Starting phenix.real_space_refine on Thu Feb 15 18:09:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5n_33621/02_2024/7y5n_33621.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5n_33621/02_2024/7y5n_33621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5n_33621/02_2024/7y5n_33621.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5n_33621/02_2024/7y5n_33621.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5n_33621/02_2024/7y5n_33621.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5n_33621/02_2024/7y5n_33621.pdb" } resolution = 3.45 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= 0.004 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: 6 Type Number sf(0) Gaussians Ca 7 9.91 5 Zn 1 6.06 5 S 112 5.16 5 C 8147 2.51 5 N 2270 2.21 5 O 2497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 841": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1077": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13034 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1109 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "C" Number of atoms: 8767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1115, 8767 Classifications: {'peptide': 1115} Link IDs: {'PTRANS': 69, 'TRANS': 1045} Chain: "D" Number of atoms: 2982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2982 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 29, 'TRANS': 358} Chain breaks: 2 Chain: "B" 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: "C" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 134 Unusual residues: {' CA': 7, ' ZN': 1, 'NAG': 9} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.71, per 1000 atoms: 0.51 Number of scatterers: 13034 At special positions: 0 Unit cell: (146.228, 116.772, 127.292, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Ca 7 19.99 S 112 16.00 O 2497 8.00 N 2270 7.00 C 8147 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 89 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 107 " distance=2.03 Simple disulfide: pdb=" SG CYS A 125 " - pdb=" SG CYS A 220 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS C 652 " distance=2.03 Simple disulfide: pdb=" SG CYS A 197 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 247 " - pdb=" SG CYS C 507 " distance=2.03 Simple disulfide: pdb=" SG CYS C 252 " - pdb=" SG CYS C 577 " distance=2.02 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 348 " distance=2.03 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 360 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 393 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 405 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 542 " distance=2.03 Simple disulfide: pdb=" SG CYS C 532 " - pdb=" SG CYS C 563 " distance=2.03 Simple disulfide: pdb=" SG CYS C 630 " - pdb=" SG CYS C 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 633 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS C 673 " - pdb=" SG CYS C 755 " distance=2.03 Simple disulfide: pdb=" SG CYS C 695 " - pdb=" SG CYS C 701 " distance=2.03 Simple disulfide: pdb=" SG CYS C 867 " - pdb=" SG CYS C 895 " distance=2.03 Simple disulfide: pdb=" SG CYS C 880 " - pdb=" SG CYS C 891 " distance=2.03 Simple disulfide: pdb=" SG CYS C 903 " - pdb=" SG CYS C 910 " distance=2.04 Simple disulfide: pdb=" SG CYS C 919 " - pdb=" SG CYS C 931 " distance=2.03 Simple disulfide: pdb=" SG CYS C 956 " - pdb=" SG CYS C 990 " distance=2.02 Simple disulfide: pdb=" SG CYS C 971 " - pdb=" SG CYS C1059 " distance=2.03 Simple disulfide: pdb=" SG CYS C1112 " - pdb=" SG CYS C1125 " distance=2.03 Simple disulfide: pdb=" SG CYS D1135 " - pdb=" SG CYS D1189 " distance=2.03 Simple disulfide: pdb=" SG CYS D1147 " - pdb=" SG CYS D1158 " distance=2.04 Simple disulfide: pdb=" SG CYS D1162 " - pdb=" SG CYS D1200 " distance=2.02 Simple disulfide: pdb=" SG CYS D1205 " - pdb=" SG CYS D1249 " distance=2.03 Simple disulfide: pdb=" SG CYS D1220 " - pdb=" SG CYS D1230 " distance=2.03 Simple disulfide: pdb=" SG CYS D1234 " - pdb=" SG CYS D1262 " distance=2.03 Simple disulfide: pdb=" SG CYS D1266 " - pdb=" SG CYS D1319 " distance=2.03 Simple disulfide: pdb=" SG CYS D1282 " - pdb=" SG CYS D1293 " distance=2.03 Simple disulfide: pdb=" SG CYS D1297 " - pdb=" SG CYS D1330 " distance=2.03 Simple disulfide: pdb=" SG CYS D1335 " - pdb=" SG CYS D1378 " distance=2.03 Simple disulfide: pdb=" SG CYS D1348 " - pdb=" SG CYS D1358 " distance=2.03 Simple disulfide: pdb=" SG CYS D1412 " - pdb=" SG CYS D1422 " distance=2.03 Simple disulfide: pdb=" SG CYS D1426 " - pdb=" SG CYS D1474 " distance=2.04 Simple disulfide: pdb=" SG CYS D1478 " - pdb=" SG CYS D1496 " distance=2.03 Simple disulfide: pdb=" SG CYS D1487 " - pdb=" SG CYS D1503 " distance=2.03 Simple disulfide: pdb=" SG CYS D1504 " - pdb=" SG CYS D1528 " distance=2.03 Simple disulfide: pdb=" SG CYS D1520 " - pdb=" SG CYS D1526 " 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-ASN " NAG B 1 " - " ASN C 310 " " NAG C1601 " - " ASN C 322 " " NAG C1602 " - " ASN C 349 " " NAG C1603 " - " ASN C 400 " " NAG C1604 " - " ASN C 521 " " NAG C1605 " - " ASN C 645 " " NAG C1606 " - " ASN C 745 " " NAG C1607 " - " ASN C 946 " " NAG C1609 " - " ASN C 825 " " NAG C1610 " - " ASN C 539 " " NAG D1601 " - " ASN D1142 " Time building additional restraints: 5.24 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C1608 " pdb="ZN ZN C1608 " - pdb=" NE2 HIS C 482 " pdb="ZN ZN C1608 " - pdb=" NE2 HIS C 486 " pdb="ZN ZN C1608 " - pdb=" NE2 HIS C 492 " 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3050 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 24 sheets defined 12.0% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 138 through 150 Processing helix chain 'C' and resid 152 through 154 No H-bonds generated for 'chain 'C' and resid 152 through 154' Processing helix chain 'C' and resid 184 through 194 Processing helix chain 'C' and resid 212 through 216 removed outlier: 4.470A pdb=" N ALA C 216 " --> pdb=" O ASN C 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 212 through 216' Processing