Starting phenix.real_space_refine on Sat Oct 12 01:05:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vqc_43438/10_2024/8vqc_43438.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vqc_43438/10_2024/8vqc_43438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vqc_43438/10_2024/8vqc_43438.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vqc_43438/10_2024/8vqc_43438.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vqc_43438/10_2024/8vqc_43438.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vqc_43438/10_2024/8vqc_43438.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 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 69 5.16 5 C 7242 2.51 5 N 1733 2.21 5 O 1910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 10954 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1288, 10225 Classifications: {'peptide': 1288} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 45, 'TRANS': 1242} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 417 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 187 Chain: "H" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 506 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 60} Chain: "B" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 5, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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: 9.10, per 1000 atoms: 0.83 Number of scatterers: 10954 At special positions: 0 Unit cell: (127.38, 133.98, 125.4, 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 69 16.00 O 1910 8.00 N 1733 7.00 C 7242 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 337 " distance=2.04 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 343 " distance=2.03 Simple disulfide: pdb=" SG CYS A 709 " - pdb=" SG CYS A 717 " distance=2.03 Simple disulfide: pdb=" SG CYS A1011 " - pdb=" SG CYS A1030 " distance=2.03 Simple disulfide: pdb=" SG CYS A1368 " - pdb=" SG CYS A1381 " distance=2.03 Simple disulfide: pdb=" SG CYS H 12 " - pdb=" SG CYS H 63 " distance=2.03 Simple disulfide: pdb=" SG CYS H 16 " - pdb=" SG CYS H 36 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 46 " distance=2.03 Simple disulfide: pdb=" SG CYS H 26 " - pdb=" SG CYS H 48 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 BETA1-3 " BMA B 3 " - " BMA B 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " BETA1-6 " BMA B 3 " - " BMA B 6 " " BMA B 4 " - " BMA B 5 " " BMA B 6 " - " BMA B 7 " NAG-ASN " NAG A1601 " - " ASN A 308 " " NAG A1602 " - " ASN A1028 " " NAG B 1 " - " ASN A 330 " " NAG C 1 " - " ASN A1034 " " NAG D 1 " - " ASN A1015 " " NAG E 1 " - " ASN A 312 " " NAG G 1 " - " ASN A 300 " Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.5 seconds 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2568 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 3 sheets defined 70.3% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 95 through 111 Processing helix chain 'A' and resid 128 through 139 removed outlier: 3.622A pdb=" N VAL A 132 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 157 removed outlier: 3.679A pdb=" N SER A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 188 Processing helix chain 'A' and resid 191 through 197 removed outlier: 3.994A pdb=" N ALA A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 216 removed outlier: 3.564A pdb=" N LEU A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP A 205 " --> pdb=" O TRP A 201 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 216 " --> pdb=" O GLY A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 240 removed outlier: 3.911A pdb=" N VAL A 231 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ARG A 233 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 240 " --> pdb=" O THR A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 280 removed outlier: 4.282A pdb=" N ILE A 247 " --> pdb=" O GLY A 243 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ASP A 260 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU A 261 " --> pdb=" O SER A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 311 removed outlier: 4.058A pdb=" N PHE A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 373 Processing helix chain 'A' and resid 376 through 389 removed outlier: 4.397A pdb=" N LEU A 380 " --> pdb=" O TYR A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 402 removed outlier: 3.752A pdb=" N PHE A 396 " --> pdb=" O HIS A 392 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 431 removed outlier: 4.625A pdb=" N ASN A 409 " --> pdb=" O PHE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 518 Processing helix chain 'A' and resid 518 through 537 removed outlier: 3.712A pdb=" N GLU A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 573 Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 581 through 601 removed outlier: 3.879A pdb=" N VAL A 585 " --> pdb=" O ASP A 581 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A 601 " --> pdb=" O GLU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 613 removed outlier: 4.202A pdb=" N PHE A 612 " --> pdb=" O VAL A 608 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG A 613 " --> pdb=" O PHE A 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 608 through 613' Processing helix chain 'A' and resid 614 through 619 removed outlier: 4.144A pdb=" N PHE A 618 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 614 through 619' Processing helix chain 'A' and resid 620 through 623 Processing helix chain 'A' and resid 626 through 636 removed outlier: 4.188A pdb=" N LYS A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 670 removed outlier: 3.776A pdb=" N VAL A 642 " --> pdb=" O TYR A 638 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ASN A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N MET A 665 " --> pdb=" O GLN A 661 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ASN A 666 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN A 670 " --> pdb=" O ASN A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 700 Processing helix chain 'A' and resid 702 through 712 removed outlier: 3.533A pdb=" N VAL A 712 " --> pdb=" O ASP A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 716 No H-bonds generated for 'chain 'A' and resid 714 through 716' Processing helix chain 'A' and resid 717 through 727 removed outlier: 3.797A pdb=" N PHE A 721 " --> pdb=" O CYS A 717 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 722 " --> pdb=" O ILE A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 744 Processing helix chain 'A' and resid 834 through 855 Processing helix chain 'A' and resid 855 through 875 removed outlier: 3.812A pdb=" N GLN A 859 " --> pdb=" O ASN A 855 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 875 " --> pdb=" O VAL A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 912 removed outlier: 4.081A pdb=" N VAL A 887 " --> pdb=" O ARG A 883 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN A 888 " --> pdb=" O PRO A 884 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ILE A 889 " --> pdb=" O VAL A 885 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 896 " --> pdb=" O TYR A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 920 Processing helix chain 'A' and resid 920 through 942 removed outlier: 3.743A pdb=" N TRP A 924 " --> pdb=" O SER A 920 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP A 926 " --> pdb=" O TRP A 922 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 942 " --> pdb=" O VAL A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 958 removed outlier: 3.793A pdb=" N ARG A 957 " --> pdb=" O LEU A 953 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 958 " --> pdb=" O ARG A 954 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 953 through 958' Processing helix chain 'A' and resid 958 through 963 Processing helix chain 'A' and resid 964 through 966 No H-bonds generated for 'chain 'A' and resid 964 through 966' Processing helix chain 'A' and resid 967 through 1005 removed outlier: 4.009A pdb=" N VAL A 971 " --> pdb=" O GLY A 967 " (cutoff:3.500A) Proline residue: A 980 - end of helix removed outlier: 4.410A pdb=" N MET A 999 " --> pdb=" O VAL A 995 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN A1002 " --> pdb=" O ILE A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1033 removed outlier: 3.715A pdb=" N CYS A1030 " --> pdb=" O ASP A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1059 Processing helix chain 'A' and resid 1062 through 1071 removed outlier: 4.190A pdb=" N ILE A1066 " --> pdb=" O GLY A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1097 removed outlier: 3.719A pdb=" N PHE A1092 " --> pdb=" O MET A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1124 removed outlier: 4.092A pdb=" N CYS A1109 " --> pdb=" O LYS A1105 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP A1113 " --> pdb=" O CYS A1109 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A1114 " --> pdb=" O ILE A1110 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY A1124 " --> pdb=" O ARG A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1146 Processing helix chain 'A' and resid 1157 through 1168 Processing helix chain 'A' and resid 1169 through 1189 removed outlier: 3.699A pdb=" N GLU A1173 " --> pdb=" O ASN A1169 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE A1189 " --> pdb=" O ALA A1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 1195 through 1224 removed outlier: 3.724A pdb=" N GLU A1200 " --> pdb=" O MET A1196 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A1201 " --> pdb=" O GLU A1197 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A1222 " --> pdb=" O VAL A1218 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY A1223 " --> pdb=" O ILE A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1257 removed outlier: 3.811A pdb=" N PHE A1238 " --> pdb=" O ASN A1234 