Starting phenix.real_space_refine on Fri Mar 15 01:02:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpt_22422/03_2024/7jpt_22422.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpt_22422/03_2024/7jpt_22422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpt_22422/03_2024/7jpt_22422.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpt_22422/03_2024/7jpt_22422.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpt_22422/03_2024/7jpt_22422.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpt_22422/03_2024/7jpt_22422.pdb" } resolution = 3.2 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= 0.001 sd= 0.015 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: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 6576 2.51 5 N 1728 2.21 5 O 1850 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A ASP 151": "OD1" <-> "OD2" Residue "A ASP 176": "OD1" <-> "OD2" Residue "A ASP 203": "OD1" <-> "OD2" Residue "A PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ASP 303": "OD1" <-> "OD2" Residue "A ASP 358": "OD1" <-> "OD2" Residue "A ASP 395": "OD1" <-> "OD2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A GLU 537": "OE1" <-> "OE2" Residue "A ASP 543": "OD1" <-> "OD2" Residue "A ASP 549": "OD1" <-> "OD2" Residue "A PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 673": "OE1" <-> "OE2" Residue "A GLU 675": "OE1" <-> "OE2" Residue "A PHE 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 731": "NH1" <-> "NH2" Residue "A ARG 760": "NH1" <-> "NH2" Residue "A ASP 771": "OD1" <-> "OD2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A ARG 778": "NH1" <-> "NH2" Residue "A ARG 796": "NH1" <-> "NH2" Residue "A TYR 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 876": "NH1" <-> "NH2" Residue "A GLU 953": "OE1" <-> "OE2" Residue "A ASP 978": "OD1" <-> "OD2" Residue "A TYR 983": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1027": "OD1" <-> "OD2" Residue "A GLU 1094": "OE1" <-> "OE2" Residue "A ASP 1143": "OD1" <-> "OD2" Residue "A GLU 1171": "OE1" <-> "OE2" Residue "A PHE 1174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1196": "OD1" <-> "OD2" Residue "A ASP 1203": "OD1" <-> "OD2" Residue "A PHE 1258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1372": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10220 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1327, 10153 Classifications: {'peptide': 1327} Incomplete info: {'truncation_to_alanine': 183} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 62, 'TRANS': 1260} Chain breaks: 5 Unresolved non-hydrogen bonds: 687 Unresolved non-hydrogen angles: 865 Unresolved non-hydrogen dihedrals: 547 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 24, 'TYR:plan': 5, 'ASN:plan1': 13, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 2, 'GLU:plan': 47, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 500 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "A" 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 Time building chain proxies: 5.98, per 1000 atoms: 0.59 Number of scatterers: 10220 At special positions: 0 Unit cell: (86.92, 99.64, 125.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1850 8.00 N 1728 7.00 C 6576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 59 " distance=2.03 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 100 " distance=2.03 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS A 229 " distance=2.03 Simple disulfide: pdb=" SG CYS A 247 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 332 " distance=2.03 Simple disulfide: pdb=" SG CYS A 361 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 485 " distance=2.04 Simple disulfide: pdb=" SG CYS A 462 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 514 " distance=2.03 Simple disulfide: pdb=" SG CYS A 528 " - pdb=" SG CYS A 623 " distance=2.03 Simple disulfide: pdb=" SG CYS A 597 " - pdb=" SG CYS A 614 " distance=2.03 Simple disulfide: pdb=" SG CYS A 678 " - pdb=" SG CYS A 782 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 930 " distance=2.03 Simple disulfide: pdb=" SG CYS A 904 " - pdb=" SG CYS A 922 " distance=2.03 Simple disulfide: pdb=" SG CYS A 980 " - pdb=" SG CYS A1089 " distance=2.03 Simple disulfide: pdb=" SG CYS A1060 " - pdb=" SG CYS A1080 " distance=2.03 Simple disulfide: pdb=" SG CYS A1131 " - pdb=" SG CYS A1220 " distance=2.03 Simple disulfide: pdb=" SG CYS A1197 " - pdb=" SG CYS A1211 " distance=2.03 Simple disulfide: pdb=" SG CYS A1239 " - pdb=" SG CYS A1255 " distance=2.03 Simple disulfide: pdb=" SG CYS A1277 " - pdb=" SG CYS A1380 " 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 B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A1801 " - " ASN A1253 " " NAG B 1 " - " ASN A1076 " Time building additional restraints: 4.06 Conformation dependent library (CDL) restraints added in 2.0 seconds 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2508 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 28 sheets defined 19.0% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 61 through 65 removed outlier: 4.017A pdb=" N ASP A 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 239 through 250 removed outlier: 3.800A pdb=" N GLN A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 268 Processing helix chain 'A' and resid 382 through 391 removed outlier: 3.599A pdb=" N ALA A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 411 removed outlier: 3.771A pdb=" N VAL A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 417 removed outlier: 3.557A pdb=" N GLU A 415 " --> pdb=" O LYS A 411 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE A 417 " --> pdb=" O HIS A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 removed outlier: 4.357A pdb=" N GLU A 505 " --> pdb=" O PRO A 