helix chain 'C' and resid 250 through 253 Processing helix chain 'C' and resid 254 through 264 Processing helix chain 'C' and resid 291 through 306 Processing helix chain 'C' and resid 322 through 327 Processing helix chain 'C' and resid 335 through 339 Processing helix chain 'C' and resid 383 through 385 No H-bonds generated for 'chain 'C' and resid 383 through 385' Processing helix chain 'C' and resid 386 through 391 removed outlier: 4.036A pdb=" N GLY C 390 " --> pdb=" O PHE C 386 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY C 391 " --> pdb=" O ASN C 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 391' Processing helix chain 'C' and resid 400 through 405 removed outlier: 3.700A pdb=" N THR C 404 " --> pdb=" O ASN C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 426 Processing helix chain 'C' and resid 478 through 487 Processing helix chain 'C' and resid 492 through 496 removed outlier: 4.440A pdb=" N GLY C 496 " --> pdb=" O VAL C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 582 Processing helix chain 'C' and resid 583 through 587 removed outlier: 3.506A pdb=" N TRP C 586 " --> pdb=" O TYR C 583 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN C 587 " --> pdb=" O GLN C 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 583 through 587' Processing helix chain 'C' and resid 815 through 820 removed outlier: 3.949A pdb=" N SER C 820 " --> pdb=" O MET C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 873 through 877 Processing helix chain 'C' and resid 993 through 1000 Processing helix chain 'C' and resid 1105 through 1112 removed outlier: 3.510A pdb=" N SER C1111 " --> pdb=" O VAL C1107 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS C1112 " --> pdb=" O THR C1108 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1283 Processing helix chain 'D' and resid 1339 through 1343 removed outlier: 3.755A pdb=" N HIS D1343 " --> pdb=" O PRO D1340 " (cutoff:3.500A) Processing helix chain 'D' and resid 1493 through 1502 removed outlier: 3.809A pdb=" N ASN D1497 " --> pdb=" O ALA D1494 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR D1498 " --> pdb=" O PHE D1495 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP D1502 " --> pdb=" O ASP D1499 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 95 through 98 removed outlier: 5.817A pdb=" N SER A 114 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU A 216 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 174 removed outlier: 3.633A pdb=" N ILE A 159 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL A 198 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 135 through 140 removed outlier: 5.412A pdb=" N GLN C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL C 132 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 176 " --> pdb=" O GLU C 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 135 through 140 removed outlier: 5.412A pdb=" N GLN C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL C 132 " --> pdb=" O GLN C 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 103 through 106 removed outlier: 6.480A pdb=" N ILE C 77 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N VAL C 56 " --> pdb=" O ILE C 77 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N THR C 79 " --> pdb=" O PRO C 54 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LEU C 158 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 311 through 321 removed outlier: 4.862A pdb=" N PHE C 437 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N LEU C 280 " --> pdb=" O PHE C 437 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 329 through 331 Processing sheet with id=AA8, first strand: chain 'C' and resid 600 through 604 removed outlier: 6.925A pdb=" N THR C 610 " --> pdb=" O LEU C 602 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 640 through 642 removed outlier: 6.648A pdb=" N ILE C 784 " --> pdb=" O VAL C 720 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL C 720 " --> pdb=" O ILE C 784 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA C 786 " --> pdb=" O ILE C 718 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ILE C 718 " --> pdb=" O ALA C 786 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N MET C 788 " --> pdb=" O LEU C 716 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU C 716 " --> pdb=" O MET C 788 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR C 790 " --> pdb=" O GLU C 714 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 645 through 647 removed outlier: 11.614A pdb=" N LEU C 705 " --> pdb=" O TYR C 776 " (cutoff:3.500A) removed outlier: 10.956A pdb=" N TYR C 776 " --> pdb=" O LEU C 705 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N PHE C 707 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 11.668A pdb=" N GLN C 774 " --> pdb=" O PHE C 707 " (cutoff:3.500A) removed outlier: 10.783A pdb=" N TYR C 709 " --> pdb=" O GLY C 772 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLY C 772 " --> pdb=" O TYR C 709 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP C 735 " --> pdb=" O TYR C 776 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE C 736 " --> pdb=" O LEU C 748 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 805 through 810 Processing sheet with id=AB3, first strand: chain 'C' and resid 901 through 903 Processing sheet with id=AB4, first strand: chain 'C' and resid 939 through 943 removed outlier: 3.548A pdb=" N GLY C1095 " --> pdb=" O HIS C1022 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 948 through 949 removed outlier: 6.742A pdb=" N GLN C1080 " --> pdb=" O PHE C1010 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL C1040 " --> pdb=" O GLY C1053 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY C1053 " --> pdb=" O VAL C1040 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU C1042 " --> pdb=" O ASP C1051 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ASP C1051 " --> pdb=" O LEU C1042 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASP C1044 " --> pdb=" O SER C1049 