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A1243 " --> pdb=" O LEU A1239 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ASP A1252 " --> pdb=" O LEU A1248 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL A1253 " --> pdb=" O MET A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1268 removed outlier: 4.658A pdb=" N LEU A1263 " --> pdb=" O ILE A1259 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU A1264 " --> pdb=" O SER A1260 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ARG A1265 " --> pdb=" O PRO A1261 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A1268 " --> pdb=" O LEU A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1273 removed outlier: 3.632A pdb=" N GLY A1273 " --> pdb=" O LEU A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1295 removed outlier: 4.047A pdb=" N ARG A1286 " --> pdb=" O ALA A1282 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A1295 " --> pdb=" O ALA A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1321 Processing helix chain 'A' and resid 1338 through 1351 removed outlier: 4.260A pdb=" N THR A1351 " --> pdb=" O PHE A1347 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1363 removed outlier: 3.709A pdb=" N VAL A1358 " --> pdb=" O GLY A1354 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1398 removed outlier: 3.973A pdb=" N SER A1393 " --> pdb=" O ALA A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1401 through 1424 removed outlier: 3.688A pdb=" N ILE A1410 " --> pdb=" O TYR A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1439 removed outlier: 3.728A pdb=" N GLN A1439 " --> pdb=" O GLU A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1451 through 1459 removed outlier: 3.889A pdb=" N GLU A1455 " --> pdb=" O ASP A1451 " (cutoff:3.500A) Processing helix chain 'A' and resid 1470 through 1477 Processing helix chain 'A' and resid 1488 through 1505 removed outlier: 3.523A pdb=" N VAL A1492 " --> pdb=" O PHE A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1521 Proline residue: A1516 - end of helix removed outlier: 3.507A pdb=" N ALA A1521 " --> pdb=" O ASN A1517 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 29 removed outlier: 3.610A pdb=" N CYS H 26 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASN H 29 " --> pdb=" O LEU H 25 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 289 through 290 Processing sheet with id=AA2, first strand: chain 'A' and resid 1009 through 1012 Processing sheet with id=AA3, first strand: chain 'H' and resid 34 through 35 631 hydrogen bonds defined for protein. 1857 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.47 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3306 1.34 - 1.46: 3016 1.46 - 1.58: 4817 1.58 - 1.70: 0 1.70 - 1.82: 111 Bond restraints: 11250 Sorted by residual: bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C LEU A1276 " pdb=" N ARG A1277 " ideal model delta sigma weight residual 1.335 1.308 0.027 1.30e-02 5.92e+03 4.25e+00 bond pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sigma weight residual 1.417 1.452 -0.035 2.00e-02 2.50e+03 3.01e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.80e+00 bond pdb=" CA LEU A1276 " pdb=" C LEU A1276 " ideal model delta sigma weight residual 1.522 1.500 0.022 1.39e-02 5.18e+03 2.59e+00 ... (remaining 11245 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 15025 2.36 - 4.72: 228 4.72 - 7.08: 47 7.08 - 9.44: 10 9.44 - 11.79: 5 Bond angle restraints: 15315 Sorted by residual: angle pdb=" CA GLU A1443 " pdb=" CB GLU A1443 " pdb=" CG GLU A1443 " ideal model delta sigma weight residual 114.10 123.56 -9.46 2.00e+00 2.50e-01 2.24e+01 angle pdb=" CB ARG H 2 " pdb=" CG ARG H 2 " pdb=" CD ARG H 2 " ideal model delta sigma weight residual 111.30 120.75 -9.45 2.30e+00 1.89e-01 1.69e+01 angle pdb=" CB MET A1196 " pdb=" CG MET A1196 " pdb=" SD MET A1196 " ideal model delta sigma weight residual 112.70 124.49 -11.79 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CB GLU A1443 " pdb=" CG GLU A1443 " pdb=" CD GLU A1443 " ideal model delta sigma weight residual 112.60 119.20 -6.60 1.70e+00 3.46e-01 1.51e+01 angle pdb=" C ILE A 146 " pdb=" N MET A 147 " pdb=" CA MET A 147 " ideal model delta sigma weight residual 121.14 115.02 6.12 1.75e+00 3.27e-01 1.22e+01 ... (remaining 15310 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.84: 5957 21.84 - 43.68: 642 43.68 - 65.52: 78 65.52 - 87.37: 43 87.37 - 109.21: 29 Dihedral angle restraints: 6749 sinusoidal: 2766 harmonic: 3983 Sorted by residual: dihedral pdb=" CB CYS A1368 " pdb=" SG CYS A1368 " pdb=" SG CYS A1381 " pdb=" CB CYS A1381 " ideal model delta sinusoidal sigma weight residual -86.00 -3.84 -82.16 1 1.00e+01 1.00e-02 8.29e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 46 " pdb=" CB CYS H 46 " ideal model delta sinusoidal sigma weight residual -86.00 -163.21 77.21 1 1.00e+01 1.00e-02 7.47e+01 dihedral pdb=" CB CYS A1011 " pdb=" SG CYS A1011 " pdb=" SG CYS A1030 " pdb=" CB CYS A1030 " ideal model delta sinusoidal sigma weight residual -86.00 -148.92 62.92 1 1.00e+01 1.00e-02 5.23e+01 ... (remaining 6746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1639 0.078 - 0.156: 134 0.156 - 0.234: 6 0.234 - 0.312: 5 0.312 - 0.389: 2 Chirality restraints: 1786 Sorted by residual: chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 330 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.79 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" C4 NAG B 1 " pdb=" C3 NAG B 1 " pdb=" C5 NAG B 1 " pdb=" O4 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.20 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" C5 BMA B 6 " pdb=" C4 BMA B 6 " pdb=" C6 BMA B 6 " pdb=" O5 BMA B 6 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 1783 not shown) Planarity restraints: 1883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 244 " 0.016 2.00e-02 2.50e+03 1.69e-02 7.13e+00 pdb=" CG TRP A 244 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP A 244 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 244 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 244 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 244 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 244 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 244 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 244 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 244 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1443 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.12e+00 pdb=" C GLU A1443 " -0.035 2.00e-02 2.50e+03 pdb=" O GLU A1443 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA A1444 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 192 " -0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO A 193 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 193 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 193 " -0.028 5.00e-02 4.00e+02 ... (remaining 1880 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 40 2.41 - 3.03: 7161 3.03 - 3.66: 16889 3.66 - 4.28: 22951 4.28 - 4.90: 36867 Nonbonded interactions: 83908 Sorted by model distance: nonbonded pdb=" O THR A1059 " pdb=" NZ LYS A1061 " model vdw 1.791 3.120 nonbonded pdb=" O SER A 632 " pdb=" OG1 THR A 635 " model vdw 2.173 3.040 nonbonded pdb=" OD1 ASP A1129 " pdb=" N SER A1130 " model vdw 2.185 3.120 nonbonded pdb=" ND2 ASN H 23 " pdb=" O GLY H 34 " model vdw 2.243 3.120 nonbonded pdb=" O LYS A 915 " pdb=" OG1 THR A 919 " model vdw 2.243 3.040 ... (remaining 83903 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.980 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: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.470 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11250 Z= 0.246 Angle : 0.756 11.795 15315 Z= 0.369 Chirality : 0.047 0.389 1786 Planarity : 0.004 0.058 1876 Dihedral : 19.496 109.206 4154 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.45 % Favored : 92.40 % Rotamer: Outliers : 0.72 % Allowed : 28.18 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.24), residues: 1342 helix: 0.88 (0.18), residues: 854 sheet: -2.32 (1.42), residues: 12 loop : -2.01 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP A 244 HIS 0.003 0.001 HIS A1486 PHE 0.027 0.001 PHE A 861 TYR 0.022 0.001 TYR H 21 ARG 0.014 0.000 ARG H 2 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 230 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 947 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7529 (tt) REVERT: A 1275 LEU cc_start: 0.8036 (mp) cc_final: 0.7704 (tt) outliers start: 8 outliers final: 4 residues processed: 234 average time/residue: 0.2260 time to fit residues: 76.7852 Evaluate side-chains 228 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 223 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1226 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 0.0270 chunk 101 optimal weight: 10.0000 chunk 56 optimal weight: 0.1980 chunk 34 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 105 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1079 GLN A1169 ASN A1227 HIS H 23 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11250 Z= 0.174 Angle : 0.636 9.765 15315 Z= 0.315 Chirality : 0.044 0.307 1786 Planarity : 0.004 0.053 1876 Dihedral : 12.730 88.702 1829 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.00 % Favored : 92.85 % Rotamer: Outliers : 3.88 % Allowed : 24.57 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.24), residues: 1342 helix: 0.96 (0.18), residues: 891 sheet: -2.73 (1.23), residues: 12 loop : -2.18 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 244 HIS 0.002 0.001 HIS A 291 PHE 0.016 0.001 PHE A 861 TYR 0.022 0.001 TYR A1240 ARG 0.010 0.001 ARG H 2 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 242 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8146 (p) REVERT: A 715 TRP cc_start: 0.6716 (p90) cc_final: 0.6228 (p90) REVERT: A 1054 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8670 (mt) REVERT: A 1102 PHE cc_start: 0.8712 (t80) cc_final: 0.8493 (t80) REVERT: H 2 ARG cc_start: 0.7647 (mmm160) cc_final: 0.7328 (mmm160) outliers start: 43 outliers final: 21 residues processed: 268 average time/residue: 0.2093 time to fit residues: 82.5641 Evaluate side-chains 250 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 227 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 924 TRP Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1248 LEU Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1343 ILE Chi-restraints excluded: chain A residue 1362 ILE Chi-restraints excluded: chain A residue 1406 TYR Chi-restraints excluded: chain A residue 1418 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 101 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 ASN A1056 GLN ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1234 ASN ** A1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1439 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11250 Z= 0.206 Angle : 0.641 8.854 15315 Z= 0.317 Chirality : 0.044 0.290 1786 Planarity : 0.004 0.054 1876 Dihedral : 9.961 77.604 1822 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.00 % Favored : 92.85 % Rotamer: Outliers : 4.88 % Allowed : 25.38 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.24), residues: 1342 helix: 0.93 (0.18), residues: 892 sheet: -2.89 (1.18), residues: 12 loop : -2.11 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 244 HIS 0.004 0.001 HIS A1227 PHE 0.017 0.001 PHE A1321 TYR 0.017 0.001 TYR A 895 ARG 0.007 0.000 ARG A 613 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 231 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 547 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8280 (t80) REVERT: A 715 TRP cc_start: 0.6800 (p90) cc_final: 0.6323 (p90) REVERT: A 984 ASN cc_start: 0.8195 (t0) cc_final: 0.7946 (t0) REVERT: A 1276 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8377 (tt) REVERT: A 1432 MET cc_start: 0.7570 (ptt) cc_final: 0.7104 (ptt) outliers start: 54 outliers final: 29 residues processed: 264 average time/residue: 0.2085 time to fit residues: 81.1306 Evaluate side-chains 253 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 222 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 924 TRP Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1248 LEU Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1343 ILE Chi-restraints excluded: chain A residue 1418 TYR Chi-restraints excluded: chain A residue 1439 GLN Chi-restraints excluded: chain A residue 1492 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.0050 chunk 91 optimal weight: 0.0970 chunk 63 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 122 optimal weight: 0.2980 chunk 129 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11250 Z= 0.168 Angle : 0.643 13.911 15315 Z= 0.314 Chirality : 0.044 0.281 1786 Planarity : 0.004 0.054 1876 Dihedral : 8.395 66.116 1822 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.86 % Favored : 93.07 % Rotamer: Outliers : 4.34 % Allowed : 26.56 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.24), residues: 1342 helix: 0.96 (0.18), residues: 891 sheet: -2.62 (1.25), residues: 12 loop : -2.11 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 244 HIS 0.007 0.001 HIS A1226 PHE 0.020 0.001 PHE A 900 TYR 0.016 0.001 TYR A 895 ARG 0.008 0.000 ARG A 613 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 229 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 342 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.8180 (p) REVERT: A 378 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: A 420 THR cc_start: 0.9158 (t) cc_final: 0.8892 (t) REVERT: A 715 TRP cc_start: 0.6709 (p90) cc_final: 0.6248 (p90) REVERT: A 984 ASN cc_start: 0.8171 (t0) cc_final: 0.7912 (t0) REVERT: A 1042 MET cc_start: 0.7270 (tpp) cc_final: 0.7026 (tpp) REVERT: A 1054 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8568 (mt) REVERT: A 1197 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6537 (tt0) REVERT: A 1276 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8398 (tt) outliers start: 48 outliers final: 27 residues processed: 259 average time/residue: 0.2086 time to fit residues: 79.8990 Evaluate side-chains 256 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 224 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 924 TRP Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1343 ILE Chi-restraints excluded: chain A residue 1345 LEU Chi-restraints excluded: chain A residue 1362 ILE Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1418 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 2.9990 chunk 1 optimal weight: 30.0000 chunk 96 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 0 optimal weight: 50.0000 chunk 66 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 