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 502 through 505' Processing helix chain 'A' and resid 534 through 549 Processing helix chain 'A' and resid 670 through 681 removed outlier: 3.540A pdb=" N LEU A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 702 removed outlier: 4.104A pdb=" N ILE A 694 " --> pdb=" O HIS A 690 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS A 695 " --> pdb=" O VAL A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 723 Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 804 through 813 Processing helix chain 'A' and resid 832 through 841 Processing helix chain 'A' and resid 852 through 867 Processing helix chain 'A' and resid 973 through 983 removed outlier: 3.968A pdb=" N ASP A 978 " --> pdb=" O SER A 974 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TYR A 983 " --> pdb=" O THR A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1003 removed outlier: 3.604A pdb=" N GLN A 996 " --> pdb=" O SER A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1006 No H-bonds generated for 'chain 'A' and resid 1004 through 1006' Processing helix chain 'A' and resid 1123 through 1134 Processing helix chain 'A' and resid 1143 through 1158 Processing helix chain 'A' and resid 1268 through 1281 removed outlier: 3.719A pdb=" N HIS A1274 " --> pdb=" O GLN A1270 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN A1281 " --> pdb=" O CYS A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1292 through 1304 removed outlier: 3.605A pdb=" N TYR A1304 " --> pdb=" O GLU A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1318 through 1322 removed outlier: 3.689A pdb=" N LYS A1321 " --> pdb=" O TYR A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1368 Processing helix chain 'A' and resid 1369 through 1375 removed outlier: 3.598A pdb=" N HIS A1375 " --> pdb=" O TYR A1371 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 70 removed outlier: 3.573A pdb=" N ARG A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 125 through 126 Processing sheet with id=AA5, first strand: chain 'A' and resid 159 through 162 removed outlier: 6.479A pdb=" N ILE A 208 " --> pdb=" O ARG A 160 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLY A 162 " --> pdb=" O TRP A 206 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N TRP A 206 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 173 through 175 Processing sheet with id=AA7, first strand: chain 'A' and resid 228 through 238 removed outlier: 3.993A pdb=" N ASN A 233 " --> pdb=" O TYR A 338 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TYR A 338 " --> pdb=" O ASN A 233 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N GLN A 235 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N LEU A 336 " --> pdb=" O GLN A 235 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 275 through 276 Processing sheet with id=AA9, first strand: chain 'A' and resid 299 through 300 Processing sheet with id=AB1, first strand: chain 'A' and resid 366 through 368 removed outlier: 3.853A pdb=" N TYR A 483 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLU A 378 " --> pdb=" O LEU A 481 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU A 481 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 484 " --> pdb=" O TRP A 422 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLY A 424 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 10.205A pdb=" N LYS A 486 " --> pdb=" O GLY A 424 " (cutoff:3.500A) removed outlier: 15.113A pdb=" N LYS A 426 " --> pdb=" O LYS A 486 " (cutoff:3.500A) removed outlier: 20.743A pdb=" N LYS A 488 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 395 through 396 removed outlier: 3.979A pdb=" N VAL A 484 " --> pdb=" O TRP A 422 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLY A 424 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 10.205A pdb=" N LYS A 486 " --> pdb=" O GLY A 424 " (cutoff:3.500A) removed outlier: 15.113A pdb=" N LYS A 426 " --> pdb=" O LYS A 486 " (cutoff:3.500A) removed outlier: 20.743A pdb=" N LYS A 488 " --> pdb=" O LYS A 426 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL A 421 " --> pdb=" O TYR A 465 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A 423 " --> pdb=" O VAL A 463 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL A 463 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU A 425 " --> pdb=" O ASN A 461 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASN A 461 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N CYS A 462 " --> pdb=" O GLN A 475 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 507 through 508 Processing sheet with id=AB4, first strand: chain 'A' and resid 570 through 571 removed outlier: 4.541A pdb=" N VAL A 598 " --> pdb=" O THR A 558 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 655 through 660 removed outlier: 3.932A pdb=" N PHE A 780 " --> pdb=" O PHE A 660 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 716 removed outlier: 4.923A pdb=" N ALA A 753 " --> pdb=" O ILE A 713 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 823 through 831 removed outlier: 7.722A pdb=" N ASP A 828 " --> pdb=" O LEU A 926 " (cutoff:3.500A) removed outlier: 9.579A pdb=" N LEU A 926 " --> pdb=" O ASP A 828 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 849 through 850 Processing sheet with id=AB9, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AC1, first strand: chain 'A' and resid 956 through 958 Processing sheet with id=AC2, first strand: chain 'A' and resid 970 through 972 Processing sheet with id=AC3, first strand: chain 'A' and resid 1009 through 1010 Processing sheet with id=AC4, first strand: chain 'A' and resid 1009 through 1010 Processing sheet with id=AC5, first strand: chain 'A' and resid 1108 through 1110 Processing sheet with id=AC6, first strand: chain 'A' and resid 1161 through 1162 Processing sheet with id=AC7, first strand: chain 'A' and resid 1165 through 1167 Processing sheet with id=AC8, first strand: chain 'A' and resid 1249 through 1250 Processing sheet with id=AC9, first strand: chain 'A' and resid 1258 through 1259 removed outlier: 3.842A pdb=" N LEU A1378 " --> pdb=" O ILE A1259 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ALA A1379 " --> pdb=" O MET A1313 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1316 through 1317 274 hydrogen bonds defined for protein. 