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N SER C1049 " --> pdb=" O ASP C1044 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 1117 through 1119 Processing sheet with id=AB7, first strand: chain 'D' and resid 1143 through 1147 removed outlier: 3.581A pdb=" N VAL D1185 " --> pdb=" O VAL D1160 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 1175 through 1176 removed outlier: 3.566A pdb=" N GLU D1175 " --> pdb=" O ARG D1172 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA D1199 " --> pdb=" O GLN D1169 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG D1171 " --> pdb=" O GLN D1197 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN D1197 " --> pdb=" O ARG D1171 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 1216 through 1219 Processing sheet with id=AC1, first strand: chain 'D' and resid 1239 through 1242 Processing sheet with id=AC2, first strand: chain 'D' and resid 1275 through 1277 Processing sheet with id=AC3, first strand: chain 'D' and resid 1301 through 1302 removed outlier: 3.563A pdb=" N HIS D1302 " --> pdb=" O VAL D1331 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 1358 through 1359 removed outlier: 4.308A pdb=" N CYS D1358 " --> pdb=" O ILE D1376 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE D1376 " --> pdb=" O CYS D1358 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 1408 through 1411 Processing sheet with id=AC6, first strand: chain 'D' and resid 1431 through 1435 308 hydrogen bonds defined for protein. 801 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: 5.37 Time building geometry restraints manager: 5.62 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: 4233 1.34 - 1.46: 3086 1.46 - 1.58: 5923 1.58 - 1.70: 0 1.70 - 1.82: 134 Bond restraints: 13376 Sorted by residual: bond pdb=" N VAL D1513 " pdb=" CA VAL D1513 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.19e-02 7.06e+03 9.95e+00 bond pdb=" C1 NAG C1609 " pdb=" O5 NAG C1609 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.69e+00 bond pdb=" N PHE D1516 " pdb=" CA PHE D1516 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.04e-02 9.25e+03 8.15e+00 bond pdb=" N TRP A 207 " pdb=" CA TRP A 207 " ideal model delta sigma weight residual 1.453 1.489 -0.035 1.27e-02 6.20e+03 7.65e+00 bond pdb=" N LEU C 940 " pdb=" CA LEU C 940 " ideal model delta sigma weight residual 1.455 1.488 -0.034 1.26e-02 6.30e+03 7.08e+00 ... (remaining 13371 not shown) Histogram of bond angle deviations from ideal: 99.43 - 106.39: 518 106.39 - 113.34: 7154 113.34 - 120.30: 4736 120.30 - 127.25: 5571 127.25 - 134.21: 223 Bond angle restraints: 18202 Sorted by residual: angle pdb=" C THR D1334 " pdb=" N CYS D1335 " pdb=" CA CYS D1335 " ideal model delta sigma weight residual 121.54 130.05 -8.51 1.91e+00 2.74e-01 1.98e+01 angle pdb=" CA MET C 473 " pdb=" C MET C 473 " pdb=" O MET C 473 " ideal model delta sigma weight residual 120.19 116.61 3.58 8.40e-01 1.42e+00 1.81e+01 angle pdb=" N GLN A 189 " pdb=" CA GLN A 189 " pdb=" C GLN A 189 " ideal model delta sigma weight residual 109.81 118.28 -8.47 2.21e+00 2.05e-01 1.47e+01 angle pdb=" C GLU C 442 " pdb=" N GLU C 443 " pdb=" CA GLU C 443 " ideal model delta sigma weight residual 122.08 127.54 -5.46 1.47e+00 4.63e-01 1.38e+01 angle pdb=" C TRP C 727 " pdb=" N ASP C 728 " pdb=" CA ASP C 728 " ideal model delta sigma weight residual 121.54 128.39 -6.85 1.91e+00 2.74e-01 1.28e+01 ... (remaining 18197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.77: 7775 22.77 - 45.54: 360 45.54 - 68.31: 64 68.31 - 91.08: 8 91.08 - 113.85: 14 Dihedral angle restraints: 8221 sinusoidal: 3480 harmonic: 4741 Sorted by residual: dihedral pdb=" CB CYS C 252 " pdb=" SG CYS C 252 " pdb=" SG CYS C 577 " pdb=" CB CYS C 577 " ideal model delta sinusoidal sigma weight residual 93.00 155.15 -62.15 1 1.00e+01 1.00e-02 5.12e+01 dihedral pdb=" CB CYS C 867 " pdb=" SG CYS C 867 " pdb=" SG CYS C 895 " pdb=" CB CYS C 895 " ideal model delta sinusoidal sigma weight residual -86.00 -141.45 55.45 1 1.00e+01 1.00e-02 4.16e+01 dihedral pdb=" CA ASP C 811 " pdb=" C ASP C 811 " pdb=" N PRO C 812 " pdb=" CA PRO C 812 " ideal model delta harmonic sigma weight residual 180.00 151.58 28.42 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 8218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1424 0.049 - 0.099: 408 0.099 - 0.148: 127 0.148 - 0.197: 16 0.197 - 0.247: 4 Chirality restraints: 1979 Sorted by residual: chirality pdb=" C1 NAG C1610 " pdb=" ND2 ASN C 539 " pdb=" C2 NAG C1610 " pdb=" O5 NAG C1610 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA GLN A 189 " pdb=" N GLN A 189 " pdb=" C GLN A 189 " pdb=" CB GLN A 189 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA LEU C 940 " pdb=" N LEU C 940 " pdb=" C LEU C 940 " pdb=" CB LEU C 940 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1976 not shown) Planarity restraints: 2395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 988 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.78e+00 pdb=" N PRO C 989 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 989 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 989 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 681 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO C 682 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 682 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 682 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 101 " 0.035 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO A 102 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " 0.029 5.00e-02 4.00e+02 ... (remaining 2392 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2709 2.78 - 3.31: 10699 3.31 - 3.84: 21453 3.84 - 4.37: 24874 4.37 - 4.90: 43251 Nonbonded interactions: 102986 Sorted by model distance: nonbonded pdb=" O GLY D1300 " pdb=" OG1 THR D1334 " model vdw 2.249 2.440 nonbonded pdb=" OD1 ASP C 87 " pdb=" OG SER C 110 " model vdw 2.314 2.440 nonbonded pdb=" OG1 THR D1320 " pdb=" OD1 ASP D1322 " model vdw 2.322 2.440 nonbonded pdb=" O GLY C 49 " pdb=" OH