Starting phenix.real_space_refine on Tue Mar 19 04:06:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2p_11989/03_2024/7b2p_11989_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2p_11989/03_2024/7b2p_11989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2p_11989/03_2024/7b2p_11989.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2p_11989/03_2024/7b2p_11989.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2p_11989/03_2024/7b2p_11989_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2p_11989/03_2024/7b2p_11989_trim.pdb" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 42 5.16 5 C 7400 2.51 5 N 2019 2.21 5 O 2229 1.98 5 H 11497 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 138": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 157": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 159": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 168": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A ARG 269": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 351": "OE1" <-> "OE2" Residue "A ASP 487": "OD1" <-> "OD2" Residue "A ASP 561": "OD1" <-> "OD2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A ARG 582": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 658": "OD1" <-> "OD2" Residue "B PHE 777": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 787": "OE1" <-> "OE2" Residue "B ARG 791": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 847": "OE1" <-> "OE2" Residue "B ASP 860": "OD1" <-> "OD2" Residue "B TYR 946": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 959": "OE1" <-> "OE2" Residue "B ASP 973": "OD1" <-> "OD2" Residue "B TYR 977": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 1005": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1055": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 1091": "OE1" <-> "OE2" Residue "B GLU 1098": "OE1" <-> "OE2" Residue "B GLU 1137": "OE1" <-> "OE2" Residue "B GLU 1169": "OE1" <-> "OE2" Residue "B GLU 1181": "OE1" <-> "OE2" Residue "B GLU 1280": "OE1" <-> "OE2" Residue "B ARG 1291": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 1465": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 1474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 1494": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 1498": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 1533": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 1539": "OE1" <-> "OE2" Residue "C TYR 1559": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 1570": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 1577": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 1592": "OE1" <-> "OE2" Residue "D ARG 59": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 73": "OD1" <-> "OD2" Residue "D TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23187 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 10007 Classifications: {'peptide': 650} Link IDs: {'PCIS': 3, 'PTRANS': 41, 'TRANS': 605} Chain: "B" Number of atoms: 9363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 9363 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 27, 'TRANS': 582} Chain breaks: 3 Chain: "C" Number of atoms: 1980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1980 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "D" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1767 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 9.34, per 1000 atoms: 0.40 Number of scatterers: 23187 At special positions: 0 Unit cell: (141.933, 118.277, 114.163, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 O 2229 8.00 N 2019 7.00 C 7400 6.00 H 11497 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 567 " - pdb=" SG CYS B 820 " distance=2.03 Simple disulfide: pdb=" SG CYS A 635 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 876 " - pdb=" SG CYS C1590 " distance=2.03 Simple disulfide: pdb=" SG CYS B1394 " - pdb=" SG CYS C1566 " distance=2.03 Simple disulfide: pdb=" SG CYS C1471 " - pdb=" SG CYS C1535 " distance=2.03 Simple disulfide: pdb=" SG CYS C1583 " - pdb=" SG CYS C1588 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG B1801 " - " ASN B 862 " " NAG B1802 " - " ASN B1328 " " NAG B1803 " - " ASN B1391 " " NAG E 1 " - " ASN A 226 " Time building additional restraints: 17.38 Conformation dependent library (CDL) restraints added in 2.3 seconds 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2780 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 28 sheets defined 18.9% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 61 through 64 Processing helix chain 'A' and resid 90 through 97 Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 315 through 326 Processing helix chain 'A' and resid 329 through 333 Processing helix chain 'A' and resid 606 through 611 Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 642 through 650 Processing helix chain 'B' and resid 996 through 1002 removed outlier: 3.533A pdb=" N VAL B1000 " --> pdb=" O SER B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1032 Proline residue: B1020 - end of helix Processing helix chain 'B' and resid 1038 through 1058 removed outlier: 3.993A pdb=" N LYS B1042 " --> pdb=" O PRO B1038 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP B1043 " --> pdb=" O PRO B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1090 Processing helix chain 'B' and resid 1096 through 1110 removed outlier: 4.400A pdb=" N LEU B1100 " --> pdb=" O SER B1096 " (cutoff:3.500A) Processing helix chain 'B' and resid 1125 through 1130 removed outlier: 3.706A pdb=" N MET B1128 " --> pdb=" O ASP B1125 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY B1130 " --> pdb=" O SER B1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1152 Processing helix chain 'B' and resid 1161 through 1185 removed outlier: 3.550A pdb=" N ALA B1185 " --> pdb=" O GLU B1181 " (cutoff:3.500A) Processing helix chain 'B' and resid 1189 through 1203 Processing helix chain 'B' and resid 1206 through 1221 Processing helix chain 'B' and resid 1258 through 1275 Processing helix chain 'B' and resid 1281 through 1294 Processing helix chain 'B' and resid 1302 through 1320 Processing helix chain 'C' and resid 1498 through 1507 removed outlier: 3.670A pdb=" N GLU C1502 " --> pdb=" O ARG C1498 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS C1503 " --> pdb=" O ALA C1499 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU C1504 " --> pdb=" O ASP C1500 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR C1505 " --> pdb=" O LEU C1501 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU C1507 " --> pdb=" O LYS C1503 