705 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: 4.32 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3208 1.35 - 1.47: 2866 1.47 - 1.59: 4381 1.59 - 1.71: 0 1.71 - 1.83: 79 Bond restraints: 10534 Sorted by residual: bond pdb=" C1 NAG A1802 " pdb=" O5 NAG A1802 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.92e+00 bond pdb=" C THR A 459 " pdb=" N PRO A 460 " ideal model delta sigma weight residual 1.334 1.356 -0.022 1.11e-02 8.12e+03 3.97e+00 bond pdb=" C1 BMA B 3 " pdb=" C2 BMA B 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" C1 NAG A1801 " pdb=" O5 NAG A1801 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 ... (remaining 10529 not shown) Histogram of bond angle deviations from ideal: 99.96 - 106.78: 358 106.78 - 113.60: 5664 113.60 - 120.41: 3692 120.41 - 127.23: 4463 127.23 - 134.04: 199 Bond angle restraints: 14376 Sorted by residual: angle pdb=" C TRP A1025 " pdb=" N THR A1026 " pdb=" CA THR A1026 " ideal model delta sigma weight residual 121.54 127.44 -5.90 1.91e+00 2.74e-01 9.54e+00 angle pdb=" CA CYS A 485 " pdb=" CB CYS A 485 " pdb=" SG CYS A 485 " ideal model delta sigma weight residual 114.40 120.20 -5.80 2.30e+00 1.89e-01 6.35e+00 angle pdb=" CA LEU A 654 " pdb=" CB LEU A 654 " pdb=" CG LEU A 654 " ideal model delta sigma weight residual 116.30 124.75 -8.45 3.50e+00 8.16e-02 5.83e+00 angle pdb=" N LEU A1172 " pdb=" CA LEU A1172 " pdb=" C LEU A1172 " ideal model delta sigma weight residual 113.18 110.00 3.18 1.33e+00 5.65e-01 5.72e+00 angle pdb=" N THR A 440 " pdb=" CA THR A 440 " pdb=" C THR A 440 " ideal model delta sigma weight residual 114.04 111.18 2.86 1.24e+00 6.50e-01 5.31e+00 ... (remaining 14371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.55: 5776 22.55 - 45.10: 364 45.10 - 67.66: 54 67.66 - 90.21: 18 90.21 - 112.76: 7 Dihedral angle restraints: 6219 sinusoidal: 2341 harmonic: 3878 Sorted by residual: dihedral pdb=" CB CYS A 389 " pdb=" SG CYS A 389 " pdb=" SG CYS A 485 " pdb=" CB CYS A 485 " ideal model delta sinusoidal sigma weight residual 93.00 -179.27 -87.73 1 1.00e+01 1.00e-02 9.22e+01 dihedral pdb=" CB CYS A 317 " pdb=" SG CYS A 317 " pdb=" SG CYS A 332 " pdb=" CB CYS A 332 " ideal model delta sinusoidal sigma weight residual -86.00 0.38 -86.38 1 1.00e+01 1.00e-02 8.99e+01 dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS A 514 " pdb=" CB CYS A 514 " ideal model delta sinusoidal sigma weight residual -86.00 -165.64 79.64 1 1.00e+01 1.00e-02 7.87e+01 ... (remaining 6216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1315 0.054 - 0.108: 205 0.108 - 0.162: 34 0.162 - 0.216: 0 0.216 - 0.269: 1 Chirality restraints: 1555 Sorted by residual: chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA CYS A1211 " pdb=" N CYS A1211 " pdb=" C CYS A1211 " pdb=" CB CYS A1211 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CB ILE A 737 " pdb=" CA ILE A 737 " pdb=" CG1 ILE A 737 " pdb=" CG2 ILE A 737 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 1552 not shown) Planarity restraints: 1818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 967 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO A 968 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 968 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 968 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 813 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO A 814 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 814 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 814 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 697 " -0.013 2.00e-02 2.50e+03 1.06e-02 1.95e+00 pdb=" CG PHE A 697 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 697 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 697 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 697 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 697 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 697 " -0.005 2.00e-02 2.50e+03 ... (remaining 1815 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2673 2.79 - 3.32: 8847 3.32 - 3.85: 16455 3.85 - 4.37: 18978 4.37 - 4.90: 32978 Nonbonded interactions: 79931 Sorted by model distance: nonbonded pdb=" OH TYR A 165 " pdb=" OE1 GLN A1301 " model vdw 2.267 2.440 nonbonded pdb=" O SER A 329 " pdb=" OG SER A 329 " model vdw 2.286 2.440 nonbonded pdb=" O SER A1097 " pdb=" OG SER A1097 " model vdw 2.316 2.440 nonbonded pdb=" OE1 GLU A1195 " pdb=" N ASP A1210 " model vdw 2.318 2.520 nonbonded pdb=" NH1 ARG A 160 " pdb=" OD2 ASP A 161 " model vdw 2.324 2.520 ... (remaining 79926 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.53 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: 0.140 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: 0.000 Extract box with map and model: 1.480 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 33.010 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 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 : 0.002 0.053 10534 Z= 0.162 Angle : 0.548 8.452 14376 Z= 0.292 Chirality : 0.042 0.269 1555 Planarity : 0.003 0.036 1816 Dihedral : 15.001 112.760 3642 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.77 % Favored : 93.16 % Rotamer: Outliers : 3.48 % Allowed : 18.97 