TYR C 111 " model vdw 2.323 2.440 nonbonded pdb=" OD1 ASN C 322 " pdb=" OG SER C 324 " model vdw 2.331 2.440 ... (remaining 102981 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.100 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 38.820 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 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 : 0.005 0.066 13376 Z= 0.315 Angle : 0.693 8.855 18202 Z= 0.376 Chirality : 0.051 0.247 1979 Planarity : 0.006 0.055 2384 Dihedral : 14.101 113.850 5045 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 5.43 % Allowed : 7.24 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.19), residues: 1629 helix: -2.27 (0.31), residues: 153 sheet: 0.18 (0.28), residues: 354 loop : -1.27 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 842 HIS 0.006 0.001 HIS C 78 PHE 0.015 0.002 PHE C 92 TYR 0.017 0.002 TYR C 131 ARG 0.003 0.000 ARG C 274 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 210 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 VAL cc_start: 0.8713 (p) cc_final: 0.8505 (p) REVERT: C 221 LYS cc_start: 0.5997 (OUTLIER) cc_final: 0.5253 (mmtm) REVERT: C 590 ARG cc_start: 0.6686 (mtp85) cc_final: 0.6127 (tpt170) REVERT: C 632 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8376 (mt) REVERT: C 728 ASP cc_start: 0.5535 (m-30) cc_final: 0.4961 (t0) REVERT: C 745 ASN cc_start: 0.7008 (OUTLIER) cc_final: 0.6773 (m-40) REVERT: C 778 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7970 (mp) REVERT: C 889 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7338 (m-30) REVERT: C 961 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7383 (mp) REVERT: C 1109 LEU cc_start: 0.8180 (mt) cc_final: 0.7961 (mm) REVERT: D 1170 ILE cc_start: 0.5968 (OUTLIER) cc_final: 0.5612 (pt) REVERT: D 1177 ILE cc_start: 0.3542 (OUTLIER) cc_final: 0.3166 (mt) REVERT: D 1283 ARG cc_start: 0.6896 (mtt180) cc_final: 0.5530 (ttp80) REVERT: D 1388 PHE cc_start: 0.5103 (m-10) cc_final: 0.4809 (m-80) REVERT: D 1512 LYS cc_start: 0.8266 (tttt) cc_final: 0.7965 (ttpt) REVERT: D 1532 GLN cc_start: 0.5989 (mt0) cc_final: 0.5774 (mp10) outliers start: 78 outliers final: 23 residues processed: 274 average time/residue: 0.2504 time to fit residues: 99.5240 Evaluate side-chains 173 residues out of total 1437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 142 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 638 ILE Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 778 LEU Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 889 ASP Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 961 ILE Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain D residue 1170 ILE Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1220 CYS Chi-restraints excluded: chain D residue 1447 HIS Chi-restraints excluded: chain D residue 1486 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN A 173 GLN A 188 HIS ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN C 78 HIS ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 HIS C1062 ASN D1154 HIS D1211 HIS D1274 ASN D1377 HIS ** D1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13376 Z= 0.273 Angle : 0.596 9.253 18202 Z= 0.305 Chirality : 0.047 0.240 1979 Planarity : 0.005 0.040 2384 Dihedral : 10.960 108.975 2077 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.69 % Allowed : 11.48 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.20), residues: 1629 helix: -0.74 (0.40), residues: 140 sheet: -0.03 (0.27), residues: 381 loop : -0.91 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 680 HIS 0.006 0.001 HIS D1154 PHE 0.019 0.001 PHE D1342 TYR 0.017 0.001 TYR C 131 ARG 0.003 0.000 ARG C 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 142 time to evaluate : 1.427 Fit side-chains revert: symmetry clash REVERT: C 221 LYS cc_start: 0.6061 (OUTLIER) cc_final: 0.5313 (mmtm) REVERT: C 590 ARG cc_start: 0.6818 (mtp85) cc_final: 0.6256 (tpt170) REVERT: C 632 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8413 (mt) REVERT: C 728 ASP cc_start: 0.5488 (m-30) cc_final: 0.5050 (t0) REVERT: C 745 ASN cc_start: 0.6892 (OUTLIER) cc_final: 0.6669 (m-40) REVERT: C 778 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8019 (mp) REVERT: C 889 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7296 (m-30) REVERT: C 961 ILE cc_start: 0.7584 (OUTLIER) cc_final: 0.7370 (mp) REVERT: D 1170 ILE cc_start: 0.5877 (tt) cc_final: 0.5478 (pt) REVERT: D 1177 ILE cc_start: 0.3344 (OUTLIER) cc_final: 0.2935 (mt) REVERT: D 1283 ARG cc_start: 0.6960 (mtt180) cc_final: 0.5661 (ttp80) REVERT: D 1388 PHE cc_start: 0.5227 (m-10) cc_final: 0.4637 (m-80) REVERT: D 1512 LYS cc_start: 0.8215 (tttt) cc_final: 0.7830 (ttpt) outliers start: 53 outliers final: 32 residues processed: 189 average time/residue: 0.2434 time to fit residues: 68.2937 Evaluate side-chains 161 residues out of total 1437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 122 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 549 ASN Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 638 ILE Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 778 LEU Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 889 ASP Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 927 SER Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 961 ILE Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1082 VAL Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1185 VAL Chi-restraints excluded: chain D residue 1220 CYS Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1289 VAL Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1447 HIS Chi-restraints excluded: chain D residue 1486 TYR Chi-restraints excluded: chain D residue 1525 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 159 optimal weight: 0.0870 chunk 131 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 118 optimal weight: 0.1980 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 HIS ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1389 HIS D1429 HIS ** D1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13376 