43 optimal weight: 0.0870 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1194 GLN A1226 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11250 Z= 0.189 Angle : 0.648 13.925 15315 Z= 0.313 Chirality : 0.043 0.274 1786 Planarity : 0.004 0.053 1876 Dihedral : 7.371 57.327 1820 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.08 % Favored : 92.85 % Rotamer: Outliers : 5.06 % Allowed : 26.20 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.24), residues: 1342 helix: 1.01 (0.18), residues: 891 sheet: -2.77 (1.24), residues: 12 loop : -2.08 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 244 HIS 0.005 0.001 HIS A1226 PHE 0.023 0.001 PHE A 900 TYR 0.017 0.001 TYR A 895 ARG 0.009 0.000 ARG A 613 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 229 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8200 (p) REVERT: A 378 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7718 (mt-10) REVERT: A 379 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7267 (t0) REVERT: A 420 THR cc_start: 0.9159 (t) cc_final: 0.8909 (t) REVERT: A 636 LYS cc_start: 0.7866 (pttm) cc_final: 0.7617 (tppt) REVERT: A 715 TRP cc_start: 0.6743 (p90) cc_final: 0.6308 (p90) REVERT: A 876 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6663 (tm-30) REVERT: A 947 LEU cc_start: 0.8129 (tp) cc_final: 0.7910 (tt) REVERT: A 984 ASN cc_start: 0.8187 (t0) cc_final: 0.7929 (t0) REVERT: A 1019 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8604 (mm) REVERT: A 1197 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6468 (tt0) REVERT: A 1224 LEU cc_start: 0.7251 (tp) cc_final: 0.6952 (tt) REVERT: A 1276 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8668 (tt) REVERT: A 1432 MET cc_start: 0.7623 (ptt) cc_final: 0.7278 (ptt) outliers start: 56 outliers final: 35 residues processed: 267 average time/residue: 0.2120 time to fit residues: 83.4560 Evaluate side-chains 259 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 217 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 924 TRP Chi-restraints excluded: chain A residue 933 TYR Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1343 ILE Chi-restraints excluded: chain A residue 1345 LEU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1418 TYR Chi-restraints excluded: chain H residue 1 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11250 Z= 0.198 Angle : 0.659 12.638 15315 Z= 0.318 Chirality : 0.043 0.268 1786 Planarity : 0.004 0.053 1876 Dihedral : 6.730 57.904 1820 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.30 % Favored : 92.62 % Rotamer: Outliers : 5.24 % Allowed : 26.11 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.24), residues: 1342 helix: 1.03 (0.18), residues: 887 sheet: -2.88 (1.25), residues: 12 loop : -1.98 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 244 HIS 0.002 0.001 HIS A 291 PHE 0.019 0.001 PHE A1238 TYR 0.015 0.001 TYR H 21 ARG 0.012 0.000 ARG A 613 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 226 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8259 (p) REVERT: A 378 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7725 (mt-10) REVERT: A 379 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.7288 (t0) REVERT: A 715 TRP cc_start: 0.6677 (p90) cc_final: 0.6259 (p90) REVERT: A 984 ASN cc_start: 0.8183 (t0) cc_final: 0.7937 (t0) REVERT: A 1019 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8639 (mm) REVERT: A 1049 ASN cc_start: 0.8797 (OUTLIER) cc_final: 0.8115 (t0) REVERT: A 1196 MET cc_start: 0.8429 (mmm) cc_final: 0.8218 (mmm) REVERT: A 1197 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6582 (tt0) REVERT: A 1224 LEU cc_start: 0.7380 (tp) cc_final: 0.7074 (tt) REVERT: H 2 ARG cc_start: 0.8270 (mmm160) cc_final: 0.7682 (mmm160) outliers start: 58 outliers final: 39 residues processed: 267 average time/residue: 0.2052 time to fit residues: 81.5167 Evaluate side-chains 262 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 217 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 924 TRP Chi-restraints excluded: chain A residue 933 TYR Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1049 ASN Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1343 ILE Chi-restraints excluded: chain A residue 1345 LEU Chi-restraints excluded: chain A residue 1346 LEU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1406 TYR Chi-restraints excluded: chain A residue 1418 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.0000 chunk 73 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 129 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11250 Z= 0.191 Angle : 0.669 11.528 15315 Z= 0.324 Chirality : 0.043 0.261 1786 Planarity : 0.004 0.052 1876 Dihedral : 6.387 58.546 1820 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.53 % Favored : 92.40 % Rotamer: Outliers : 4.97 % Allowed : 27.28 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.24), residues: 1342 helix: 1.05 (0.18), residues: 887 sheet: -2.59 (1.35), residues: 12 loop : -2.02 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 244 HIS 0.002 0.001 HIS A 421 PHE 0.026 0.001 PHE A 900 TYR 0.012 0.001 TYR A 895 ARG 0.012 0.000 ARG A 613 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 232 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 THR cc_start: 0.8568 (OUTLIER) cc_final: 0.7794 (p) REVERT: A 344 LEU cc_start: 0.8837 (mp) cc_final: 0.8553 (mp) REVERT: A 378 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7734 (mt-10) REVERT: A 379 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7286 (t0) REVERT: A 715 TRP cc_start: 0.6665 (p90) cc_final: 0.6244 (p90) REVERT: A 876 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6571 (tm-30) REVERT: A 984 ASN cc_start: 0.8182 (t0) cc_final: 0.7934 (t0) REVERT: A 1019 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8671 (mm) REVERT: A 1049 ASN cc_start: 0.8346 (OUTLIER) cc_final: 0.8121 (t0) REVERT: A 1197 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6564 (tt0) REVERT: A 1224 LEU cc_start: 0.7340 (tp) cc_final: 0.7045 (tt) outliers start: 55 outliers final: 39 residues processed: 272 average time/residue: 0.2177 time to fit residues: 88.2234 Evaluate side-chains 267 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 221 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 924 TRP Chi-restraints excluded: chain A residue 933 TYR Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1038 GLU Chi-restraints excluded: chain A residue 1049 ASN Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1343 ILE Chi-restraints excluded: chain A residue 1345 LEU Chi-restraints excluded: chain A residue 1346 LEU Chi-restraints excluded: chain A residue 1362 ILE Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1406 TYR Chi-restraints excluded: chain A residue 1418 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 82 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 117 optimal weight: 0.5980 chunk 123 optimal weight: 0.0970 chunk 112 optimal weight: 0.0980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 742 ASN A 948 GLN ** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11250 Z= 0.173 Angle : 0.671 11.026 15315 Z= 0.323 Chirality : 0.043 0.253 1786 Planarity : 0.004 0.055 1876 Dihedral : 6.123 59.555 1820 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.00 % Favored : 92.92 % Rotamer: Outliers : 4.43 % Allowed : 27.91 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.24), residues: 1342 helix: 1.03 (0.18), residues: 888 sheet: -2.62 (1.37), residues: 12 loop : -2.08 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 244 HIS 0.003 0.001 HIS A1021 PHE 0.034 0.001 PHE A 900 TYR 0.015 0.001 TYR H 21 ARG 0.012 0.001 ARG A 613 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 235 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.7764 (p) REVERT: A 344 LEU cc_start: 0.8789 (mp) cc_final: 0.8536 (mp) REVERT: A 378 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7691 (mt-10) REVERT: A 379 ASP cc_start: 0.7600 (OUTLIER) cc_final: 0.7217 (t0) REVERT: A 715 TRP cc_start: 0.6636 (p90) cc_final: 0.6191 (p90) REVERT: A 984 ASN cc_start: 0.8150 (t0) cc_final: 0.7907 (t0) REVERT: A 1019 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8620 (mm) REVERT: A 1197 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6562 (tt0) REVERT: A 1224 LEU cc_start: 0.7405 (tp) cc_final: 0.7140 (tt) REVERT: A 1275 LEU cc_start: 0.8167 (mp) cc_final: 0.7667 (tt) REVERT: H 2 ARG cc_start: 0.8253 (mmm160) cc_final: 0.7619 (mmm160) outliers start: 49 outliers final: 33 residues processed: 270 average time/residue: 0.2090 time to fit residues: 83.7211 Evaluate side-chains 264 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 226 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 924 TRP Chi-restraints excluded: chain A residue 933 TYR Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1343 ILE Chi-restraints excluded: chain A residue 1345 LEU Chi-restraints excluded: chain A residue 1346 LEU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1406 TYR Chi-restraints excluded: chain A residue 1418 TYR Chi-restraints excluded: chain H residue 1 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 3.9990 chunk 123 optimal weight: 0.0070 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 36 optimal weight: 40.0000 chunk 108 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 ASN ** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11250 Z= 0.199 Angle : 0.702 12.052 15315 Z= 0.337 Chirality : 0.043 0.252 1786 Planarity : 0.004 0.052 1876 Dihedral : 6.006 59.454 1820 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.30 % Favored : 92.62 % Rotamer: Outliers : 4.34 % Allowed : 28.64 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.24), residues: 1342 helix: 1.01 (0.18), residues: 888 sheet: -2.91 (1.39), residues: 10 loop : -2.07 