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % 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: -4.02 (0.19), residues: 1315 helix: -1.24 (0.30), residues: 208 sheet: -2.36 (0.36), residues: 150 loop : -3.33 (0.16), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1025 HIS 0.003 0.000 HIS A 40 PHE 0.024 0.001 PHE A 697 TYR 0.009 0.001 TYR A 116 ARG 0.001 0.000 ARG A 796 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 202 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.2372 (OUTLIER) cc_final: 0.1032 (t) REVERT: A 109 LYS cc_start: 0.6901 (tptt) cc_final: 0.6624 (tptt) REVERT: A 140 TRP cc_start: 0.6619 (m100) cc_final: 0.6344 (m100) REVERT: A 222 LYS cc_start: 0.6934 (OUTLIER) cc_final: 0.6620 (ttpm) REVERT: A 561 ARG cc_start: 0.4794 (ptm160) cc_final: 0.4588 (ptm160) REVERT: A 695 LYS cc_start: 0.5972 (mtpt) cc_final: 0.5410 (mmtm) REVERT: A 771 ASP cc_start: 0.7619 (m-30) cc_final: 0.7192 (m-30) REVERT: A 910 LYS cc_start: 0.8137 (ttpm) cc_final: 0.7843 (ttpp) REVERT: A 911 THR cc_start: 0.8116 (OUTLIER) cc_final: 0.7893 (p) REVERT: A 996 GLN cc_start: 0.8435 (tp40) cc_final: 0.7983 (tm-30) REVERT: A 1021 LYS cc_start: 0.7043 (OUTLIER) cc_final: 0.6721 (mtmt) REVERT: A 1117 ILE cc_start: 0.8628 (mm) cc_final: 0.8421 (mm) REVERT: A 1136 MET cc_start: 0.7211 (mtt) cc_final: 0.6982 (mtm) REVERT: A 1266 MET cc_start: 0.3359 (tpt) cc_final: 0.2535 (tpt) REVERT: A 1313 MET cc_start: 0.7704 (ttt) cc_final: 0.7210 (ttm) REVERT: A 1361 GLN cc_start: 0.7390 (tm-30) cc_final: 0.7127 (tm-30) REVERT: A 1370 VAL cc_start: 0.8401 (m) cc_final: 0.8155 (t) outliers start: 35 outliers final: 19 residues processed: 230 average time/residue: 0.2435 time to fit residues: 76.5505 Evaluate side-chains 144 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1021 LYS Chi-restraints excluded: chain A residue 1069 SER Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain A residue 1317 THR Chi-restraints excluded: chain A residue 1362 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 6.9990 chunk 100 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 0.0370 chunk 67 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 overall best weight: 1.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 GLN A 369 ASN A 510 HIS A 529 ASN A 538 GLN A 542 ASN ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 ASN A 993 GLN A1059 HIS A1065 ASN A1084 HIS A1173 ASN A1274 HIS A1306 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10534 Z= 0.228 Angle : 0.595 8.577 14376 Z= 0.298 Chirality : 0.043 0.220 1555 Planarity : 0.004 0.046 1816 Dihedral : 7.894 53.284 1543 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 5.96 % Allowed : 21.15 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % 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: -3.32 (0.20), residues: 1315 helix: -0.18 (0.33), residues: 212 sheet: -2.08 (0.37), residues: 152 loop : -2.95 (0.17), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 912 HIS 0.005 0.001 HIS A 40 PHE 0.013 0.002 PHE A 998 TYR 0.017 0.001 TYR A 116 ARG 0.006 0.001 ARG A1290 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 131 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.2774 (OUTLIER) cc_final: 0.1097 (t) REVERT: A 67 TRP cc_start: 0.7068 (m100) cc_final: 0.6288 (m100) REVERT: A 69 TRP cc_start: 0.8756 (m100) cc_final: 0.8450 (m100) REVERT: A 112 HIS cc_start: 0.7411 (OUTLIER) cc_final: 0.7203 (t-90) REVERT: A 140 TRP cc_start: 0.6798 (m100) cc_final: 0.6364 (m100) REVERT: A 406 GLU cc_start: 0.7282 (tm-30) cc_final: 0.6877 (tm-30) REVERT: A 590 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.5857 (mm-30) REVERT: A 600 MET cc_start: 0.7789 (mtp) cc_final: 0.7534 (mtm) REVERT: A 617 PHE cc_start: 0.5289 (t80) cc_final: 0.5004 (t80) REVERT: A 695 LYS cc_start: 0.6409 (mtpt) cc_final: 0.5804 (mmtm) REVERT: A 910 LYS cc_start: 0.8227 (ttpm) cc_final: 0.7894 (ttpp) REVERT: A 911 THR cc_start: 0.8180 (OUTLIER) cc_final: 0.7976 (p) REVERT: A 996 GLN cc_start: 0.8591 (tp40) cc_final: 0.8327 (tm-30) REVERT: A 1136 MET cc_start: 0.7047 (mtt) cc_final: 0.6720 (mtm) REVERT: A 1266 MET cc_start: 0.3728 (tpt) cc_final: 0.2778 (tpt) REVERT: A 1313 MET cc_start: 0.7764 (ttt) cc_final: 0.7247 (ttm) REVERT: A 1361 GLN cc_start: 0.7448 (tm-30) cc_final: 0.7167 (tm-30) REVERT: A 1370 VAL cc_start: 0.8226 (m) cc_final: 0.7840 (t) REVERT: A 1374 GLN cc_start: 0.8221 (mt0) cc_final: 0.7846 (mm-40) outliers start: 60 outliers final: 34 residues processed: 183 average time/residue: 0.2118 time to fit residues: 55.8434 Evaluate side-chains 155 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 117 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 590 GLU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1025 TRP Chi-restraints excluded: chain A residue 1026 THR Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain A residue 1241 SER Chi-restraints excluded: chain A residue 1326 PHE Chi-restraints excluded: chain A residue 1380 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 120 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 HIS ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 ASN A1146 GLN A1153 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 10534 Z= 0.372 Angle : 0.665 7.864 14376 Z= 0.340 Chirality : 0.046 0.206 1555 Planarity : 0.004 0.052 1816 Dihedral : 7.059 50.916 1528 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 7.35 % Allowed : 19.66 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % 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: -3.08 (0.21), residues: 1315 helix: 0.09 (0.34), residues: 211 sheet: -1.86 (0.38), residues: 152 loop : -2.82 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 277 HIS 0.007 0.001 HIS A 113 PHE 0.021 0.002 PHE A 