Z= 0.207 Angle : 0.552 8.621 18202 Z= 0.278 Chirality : 0.045 0.256 1979 Planarity : 0.004 0.040 2384 Dihedral : 9.289 104.982 2068 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.69 % Allowed : 12.11 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.20), residues: 1629 helix: -0.07 (0.44), residues: 140 sheet: -0.08 (0.27), residues: 379 loop : -0.79 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 842 HIS 0.005 0.001 HIS C 78 PHE 0.010 0.001 PHE C 92 TYR 0.016 0.001 TYR C 131 ARG 0.005 0.000 ARG D1456 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 131 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 221 LYS cc_start: 0.6106 (OUTLIER) cc_final: 0.5360 (mmtm) REVERT: C 319 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7022 (mm-30) REVERT: C 590 ARG cc_start: 0.6796 (mtp85) cc_final: 0.6243 (tpt170) REVERT: C 632 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8367 (mt) REVERT: C 728 ASP cc_start: 0.5389 (m-30) cc_final: 0.4981 (t0) REVERT: C 745 ASN cc_start: 0.6904 (OUTLIER) cc_final: 0.6660 (m-40) REVERT: C 778 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8009 (mp) REVERT: C 889 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7371 (m-30) REVERT: D 1170 ILE cc_start: 0.5885 (tt) cc_final: 0.5475 (pt) REVERT: D 1177 ILE cc_start: 0.3508 (OUTLIER) cc_final: 0.3102 (mt) REVERT: D 1283 ARG cc_start: 0.6988 (mtt180) cc_final: 0.5619 (ttp80) REVERT: D 1388 PHE cc_start: 0.5190 (m-10) cc_final: 0.4616 (m-80) REVERT: D 1512 LYS cc_start: 0.8188 (tttt) cc_final: 0.7785 (ttpt) outliers start: 53 outliers final: 35 residues processed: 179 average time/residue: 0.2463 time to fit residues: 65.4791 Evaluate side-chains 165 residues out of total 1437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 123 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 549 ASN Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 638 ILE Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 778 LEU Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 889 ASP Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 991 THR Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1082 VAL Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1185 VAL Chi-restraints excluded: chain D residue 1220 CYS Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1289 VAL Chi-restraints excluded: chain D residue 1319 CYS Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1441 THR Chi-restraints excluded: chain D residue 1447 HIS Chi-restraints excluded: chain D residue 1486 TYR Chi-restraints excluded: chain D residue 1525 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 147 optimal weight: 30.0000 chunk 156 optimal weight: 9.9990 chunk 77 optimal weight: 0.5980 chunk 140 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 HIS C 85 ASN C 234 HIS ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13376 Z= 0.204 Angle : 0.538 7.957 18202 Z= 0.272 Chirality : 0.045 0.245 1979 Planarity : 0.004 0.040 2384 Dihedral : 8.253 95.318 2061 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.04 % Allowed : 12.25 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.20), residues: 1629 helix: 0.26 (0.47), residues: 134 sheet: -0.11 (0.27), residues: 379 loop : -0.70 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 842 HIS 0.004 0.001 HIS C 78 PHE 0.012 0.001 PHE D1352 TYR 0.015 0.001 TYR C 131 ARG 0.002 0.000 ARG C 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 128 time to evaluate : 1.501 Fit side-chains REVERT: C 221 LYS cc_start: 0.6103 (OUTLIER) cc_final: 0.5452 (mmtm) REVERT: C 319 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7058 (mm-30) REVERT: C 590 ARG cc_start: 0.6874 (mtp85) cc_final: 0.6272 (tpt170) REVERT: C 728 ASP cc_start: 0.5111 (m-30) cc_final: 0.4772 (t0) REVERT: C 745 ASN cc_start: 0.6960 (OUTLIER) cc_final: 0.6691 (m-40) REVERT: C 889 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7402 (m-30) REVERT: D 1170 ILE cc_start: 0.5857 (OUTLIER) cc_final: 0.5479 (pt) REVERT: D 1177 ILE cc_start: 0.3498 (OUTLIER) cc_final: 0.3056 (mt) REVERT: D 1283 ARG cc_start: 0.7106 (mtt180) cc_final: 0.5741 (ttp80) REVERT: D 1388 PHE cc_start: 0.5284 (m-10) cc_final: 0.4677 (m-80) REVERT: D 1512 LYS cc_start: 0.8204 (tttt) cc_final: 0.7699 (ttpt) outliers start: 58 outliers final: 43 residues processed: 179 average time/residue: 0.2558 time to fit residues: 67.5385 Evaluate side-chains 169 residues out of total 1437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 120 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 549 ASN Chi-restraints excluded: chain C residue 638 ILE Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 889 ASP Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 991 THR Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain C residue 1082 VAL Chi-restraints excluded: chain D residue 1170 ILE Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1185 VAL Chi-restraints excluded: chain D residue 1195 ASN Chi-restraints excluded: chain D residue 1220 CYS Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1289 VAL Chi-restraints excluded: chain D residue 1320 THR Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1441 THR Chi-restraints excluded: chain D residue 1447 HIS Chi-restraints excluded: chain D residue 1486 TYR Chi-restraints excluded: chain D residue 1522 LEU Chi-restraints excluded: chain D residue 1525 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 133 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13376 Z= 0.334 Angle : 0.592 7.461 18202 Z= 0.302 Chirality : 0.047 0.257 1979 Planarity : 0.004 0.042 2384 Dihedral : 8.288 94.700 2056 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.24 % Allowed : 13.29 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.20), residues: 1629 helix: -0.02 (0.44), residues: 140 sheet: -0.12 (0.27), residues: 366 loop : -0.74 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 44 HIS 0.005 0.001 HIS C 492 PHE 0.014 0.002 PHE C 236 TYR 0.017 0.002 TYR C 131 ARG 0.006 0.001 