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 244 HIS 0.003 0.001 HIS A1021 PHE 0.028 0.001 PHE A 900 TYR 0.012 0.001 TYR A1334 ARG 0.011 0.000 ARG A 613 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 229 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.7742 (p) REVERT: A 344 LEU cc_start: 0.8830 (mp) cc_final: 0.8553 (mp) REVERT: A 378 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7713 (mt-10) REVERT: A 379 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7241 (t0) REVERT: A 715 TRP cc_start: 0.6646 (p90) cc_final: 0.6204 (p90) REVERT: A 984 ASN cc_start: 0.8161 (t0) cc_final: 0.7914 (t0) REVERT: A 1019 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8659 (mm) REVERT: A 1197 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6496 (tt0) REVERT: A 1224 LEU cc_start: 0.7438 (tp) cc_final: 0.7163 (tt) REVERT: A 1432 MET cc_start: 0.7661 (ptt) cc_final: 0.7369 (ttm) REVERT: H 2 ARG cc_start: 0.8221 (mmm160) cc_final: 0.7630 (mmm160) outliers start: 48 outliers final: 34 residues processed: 267 average time/residue: 0.2057 time to fit residues: 81.0403 Evaluate side-chains 264 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 225 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 924 TRP Chi-restraints excluded: chain A residue 933 TYR Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1038 GLU Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1343 ILE Chi-restraints excluded: chain A residue 1346 LEU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1418 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.8980 chunk 60 optimal weight: 20.0000 chunk 88 optimal weight: 0.6980 chunk 133 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11250 Z= 0.207 Angle : 0.715 12.006 15315 Z= 0.343 Chirality : 0.044 0.252 1786 Planarity : 0.004 0.053 1876 Dihedral : 5.935 59.328 1820 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.60 % Favored : 92.32 % Rotamer: Outliers : 4.07 % Allowed : 28.55 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.24), residues: 1342 helix: 0.98 (0.18), residues: 890 sheet: -2.89 (1.40), residues: 10 loop : -2.11 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 244 HIS 0.002 0.001 HIS A1021 PHE 0.043 0.001 PHE A 900 TYR 0.012 0.001 TYR A 895 ARG 0.010 0.000 ARG A 613 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 225 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 THR cc_start: 0.8511 (OUTLIER) cc_final: 0.7727 (p) REVERT: A 344 LEU cc_start: 0.8853 (mp) cc_final: 0.8557 (mp) REVERT: A 378 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7722 (mt-10) REVERT: A 379 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7255 (t0) REVERT: A 715 TRP cc_start: 0.6726 (p90) cc_final: 0.6271 (p90) REVERT: A 984 ASN cc_start: 0.8172 (t0) cc_final: 0.7927 (t0) REVERT: A 1019 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8670 (mm) REVERT: A 1197 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.6472 (tt0) REVERT: A 1275 LEU cc_start: 0.8159 (mp) cc_final: 0.7670 (tt) REVERT: H 2 ARG cc_start: 0.8230 (mmm160) cc_final: 0.7637 (mmm160) outliers start: 45 outliers final: 33 residues processed: 258 average time/residue: 0.2099 time to fit residues: 80.1069 Evaluate side-chains 260 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 222 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 924 TRP Chi-restraints excluded: chain A residue 933 TYR Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1038 GLU Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1343 ILE Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1418 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 29 optimal weight: 0.0970 chunk 106 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 109 optimal weight: 0.0870 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 6 optimal weight: 8.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.160608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.119774 restraints weight = 21874.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.121390 restraints weight = 12759.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.121815 restraints weight = 8472.453| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11250 Z= 0.185 Angle : 0.714 11.924 15315 Z= 0.341 Chirality : 0.043 0.248 1786 Planarity : 0.004 0.053 1876 Dihedral : 5.809 59.839 1820 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.93 % Favored : 93.00 % Rotamer: Outliers : 3.61 % Allowed : 29.00 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.24), residues: 1342 helix: 0.99 (0.18), residues: 889 sheet: -2.82 (1.43), residues: 10 loop : -2.14 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 244 HIS 0.003 0.001 HIS A1021 PHE 0.025 0.001 PHE A 858 TYR 0.013 0.001 TYR A 895 ARG 0.009 0.000 ARG A 613 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2895.77 seconds wall clock time: 53 minutes 21.21 seconds (3201.21 seconds total)