697 TYR 0.018 0.002 TYR A 888 ARG 0.008 0.001 ARG A1015 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 121 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.3270 (OUTLIER) cc_final: 0.1083 (t) REVERT: A 67 TRP cc_start: 0.7139 (m100) cc_final: 0.6924 (m100) REVERT: A 140 TRP cc_start: 0.7099 (m100) cc_final: 0.6337 (m100) REVERT: A 141 LYS cc_start: 0.7576 (mmmt) cc_final: 0.6072 (mttp) REVERT: A 320 MET cc_start: 0.8164 (ttt) cc_final: 0.7915 (ttt) REVERT: A 358 ASP cc_start: 0.7661 (p0) cc_final: 0.7262 (p0) REVERT: A 406 GLU cc_start: 0.7388 (tm-30) cc_final: 0.6985 (tm-30) REVERT: A 561 ARG cc_start: 0.4994 (ptm160) cc_final: 0.4718 (ptm160) REVERT: A 617 PHE cc_start: 0.5632 (t80) cc_final: 0.5171 (t80) REVERT: A 695 LYS cc_start: 0.6748 (mtpt) cc_final: 0.6009 (mmtm) REVERT: A 838 LEU cc_start: 0.8884 (mm) cc_final: 0.8446 (mm) REVERT: A 846 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7083 (p90) REVERT: A 996 GLN cc_start: 0.8647 (tp40) cc_final: 0.8346 (tm-30) REVERT: A 1033 TYR cc_start: 0.7698 (OUTLIER) cc_final: 0.7408 (p90) REVERT: A 1136 MET cc_start: 0.7334 (mtt) cc_final: 0.6990 (mtm) REVERT: A 1266 MET cc_start: 0.3775 (tpt) cc_final: 0.3078 (tpt) REVERT: A 1313 MET cc_start: 0.7744 (ttt) cc_final: 0.7288 (ttm) REVERT: A 1361 GLN cc_start: 0.7502 (tm-30) cc_final: 0.7181 (tm-30) REVERT: A 1370 VAL cc_start: 0.8293 (m) cc_final: 0.7969 (t) REVERT: A 1374 GLN cc_start: 0.8285 (mt0) cc_final: 0.7876 (mm110) outliers start: 74 outliers final: 51 residues processed: 182 average time/residue: 0.2063 time to fit residues: 54.2336 Evaluate side-chains 169 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 115 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1033 TYR Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1241 SER Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1326 PHE Chi-restraints excluded: chain A residue 1376 SER Chi-restraints excluded: chain A residue 1380 CYS Chi-restraints excluded: chain A residue 1382 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 chunk 114 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 ASN ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 10534 Z= 0.290 Angle : 0.620 7.658 14376 Z= 0.317 Chirality : 0.044 0.238 1555 Planarity : 0.004 0.076 1816 Dihedral : 6.689 53.044 1528 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 6.75 % Allowed : 21.25 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % 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: -2.92 (0.21), residues: 1315 helix: 0.40 (0.34), residues: 213 sheet: -1.95 (0.34), residues: 187 loop : -2.72 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 277 HIS 0.005 0.001 HIS A 113 PHE 0.022 0.002 PHE A 697 TYR 0.016 0.001 TYR A 116 ARG 0.006 0.001 ARG A1015 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 129 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.2432 (OUTLIER) cc_final: 0.1820 (t) REVERT: A 67 TRP cc_start: 0.6877 (m100) cc_final: 0.6296 (m100) REVERT: A 140 TRP cc_start: 0.7202 (m100) cc_final: 0.6437 (m100) REVERT: A 141 LYS cc_start: 0.7600 (mmmt) cc_final: 0.6226 (mttp) REVERT: A 222 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.7265 (mtpt) REVERT: A 320 MET cc_start: 0.8148 (ttt) cc_final: 0.7835 (ttt) REVERT: A 358 ASP cc_start: 0.7644 (p0) cc_final: 0.7225 (p0) REVERT: A 406 GLU cc_start: 0.7347 (tm-30) cc_final: 0.6955 (tm-30) REVERT: A 481 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6501 (pp) REVERT: A 561 ARG cc_start: 0.5000 (ptm160) cc_final: 0.4745 (ptm160) REVERT: A 688 PHE cc_start: 0.7813 (OUTLIER) cc_final: 0.7303 (p90) REVERT: A 695 LYS cc_start: 0.6798 (mtpt) cc_final: 0.6028 (mmtm) REVERT: A 723 GLN cc_start: 0.8356 (mt0) cc_final: 0.8113 (mt0) REVERT: A 838 LEU cc_start: 0.8830 (mm) cc_final: 0.8408 (mm) REVERT: A 1033 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.7465 (p90) REVERT: A 1117 ILE cc_start: 0.8889 (mm) cc_final: 0.8566 (mt) REVERT: A 1136 MET cc_start: 0.7309 (mtt) cc_final: 0.6972 (mtm) REVERT: A 1313 MET cc_start: 0.7772 (ttt) cc_final: 0.7295 (ttm) REVERT: A 1370 VAL cc_start: 0.8257 (m) cc_final: 0.7962 (t) REVERT: A 1374 GLN cc_start: 0.8221 (mt0) cc_final: 0.7870 (mm110) outliers start: 68 outliers final: 49 residues processed: 181 average time/residue: 0.2055 time to fit residues: 54.3181 Evaluate side-chains 170 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 116 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain A residue 880 TRP Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1033 TYR Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1151 SER Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1241 SER Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1326 PHE Chi-restraints excluded: chain A residue 1380 CYS Chi-restraints excluded: chain A residue 1382 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 95 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 ASN A1257 ASN A1278 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10534 Z= 0.266 Angle : 0.609 7.742 14376 Z= 0.311 Chirality : 0.044 0.214 1555 Planarity : 0.004 0.065 1816 Dihedral : 6.468 52.550 1526 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 7.15 % Allowed : 22.24 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % 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: -2.72 (0.22), residues: 1315 helix: 0.64 (0.35), residues: 213 sheet: -1.89 (0.34), residues: 189 loop : -2.59 (0.19), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 912 HIS 0.005 0.001 HIS A1373 PHE 0.024 0.002 PHE A1348 TYR 0.018 0.001 TYR A 548 ARG 0.006 0.001 ARG A1015 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 119 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 CYS cc_start: 0.3053 (OUTLIER) cc_final: 