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 124 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 221 LYS cc_start: 0.5764 (OUTLIER) cc_final: 0.5232 (mmtm) REVERT: C 319 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7145 (mm-30) REVERT: C 590 ARG cc_start: 0.6812 (mtp85) cc_final: 0.6227 (tpt170) REVERT: C 728 ASP cc_start: 0.4938 (m-30) cc_final: 0.4692 (t0) REVERT: C 759 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8563 (tp) REVERT: C 889 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7358 (m-30) REVERT: D 1177 ILE cc_start: 0.3484 (OUTLIER) cc_final: 0.3118 (mt) REVERT: D 1283 ARG cc_start: 0.7106 (mtt180) cc_final: 0.5902 (ttp80) REVERT: D 1388 PHE cc_start: 0.5359 (m-10) cc_final: 0.4757 (m-80) REVERT: D 1512 LYS cc_start: 0.8264 (tttt) cc_final: 0.7725 (ttpt) outliers start: 61 outliers final: 46 residues processed: 176 average time/residue: 0.2622 time to fit residues: 68.8864 Evaluate side-chains 168 residues out of total 1437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 117 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 549 ASN Chi-restraints excluded: chain C residue 638 ILE Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 714 GLU Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 889 ASP Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 991 THR Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain C residue 1082 VAL Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1185 VAL Chi-restraints excluded: chain D residue 1195 ASN Chi-restraints excluded: chain D residue 1220 CYS Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1289 VAL Chi-restraints excluded: chain D residue 1319 CYS Chi-restraints excluded: chain D residue 1320 THR Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1441 THR Chi-restraints excluded: chain D residue 1447 HIS Chi-restraints excluded: chain D residue 1458 VAL Chi-restraints excluded: chain D residue 1486 TYR Chi-restraints excluded: chain D residue 1522 LEU Chi-restraints excluded: chain D residue 1525 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 91 optimal weight: 0.0570 chunk 38 optimal weight: 0.7980 chunk 156 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 GLN ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13376 Z= 0.167 Angle : 0.520 7.236 18202 Z= 0.263 Chirality : 0.044 0.280 1979 Planarity : 0.004 0.038 2384 Dihedral : 7.983 93.632 2056 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.90 % Allowed : 14.20 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.57 (0.21), residues: 1629 helix: 0.56 (0.46), residues: 134 sheet: -0.08 (0.27), residues: 366 loop : -0.59 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 842 HIS 0.003 0.001 HIS C 482 PHE 0.022 0.001 PHE C 236 TYR 0.015 0.001 TYR C 131 ARG 0.002 0.000 ARG C 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 125 time to evaluate : 1.604 Fit side-chains revert: symmetry clash REVERT: C 221 LYS cc_start: 0.6131 (OUTLIER) cc_final: 0.5487 (mmtm) REVERT: C 319 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7101 (mm-30) REVERT: C 590 ARG cc_start: 0.6872 (mtp85) cc_final: 0.6257 (tpt170) REVERT: C 728 ASP cc_start: 0.5109 (m-30) cc_final: 0.4847 (t0) REVERT: C 745 ASN cc_start: 0.6871 (OUTLIER) cc_final: 0.6574 (m-40) REVERT: C 889 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7259 (m-30) REVERT: D 1177 ILE cc_start: 0.3666 (OUTLIER) cc_final: 0.3327 (mt) REVERT: D 1283 ARG cc_start: 0.7050 (mtt180) cc_final: 0.5812 (ttp80) REVERT: D 1388 PHE cc_start: 0.5396 (m-10) cc_final: 0.4763 (m-80) REVERT: D 1512 LYS cc_start: 0.8193 (tttt) cc_final: 0.7691 (ttpt) outliers start: 56 outliers final: 43 residues processed: 173 average time/residue: 0.2536 time to fit residues: 65.6738 Evaluate side-chains 167 residues out of total 1437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 119 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 549 ASN Chi-restraints excluded: chain C residue 607 ASP Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 889 ASP Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 991 THR Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain C residue 1082 VAL Chi-restraints excluded: chain C residue 1100 SER Chi-restraints excluded: chain D residue 1151 ASP Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1185 VAL Chi-restraints excluded: chain D residue 1220 CYS Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1289 VAL Chi-restraints excluded: chain D residue 1320 THR Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1383 THR Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1447 HIS Chi-restraints excluded: chain D residue 1486 TYR Chi-restraints excluded: chain D residue 1525 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13376 Z= 0.235 Angle : 0.539 7.326 18202 Z= 0.272 Chirality : 0.045 0.248 1979 Planarity : 0.004 0.035 2384 Dihedral : 7.949 92.835 2054 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.24 % Allowed : 14.06 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.60 (0.21), residues: 1629 helix: 0.51 (0.45), residues: 134 sheet: -0.14 (0.27), residues: 366 loop : -0.59 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 179 HIS 0.003 0.001 HIS C 689 PHE 0.023 0.001 PHE C 236 TYR 0.015 0.001 TYR C 131 ARG 0.002 0.000 ARG C 89 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 121 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 221 LYS cc_start: 0.5924 (OUTLIER) cc_final: 0.5391 (mmtm) REVERT: C 319 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7097 (mm-30) REVERT: C 590 ARG cc_start: 0.6793 (mtp85) cc_final: 0.6212 (tpt170) REVERT: C 728 ASP cc_start: 0.4954 (m-30) cc_final: 0.4719 (t0) REVERT: C 745 ASN cc_start: 0.6926 (OUTLIER) cc_final: 0.6610 (m-40) REVERT: C 889 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7409 (m-30) REVERT: D 1177 ILE cc_start: 0.3753 (OUTLIER) cc_final: 0.3414 (mt) REVERT: D 1283 ARG cc_start: 0.7041 (mtt180) cc_final: 0.5859 (ttp80) REVERT: D 1388 PHE cc_start: 0.5468 (m-10) cc_final: 0.4771 (m-80) REVERT: D 1512 LYS cc_start: 0.8238 (tttt) cc_final: 0.7695 (ttpt) outliers start: 61 outliers final: 50 residues processed: 173 average time/residue: 0.2460 time to fit residues: 63.6133 Evaluate side-chains 174 residues out of total 1437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 119 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 549 ASN Chi-restraints excluded: chain C residue 607 ASP Chi-restraints excluded: chain C residue 638 ILE Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 889 ASP Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 990 CYS Chi-restraints excluded: chain C residue 991 THR Chi-restraints excluded: chain C residue 1006 LEU Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain C residue 1082 VAL Chi-restraints excluded: chain C residue 1100 SER Chi-restraints excluded: chain D residue 1151 ASP Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1185 VAL Chi-restraints excluded: chain D residue 1195 ASN Chi-restraints excluded: chain D residue 1289 VAL Chi-restraints excluded: chain D residue 1320 THR Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1383 THR Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1441 THR Chi-restraints excluded: chain D residue 1447 HIS Chi-restraints excluded: chain D residue 1486 TYR Chi-restraints excluded: chain D residue 1522 LEU Chi-restraints excluded: chain D residue 1525 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 142 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13376 Z= 0.254 Angle : 0.550 7.475 18202 Z= 0.278 Chirality : 0.045 0.238 1979 Planarity : 0.004 0.037 2384 Dihedral : 7.941 92.156 2053 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.66 % Allowed : 13.78 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.69 (0.21), residues: 1629 helix: 0.22 (0.44), residues: 142 sheet: -0.14 (0.27), residues: 366 loop : -0.65 (0.19), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 842 HIS 0.003 0.001 HIS C 689 PHE 0.025 0.001 PHE C 236 TYR 0.016 0.001 TYR C 131 ARG 0.002 0.000 ARG C 385 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 123 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 221 LYS cc_start: 0.5932 (OUTLIER) cc_final: 0.5393 (mmtm) REVERT: C 319 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7114 (mm-30) REVERT: C 590 ARG cc_start: 0.6786 (mtp85) cc_final: 0.6205 (tpt170) REVERT: C 635 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: C 728 ASP cc_start: 0.4862 (m-30) cc_final: 0.4602 (t0) REVERT: C 759 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8550 (tp) REVERT: C 889 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7336 (m-30) REVERT: D 1177 ILE cc_start: 0.3820 (OUTLIER) cc_final: 0.3441 (mt) REVERT: D 1214 TYR cc_start: 0.3874 (OUTLIER) cc_final: 0.2974 (t80) REVERT: D 1283 ARG cc_start: 0.7051 (mtt180) cc_final: 0.5862 (ttp80) REVERT: D 1388 PHE cc_start: 0.5431 (m-10) cc_final: 0.4728 (m-80) REVERT: D 1512 LYS cc_start: 0.8217 (tttt) cc_final: 0.7701 (ttpt) outliers start: 67 outliers final: 53 residues processed: 179 average time/residue: 0.2524 time to fit residues: 68.2273 Evaluate side-chains 179 residues out of total 1437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 119 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 549 ASN Chi-restraints excluded: chain C residue 607 ASP Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 638 ILE Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 714 GLU Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 889 ASP Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 991 THR Chi-restraints excluded: chain C residue 1006 LEU Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain C residue 1082 VAL Chi-restraints excluded: chain D residue 1151 ASP Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1185 VAL Chi-restraints excluded: chain D residue 1195 ASN Chi-restraints excluded: chain D residue 1214 TYR Chi-restraints excluded: chain D residue 1289 VAL Chi-restraints excluded: chain D residue 1319 CYS Chi-restraints excluded: chain D residue 1320 THR Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1383 THR Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1441 THR Chi-restraints excluded: chain D residue 1447 HIS Chi-restraints excluded: chain D residue 1471 LEU Chi-restraints excluded: chain D residue 1486 TYR Chi-restraints excluded: chain D residue 1522 LEU Chi-restraints excluded: chain D residue 1525 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 145 optimal weight: 8.9990 chunk 87 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 137 optimal weight: 0.0470 chunk 144 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 overall best weight: 0.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13376 Z= 0.189 Angle : 0.524 7.535 18202 Z= 0.264 Chirality : 0.044 0.230 1979 Planarity : 0.004 0.035 2384 Dihedral : 7.797 91.329 2053 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.31 % Allowed : 14.41 % Favored : 81.28 % 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: -0.59 (0.21), residues: 1629 helix: 0.39 (0.45), residues: 142 sheet: -0.11 (0.27), residues: 366 loop : -0.59 (0.19), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 179 HIS 0.003 0.001 HIS D1468 PHE 0.024 0.001 PHE C 236 TYR 0.015 0.001 TYR C 131 ARG 0.002 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 125 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 221 LYS cc_start: 0.6009 (OUTLIER) cc_final: 0.5245 (mppt) REVERT: C 319 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7082 (mm-30) REVERT: C 590 ARG cc_start: 0.6772 (mtp85) cc_final: 0.6204 (tpt170) REVERT: C 635 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7367 (tt0) REVERT: C 728 ASP cc_start: 0.4801 (m-30) cc_final: 0.4578 (t0) REVERT: C 745 ASN cc_start: 0.6917 (OUTLIER) cc_final: 0.6574 (m-40) REVERT: C 759 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8534 (tp) REVERT: C 889 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7334 (m-30) REVERT: D 1177 ILE cc_start: 0.3592 (OUTLIER) cc_final: 