outliers : 3.31 % Allowed : 32.53 % Favored : 64.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % 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: -0.92 (0.16), residues: 2561 helix: 0.34 (0.15), residues: 1207 sheet: -0.88 (0.34), residues: 236 loop : -1.58 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 46 HIS 0.008 0.001 HIS C 276 PHE 0.019 0.002 PHE D 686 TYR 0.014 0.001 TYR A1298 ARG 0.007 0.000 ARG A 412 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 262 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6716 (mt-10) REVERT: A 515 ARG cc_start: 0.5177 (ppt170) cc_final: 0.4663 (tmt-80) REVERT: A 614 LEU cc_start: 0.6148 (OUTLIER) cc_final: 0.5925 (tt) REVERT: A 916 SER cc_start: 0.8240 (OUTLIER) cc_final: 0.7495 (m) REVERT: A 972 MET cc_start: 0.6293 (ttp) cc_final: 0.5891 (ptt) REVERT: A 1159 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8333 (ptm160) REVERT: A 1277 LEU cc_start: 0.8346 (tt) cc_final: 0.8024 (tp) REVERT: A 1390 ARG cc_start: 0.6926 (OUTLIER) cc_final: 0.6352 (mmt180) REVERT: A 1406 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8358 (tm-30) REVERT: A 1478 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8016 (ptmm) REVERT: A 1528 ASP cc_start: 0.7718 (t0) cc_final: 0.7124 (m-30) REVERT: A 1551 GLU cc_start: 0.3584 (OUTLIER) cc_final: 0.3158 (tm-30) REVERT: D 379 ASP cc_start: 0.8716 (p0) cc_final: 0.8456 (p0) REVERT: D 675 ASN cc_start: 0.6844 (t0) cc_final: 0.6606 (t0) REVERT: D 788 TYR cc_start: 0.6296 (OUTLIER) cc_final: 0.5881 (m-80) REVERT: D 805 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.7562 (mmtp) REVERT: D 848 MET cc_start: 0.4698 (OUTLIER) cc_final: 0.4445 (pmm) REVERT: D 884 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6868 (mtt90) REVERT: D 1016 ILE cc_start: 0.4757 (OUTLIER) cc_final: 0.4356 (pp) REVERT: C 204 LEU cc_start: 0.6458 (mt) cc_final: 0.6170 (tt) REVERT: C 339 GLU cc_start: 0.6933 (tp30) cc_final: 0.6476 (tm-30) REVERT: C 351 GLU cc_start: 0.5866 (mt-10) cc_final: 0.5292 (pt0) outliers start: 76 outliers final: 50 residues processed: 324 average time/residue: 1.0965 time to fit residues: 415.8881 Evaluate side-chains 311 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 250 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 898 ASN Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1159 ARG Chi-restraints excluded: chain A residue 1236 VAL Chi-restraints excluded: chain A residue 1390 ARG Chi-restraints excluded: chain A residue 1478 LYS Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain A residue 1637 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 455 GLU Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 615 THR Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 688 ASP Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 788 TYR Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 805 LYS Chi-restraints excluded: chain D residue 848 MET Chi-restraints excluded: chain D residue 850 CYS Chi-restraints excluded: chain D residue 852 ILE Chi-restraints excluded: chain D residue 884 ARG Chi-restraints excluded: chain D residue 1016 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 39 CYS Chi-restraints excluded: chain B residue 41 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 218 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 188 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 85 optimal weight: 0.3980 chunk 210 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1526 ASN ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 717 GLN ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.212286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.142425 restraints weight = 24874.410| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.92 r_work: 0.3407 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21770 Z= 0.212 Angle : 0.604 14.053 29502 Z= 0.294 Chirality : 0.042 0.268 3373 Planarity : 0.004 0.079 3692 Dihedral : 9.176 131.757 3596 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.90 % Favored : 93.83 % Rotamer: Outliers : 3.48 % Allowed : 32.40 % Favored : 64.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % 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: -0.98 (0.16), residues: 2561 helix: 0.31 (0.15), residues: 1230 sheet: -0.85 (0.34), residues: 238 loop : -1.69 (0.18), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1549 HIS 0.002 0.001 HIS B 6 PHE 0.015 0.001 PHE A 588 TYR 0.015 0.001 TYR A1298 ARG 0.008 0.000 ARG A1018 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7900.97 seconds wall clock time: 140 minutes 14.40 seconds (8414.40 seconds total)