0.2290 (t) REVERT: A 67 TRP cc_start: 0.6797 (m100) cc_final: 0.6220 (m100) REVERT: A 140 TRP cc_start: 0.7211 (m100) cc_final: 0.6378 (m100) REVERT: A 141 LYS cc_start: 0.7532 (mmmt) cc_final: 0.6233 (mttp) REVERT: A 320 MET cc_start: 0.8075 (ttt) cc_final: 0.7655 (ttt) REVERT: A 358 ASP cc_start: 0.7722 (p0) cc_final: 0.7300 (p0) REVERT: A 406 GLU cc_start: 0.7349 (tm-30) cc_final: 0.7002 (tm-30) REVERT: A 481 LEU cc_start: 0.6737 (OUTLIER) cc_final: 0.6423 (pp) REVERT: A 557 TRP cc_start: 0.8336 (m100) cc_final: 0.8000 (m100) REVERT: A 561 ARG cc_start: 0.4957 (ptm160) cc_final: 0.4717 (ptm160) REVERT: A 657 TYR cc_start: 0.7566 (m-80) cc_final: 0.7306 (m-80) REVERT: A 688 PHE cc_start: 0.8067 (OUTLIER) cc_final: 0.7497 (p90) REVERT: A 695 LYS cc_start: 0.6769 (OUTLIER) cc_final: 0.6007 (mmtm) REVERT: A 838 LEU cc_start: 0.8829 (mm) cc_final: 0.8421 (mm) REVERT: A 846 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.6981 (p90) REVERT: A 1033 TYR cc_start: 0.7757 (OUTLIER) cc_final: 0.7513 (p90) REVERT: A 1117 ILE cc_start: 0.8865 (mm) cc_final: 0.8552 (mt) REVERT: A 1278 GLN cc_start: 0.7306 (mm110) cc_final: 0.6877 (mm110) REVERT: A 1313 MET cc_start: 0.7757 (ttt) cc_final: 0.7239 (ttm) outliers start: 72 outliers final: 56 residues processed: 180 average time/residue: 0.2023 time to fit residues: 53.5050 Evaluate side-chains 173 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 111 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1033 TYR Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1241 SER Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1326 PHE Chi-restraints excluded: chain A residue 1382 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 74 optimal weight: 0.0370 chunk 31 optimal weight: 9.9990 chunk 127 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 42 optimal weight: 0.0370 chunk 67 optimal weight: 2.9990 chunk 123 optimal weight: 0.0670 overall best weight: 1.8278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10534 Z= 0.220 Angle : 0.576 7.895 14376 Z= 0.295 Chirality : 0.043 0.196 1555 Planarity : 0.004 0.063 1816 Dihedral : 6.171 53.504 1526 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 7.05 % Allowed : 22.54 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % 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: -2.54 (0.22), residues: 1315 helix: 0.89 (0.36), residues: 213 sheet: -1.78 (0.34), residues: 190 loop : -2.49 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 277 HIS 0.004 0.001 HIS A1373 PHE 0.021 0.001 PHE A 697 TYR 0.014 0.001 TYR A 116 ARG 0.004 0.000 ARG A1015 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 123 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 TRP cc_start: 0.6663 (m100) cc_final: 0.6181 (m100) REVERT: A 140 TRP cc_start: 0.7239 (m100) cc_final: 0.6364 (m100) REVERT: A 141 LYS cc_start: 0.7349 (mmmt) cc_final: 0.6198 (mttp) REVERT: A 222 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.7284 (mtpt) REVERT: A 320 MET cc_start: 0.8045 (ttt) cc_final: 0.7567 (ttt) REVERT: A 358 ASP cc_start: 0.7672 (p0) cc_final: 0.7299 (p0) REVERT: A 406 GLU cc_start: 0.7303 (tm-30) cc_final: 0.6959 (tm-30) REVERT: A 481 LEU cc_start: 0.6709 (OUTLIER) cc_final: 0.6377 (pp) REVERT: A 557 TRP cc_start: 0.8289 (m100) cc_final: 0.8015 (m100) REVERT: A 561 ARG cc_start: 0.4935 (ptm160) cc_final: 0.4706 (ptm160) REVERT: A 657 TYR cc_start: 0.7550 (m-80) cc_final: 0.7318 (m-80) REVERT: A 688 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7523 (p90) REVERT: A 695 LYS cc_start: 0.6715 (OUTLIER) cc_final: 0.5963 (mmtm) REVERT: A 771 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7476 (m-30) REVERT: A 838 LEU cc_start: 0.8791 (mm) cc_final: 0.8410 (mm) REVERT: A 846 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.6981 (p90) REVERT: A 1033 TYR cc_start: 0.7715 (OUTLIER) cc_final: 0.7472 (p90) REVERT: A 1117 ILE cc_start: 0.8848 (mm) cc_final: 0.8536 (mt) REVERT: A 1222 TYR cc_start: 0.7481 (t80) cc_final: 0.7260 (t80) REVERT: A 1313 MET cc_start: 0.7745 (ttt) cc_final: 0.7241 (ttm) outliers start: 71 outliers final: 51 residues processed: 187 average time/residue: 0.2102 time to fit residues: 57.7903 Evaluate side-chains 169 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 111 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 59 CYS Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain A residue 1033 TYR Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain A residue 1241 SER Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1326 PHE Chi-restraints excluded: chain A residue 1376 SER Chi-restraints excluded: chain A residue 1380 CYS Chi-restraints excluded: chain A residue 1382 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 77 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 50 optimal weight: 0.0980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 ASN A1278 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10534 Z= 0.235 Angle : 0.598 8.149 14376 Z= 0.304 Chirality : 0.043 0.194 1555 Planarity : 0.004 0.059 1816 Dihedral : 6.170 52.740 1526 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 7.15 % Allowed : 22.44 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % 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: -2.47 (0.22), residues: 1315 helix: 0.95 (0.36), residues: 213 sheet: -1.71 (0.35), residues: 190 loop : -2.46 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 277 HIS 0.005 0.001 HIS A 40 PHE 0.024 0.002 PHE A1348 TYR 0.021 0.001 TYR A1019 ARG 0.004 0.001 ARG A1015 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 113 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 TRP cc_start: 0.6789 (m100) cc_final: 0.6243 (m100) REVERT: A 140 TRP cc_start: 0.7315 (m100) cc_final: 0.6466 (m100) REVERT: A 141 LYS cc_start: 0.7338 (mmmt) cc_final: 0.6260 (mttp) REVERT: A 320 MET cc_start: 0.8051 (ttt) cc_final: 0.7576 (ttt) REVERT: A 358 ASP cc_start: 0.7688 (p0) cc_final: 0.7349 (p0) REVERT: A 406 GLU cc_start: 0.7310 (tm-30) cc_final: 0.6968 (tm-30) REVERT: A 481 LEU cc_start: 0.6702 (OUTLIER) cc_final: 0.6364 (pp) REVERT: A 557 TRP cc_start: 0.8331 (m100) cc_final: 0.8079 (m100) REVERT: A 561 ARG cc_start: 0.4944 (ptm160) cc_final: 0.4718 (ptm-80) REVERT: A 657 TYR cc_start: 0.7563 (m-80) cc_final: 0.7321 (m-80) REVERT: A 688 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7539 (p90) REVERT: A 695 LYS cc_start: 0.6668 (OUTLIER) cc_final: 0.5938 (mmtm) REVERT: A 771 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7423 (m-30) REVERT: A 838 LEU cc_start: 0.8830 (mm) cc_final: 0.8441 (mm) REVERT: A 846 PHE cc_start: 0.7925 (OUTLIER) cc_final: 0.7087 (p90) REVERT: A 876 ARG cc_start: 0.7955 (mtm180) cc_final: 0.7740 (mtm-85) REVERT: A 1033 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.7536 (p90) REVERT: A 1117 ILE cc_start: 0.8846 (mm) cc_final: 0.8525 (mt) REVERT: A 1222 TYR cc_start: 0.7637 (t80) cc_final: 0.7421 (t80) REVERT: A 1313 MET cc_start: 0.7748 (ttt) cc_final: 0.7252 (ttm) outliers start: 72 outliers final: 56 residues processed: 176 average time/residue: 0.1990 time to fit residues: 51.0552 Evaluate side-chains 174 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 112 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 880 TRP Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain A residue 1033 TYR Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain A residue 1241 SER Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1326 PHE Chi-restraints excluded: chain A residue 1376 SER Chi-restraints excluded: chain A residue 1380 CYS Chi-restraints excluded: chain A residue 1382 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 100 optimal weight: 0.0040 chunk 115 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 0.4980 overall best weight: 1.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 ASN A1278 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10534 Z= 0.171 Angle : 0.560 7.699 14376 Z= 0.285 Chirality : 0.042 0.168 1555 Planarity : 0.004 0.058 1816 Dihedral : 5.885 53.984 1525 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 6.06 % Allowed : 23.93 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % 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: -2.32 (0.22), residues: 1315 helix: 1.15 (0.36), residues: 213 sheet: -1.59 (0.37), residues: 173 loop : -2.37 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 277 HIS 0.005 0.001 HIS A 40 PHE 0.024 0.001 PHE A1348 TYR 0.020 0.001 TYR A1019 ARG 0.004 0.000 ARG A1015 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 122 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 TRP cc_start: 0.6663 (m100) cc_final: 0.6148 (m100) REVERT: A 140 TRP cc_start: 0.7279 (m100) cc_final: 0.6418 (m100) REVERT: A 141 LYS cc_start: 0.7257 (mmmt) cc_final: 0.6322 (mttp) REVERT: A 320 MET cc_start: 0.7999 (ttt) cc_final: 0.7541 (ttt) REVERT: A 358 ASP cc_start: 0.7582 (p0) cc_final: 0.7260 (p0) REVERT: A 406 GLU cc_start: 0.7261 (tm-30) cc_final: 0.6917 (tm-30) REVERT: A 481 LEU cc_start: 0.6656 (OUTLIER) cc_final: 0.6338 (pp) REVERT: A 557 TRP cc_start: 0.8247 (m100) cc_final: 0.8038 (m100) REVERT: A 561 ARG cc_start: 0.4801 (ptm160) cc_final: 0.4590 (ptm-80) REVERT: A 657 TYR cc_start: 0.7492 (m-80) cc_final: 0.6907 (m-80) REVERT: A 688 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7339 (p90) REVERT: A 695 LYS cc_start: 0.6574 (OUTLIER) cc_final: 0.5880 (mmtm) REVERT: A 697 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.6785 (t80) REVERT: A 771 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7428 (m-30) REVERT: A 838 LEU cc_start: 0.8796 (mm) cc_final: 0.8487 (mm) REVERT: A 1033 TYR cc_start: 0.7750 (OUTLIER) cc_final: 0.7464 (p90) REVERT: A 1117 ILE cc_start: 0.8786 (mm) cc_final: 0.8445 (mt) REVERT: A 1222 TYR cc_start: 0.7741 (t80) cc_final: 0.7462 (t80) REVERT: A 1313 MET cc_start: 0.7711 (ttt) cc_final: 0.7226 (ttm) outliers start: 61 outliers final: 47 residues processed: 175 average time/residue: 0.2090 time to fit residues: 52.9834 Evaluate side-chains 166 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 113 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 697 PHE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain A residue 1033 TYR Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1326 PHE Chi-restraints excluded: chain A residue 1376 SER Chi-restraints excluded: chain A residue 1380 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 112 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN A1065 ASN A1278 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 10534 Z= 0.480 Angle : 0.757 8.907 14376 Z= 0.387 Chirality : 0.048 0.264 1555 Planarity : 0.005 0.055 1816 Dihedral : 6.770 53.173 1521 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 7.75 % Allowed : 22.24 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % 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: -2.67 (0.22), residues: 1315 helix: 0.66 (0.36), residues: 211 sheet: -1.67 (0.36), residues: 186 loop : -2.59 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 912 HIS 0.006 0.001 HIS A 294 PHE 0.030 0.003 PHE A 846 TYR 0.024 0.002 TYR A 888 ARG 0.007 0.001 ARG A 669 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 109 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 TRP cc_start: 0.6891 (m100) cc_final: 0.6562 (m100) REVERT: A 140 TRP cc_start: 0.7617 (m100) cc_final: 0.6690 (m100) REVERT: A 141 LYS cc_start: 0.7413 (mmmt) cc_final: 0.6537 (mttp) REVERT: A 358 ASP cc_start: 0.7703 (p0) cc_final: 0.7441 (p0) REVERT: A 406 GLU cc_start: 0.7504 (tm-30) cc_final: 0.7150 (tm-30) REVERT: A 481 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6433 (pp) REVERT: A 561 ARG cc_start: 0.5105 (ptm160) cc_final: 0.4881 (ptm160) REVERT: A 688 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.7820 (p90) REVERT: A 695 LYS cc_start: 0.6791 (OUTLIER) cc_final: 0.6036 (mmtm) REVERT: A 697 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.6675 (t80) REVERT: A 771 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7580 (m-30) REVERT: A 838 LEU cc_start: 0.8937 (mm) cc_final: 0.8457 (mm) REVERT: A 846 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7410 (p90) REVERT: A 1033 TYR cc_start: 0.8157 (OUTLIER) cc_final: 0.7694 (p90) REVERT: A 1117 ILE cc_start: 0.8886 (mm) cc_final: 0.8584 (mt) REVERT: A 1313 MET cc_start: 0.7792 (ttt) cc_final: 0.7216 (ttm) outliers start: 78 outliers final: 60 residues processed: 175 average time/residue: 0.1969 time to fit residues: 50.5969 Evaluate side-chains 175 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 108 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 697 PHE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain A residue 880 TRP Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1033 TYR Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1241 SER Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1326 PHE Chi-restraints excluded: chain A residue 1362 THR Chi-restraints excluded: chain A residue 1376 SER Chi-restraints excluded: chain A residue 1380 CYS Chi-restraints excluded: chain A residue 1382 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 80 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1065 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1278 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 10534 Z= 0.342 Angle : 0.676 8.523 14376 Z= 0.347 Chirality : 0.045 0.237 1555 Planarity : 0.004 0.054 1816 Dihedral : 6.611 54.039 1521 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 6.65 % Allowed : 23.63 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % 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: -2.61 (0.22), residues: 1315 helix: 0.74 (0.36), residues: 212 sheet: -1.64 (0.36), residues: 185 loop : -2.56 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 912 HIS 0.005 0.001 HIS A1265 PHE 0.027 0.002 PHE A 697 TYR 0.019 0.002 TYR A1019 ARG 0.004 0.001 ARG A 669 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 107 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 TRP cc_start: 0.6799 (m100) cc_final: 0.6333 (m100) REVERT: A 140 TRP cc_start: 0.7572 (m100) cc_final: 0.6640 (m100) REVERT: A 141 LYS cc_start: 0.7327 (mmmt) cc_final: 0.6572 (mttp) REVERT: A 320 MET cc_start: 0.8107 (ttt) cc_final: 0.7604 (ttt) REVERT: A 358 ASP cc_start: 0.7716 (p0) cc_final: 0.7472 (p0) REVERT: A 406 GLU cc_start: 0.7368 (tm-30) cc_final: 0.6766 (tm-30) REVERT: A 481 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6470 (pp) REVERT: A 561 ARG cc_start: 0.5060 (ptm160) cc_final: 0.4832 (ptm-80) REVERT: A 688 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.7576 (p90) REVERT: A 695 LYS cc_start: 0.6726 (OUTLIER) cc_final: 0.5991 (mmtm) REVERT: A 697 PHE cc_start: 0.7687 (OUTLIER) cc_final: 0.6593 (t80) REVERT: A 771 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7489 (m-30) REVERT: A 838 LEU cc_start: 0.8866 (mm) cc_final: 0.8389 (mm) REVERT: A 1033 TYR cc_start: 0.8081 (OUTLIER) cc_final: 0.7636 (p90) REVERT: A 1117 ILE cc_start: 0.8865 (mm) cc_final: 0.8570 (mt) REVERT: A 1313 MET cc_start: 0.7731 (ttt) cc_final: 0.7250 (ttm) outliers start: 67 outliers final: 58 residues processed: 164 average time/residue: 0.2010 time to fit residues: 48.7903 Evaluate side-chains 168 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 104 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 697 PHE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain A residue 880 TRP Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain A residue 1033 TYR Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1151 SER Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1326 PHE Chi-restraints excluded: chain A residue 1362 THR Chi-restraints excluded: chain A residue 1376 SER Chi-restraints excluded: chain A residue 1380 CYS Chi-restraints excluded: chain A residue 1382 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 43 optimal weight: 0.2980 chunk 107 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 960 ASN ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1065 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.191828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.160676 restraints weight = 13061.158| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 2.60 r_work: 0.3937 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3784 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3799 r_free = 0.3799 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3799 r_free = 0.3799 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10534 Z= 0.243 Angle : 0.621 7.971 14376 Z= 0.318 Chirality : 0.043 0.206 1555 Planarity : 0.004 0.050 1816 Dihedral : 6.311 54.408 1521 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 6.95 % Allowed : 23.54 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % 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: -2.47 (0.22), residues: 1315 helix: 0.91 (0.36), residues: 213 sheet: -1.59 (0.36), residues: 185 loop : -2.47 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 912 HIS 0.005 0.001 HIS A1373 PHE 0.023 0.002 PHE A 697 TYR 0.020 0.001 TYR A1019 ARG 0.003 0.000 ARG A1015 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2376.13 seconds wall clock time: 43 minutes 25.75 seconds (2605.75 seconds total)