0.3272 (mt) REVERT: D 1214 TYR cc_start: 0.3812 (OUTLIER) cc_final: 0.2868 (t80) REVERT: D 1283 ARG cc_start: 0.7037 (mtt180) cc_final: 0.5803 (ttp80) REVERT: D 1388 PHE cc_start: 0.5398 (m-10) cc_final: 0.4734 (m-80) REVERT: D 1512 LYS cc_start: 0.8203 (tttt) cc_final: 0.7699 (ttpt) outliers start: 62 outliers final: 49 residues processed: 179 average time/residue: 0.2527 time to fit residues: 67.0975 Evaluate side-chains 177 residues out of total 1437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 120 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 549 ASN Chi-restraints excluded: chain C residue 607 ASP Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 638 ILE Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 889 ASP Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 990 CYS Chi-restraints excluded: chain C residue 991 THR Chi-restraints excluded: chain C residue 1006 LEU Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain C residue 1082 VAL Chi-restraints excluded: chain D residue 1151 ASP Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1185 VAL Chi-restraints excluded: chain D residue 1195 ASN Chi-restraints excluded: chain D residue 1214 TYR Chi-restraints excluded: chain D residue 1289 VAL Chi-restraints excluded: chain D residue 1319 CYS Chi-restraints excluded: chain D residue 1320 THR Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1383 THR Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1441 THR Chi-restraints excluded: chain D residue 1447 HIS Chi-restraints excluded: chain D residue 1458 VAL Chi-restraints excluded: chain D residue 1485 ASN Chi-restraints excluded: chain D residue 1486 TYR Chi-restraints excluded: chain D residue 1525 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 148 optimal weight: 20.0000 chunk 128 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 99 optimal weight: 0.0870 chunk 78 optimal weight: 0.8980 chunk 102 optimal weight: 0.0170 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13376 Z= 0.213 Angle : 0.537 7.719 18202 Z= 0.271 Chirality : 0.045 0.228 1979 Planarity : 0.004 0.035 2384 Dihedral : 7.793 90.850 2053 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 4.04 % Allowed : 15.03 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.21), residues: 1629 helix: 0.40 (0.44), residues: 142 sheet: -0.11 (0.27), residues: 366 loop : -0.61 (0.19), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 179 HIS 0.003 0.001 HIS D1468 PHE 0.025 0.001 PHE C 236 TYR 0.014 0.001 TYR C 131 ARG 0.006 0.000 ARG C 896 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 123 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 221 LYS cc_start: 0.6086 (OUTLIER) cc_final: 0.5315 (mppt) REVERT: C 319 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7082 (mm-30) REVERT: C 590 ARG cc_start: 0.6790 (mtp85) cc_final: 0.6209 (tpt170) REVERT: C 635 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7399 (tt0) REVERT: C 728 ASP cc_start: 0.4846 (m-30) cc_final: 0.4596 (t0) REVERT: C 745 ASN cc_start: 0.6912 (OUTLIER) cc_final: 0.6567 (m-40) REVERT: C 759 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8535 (tp) REVERT: C 889 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7425 (m-30) REVERT: D 1177 ILE cc_start: 0.3772 (OUTLIER) cc_final: 0.3413 (mt) REVERT: D 1283 ARG cc_start: 0.7044 (mtt180) cc_final: 0.5861 (ttp80) REVERT: D 1388 PHE cc_start: 0.5411 (m-10) cc_final: 0.4750 (m-80) REVERT: D 1512 LYS cc_start: 0.8225 (tttt) cc_final: 0.7707 (ttpt) outliers start: 58 outliers final: 51 residues processed: 173 average time/residue: 0.2512 time to fit residues: 64.8234 Evaluate side-chains 179 residues out of total 1437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 121 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 549 ASN Chi-restraints excluded: chain C residue 607 ASP Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 638 ILE Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 889 ASP Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 990 CYS Chi-restraints excluded: chain C residue 991 THR Chi-restraints excluded: chain C residue 1006 LEU Chi-restraints excluded: chain C residue 1015 VAL Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain C residue 1082 VAL Chi-restraints excluded: chain D residue 1151 ASP Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1185 VAL Chi-restraints excluded: chain D residue 1195 ASN Chi-restraints excluded: chain D residue 1289 VAL Chi-restraints excluded: chain D residue 1319 CYS Chi-restraints excluded: chain D residue 1320 THR Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1383 THR Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1441 THR Chi-restraints excluded: chain D residue 1447 HIS Chi-restraints excluded: chain D residue 1458 VAL Chi-restraints excluded: chain D residue 1471 LEU Chi-restraints excluded: chain D residue 1485 ASN Chi-restraints excluded: chain D residue 1486 TYR Chi-restraints excluded: chain D residue 1525 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 HIS D1146 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.157122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.122163 restraints weight = 18267.556| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.11 r_work: 0.3146 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13376 Z= 0.275 Angle : 0.561 7.817 18202 Z= 0.285 Chirality : 0.046 0.236 1979 Planarity : 0.004 0.035 2384 Dihedral : 7.885 90.623 2053 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.31 % Allowed : 14.82 % Favored : 80.86 % 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: -0.70 (0.21), residues: 1629 helix: 0.27 (0.44), residues: 142 sheet: -0.15 (0.27), residues: 366 loop : -0.67 (0.19), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 842 HIS 0.004 0.001 HIS C 689 PHE 0.018 0.001 PHE D1342 TYR 0.016 0.001 TYR C 131 ARG 0.002 0.000 ARG C 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2747.93 seconds wall clock time: 50 minutes 57.07 seconds (3057.07 seconds total)