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.510A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 87 removed outlier: 7.619A pdb=" N SER A 38 " --> pdb=" O PRO A 28 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 42 " --> pdb=" O LEU A 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 32 removed outlier: 3.835A pdb=" N ASN A 60 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL A 66 " --> pdb=" O ASN A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 145 Processing sheet with id=AA4, first strand: chain 'A' and resid 149 through 150 Processing sheet with id=AA5, first strand: chain 'A' and resid 185 through 191 removed outlier: 5.903A pdb=" N VAL A 178 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS A 188 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL A 176 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU A 190 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE A 174 " --> pdb=" O GLU A 190 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 241 through 247 removed outlier: 4.052A pdb=" N MET A 262 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 251 through 252 removed outlier: 3.613A pdb=" N ILE A 252 " --> pdb=" O TYR A 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 293 through 295 Processing sheet with id=AA9, first strand: chain 'A' and resid 293 through 295 Processing sheet with id=AB1, first strand: chain 'A' and resid 367 through 370 Processing sheet with id=AB2, first strand: chain 'A' and resid 418 through 423 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 476 removed outlier: 3.703A pdb=" N LEU A 489 " --> pdb=" O VAL A 531 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 515 through 522 removed outlier: 3.734A pdb=" N PHE A 517 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N HIS A 504 " --> pdb=" O TYR A 548 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N TYR A 548 " --> pdb=" O HIS A 504 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA A 545 " --> pdb=" O ASN A 556 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N HIS A 552 " --> pdb=" O HIS A 549 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 515 through 522 removed outlier: 3.734A pdb=" N PHE A 517 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N HIS A 504 " --> pdb=" O TYR A 548 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N TYR A 548 " --> pdb=" O HIS A 504 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 572 through 574 removed outlier: 3.573A pdb=" N GLU A 592 " --> pdb=" O GLU A 572 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 781 through 783 removed outlier: 6.093A pdb=" N ALA A 603 " --> pdb=" O TRP B 782 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 786 through 789 Processing sheet with id=AB9, first strand: chain 'B' and resid 835 through 836 removed outlier: 3.551A pdb=" N LEU B 855 " --> pdb=" O ARG B 895 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 849 through 851 Processing sheet with id=AC2, first strand: chain 'B' and resid 885 through 889 Processing sheet with id=AC3, first strand: chain 'B' and resid 938 through 948 removed outlier: 3.516A pdb=" N VAL B1380 " --> pdb=" O LEU B 944 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 978 " --> pdb=" O LEU B1358 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 959 through 960 removed outlier: 3.567A pdb=" N SER B1333 " --> pdb=" O LYS B1340 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 1397 through 1405 removed outlier: 3.588A pdb=" N GLU C1534 " --> pdb=" O ILE C1472 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1515 through 1518 Processing sheet with id=AC7, first strand: chain 'C' and resid 1581 through 1583 Processing sheet with id=AC8, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.532A pdb=" N THR D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 45 through 51 removed outlier: 5.395A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET D 34 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER D 110 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 45 through 51 removed outlier: 5.395A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET D 34 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D 93 " --> pdb=" O GLN D 39 " (cutoff:3.500A) 494 hydrogen bonds defined for protein. 1347 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: 9.68 Time building geometry restraints manager: 18.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11495 1.03 - 1.23: 31 1.23 - 1.42: 4952 1.42 - 1.62: 6895 1.62 - 1.81: 66 Bond restraints: 23439 Sorted by residual: bond pdb=" C1 NAG B1803 " pdb=" O5 NAG B1803 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.30e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.06e+00 bond pdb=" C1 NAG B1801 " pdb=" O5 NAG B1801 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" C GLN D 13 " pdb=" N PRO D 14 " ideal model delta sigma weight residual 1.332 1.349 -0.017 1.30e-02 5.92e+03 1.81e+00 bond pdb=" C1 NAG B1802 " pdb=" O5 NAG B1802 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.43e+00 ... (remaining 23434 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.50: 379 106.50 - 113.39: 27863 113.39 - 120.28: 7123 120.28 - 127.17: 6842 127.17 - 134.06: 147 Bond angle restraints: 42354 Sorted by residual: angle pdb=" N ARG A 48 " pdb=" CA ARG A 48 " pdb=" CB ARG A 48 " ideal model delta sigma weight residual 114.17 109.61 4.56 1.14e+00 7.69e-01 1.60e+01 angle pdb=" N THR A 75 " pdb=" CA THR A 75 " pdb=" C THR A 75 " ideal model delta sigma weight residual 111.17 115.63 -4.46 1.41e+00 5.03e-01 9.99e+00 angle pdb=" CA THR A 75 " pdb=" C THR A 75 " pdb=" N LEU A 76 " ideal model delta sigma weight residual 114.81 118.48 -3.67 1.42e+00 4.96e-01 6.68e+00 angle pdb=" CA TRP D 47 " pdb=" CB TRP D 47 " pdb=" CG TRP D 47 " ideal model delta sigma weight residual 113.60 118.16 -4.56 1.90e+00 2.77e-01 5.77e+00 angle pdb=" C GLY C1476 " pdb=" N LYS C1477 " pdb=" CA LYS C1477 " ideal model delta sigma weight residual 121.54 125.86 -4.32 1.91e+00 2.74e-01 5.12e+00 ... (remaining 42349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.16: 10384 22.16 - 44.32: 595 44.32 - 66.49: 152 66.49 - 88.65: 12 88.65 - 110.81: 3 Dihedral angle restraints: 11146 sinusoidal: 6156 harmonic: 4990 Sorted by residual: dihedral pdb=" CB CYS A 635 " pdb=" SG CYS A 635 " pdb=" SG CYS A 669 " pdb=" CB CYS A 669 " ideal model delta sinusoidal sigma weight residual 93.00 42.29 50.71 1 1.00e+01 1.00e-02 3.52e+01 dihedral pdb=" CB CYS B 876 " pdb=" SG CYS B 876 " pdb=" SG CYS C1590 " pdb=" CB CYS C1590 " ideal model delta sinusoidal sigma weight residual -86.00 -130.75 44.75 1 1.00e+01 1.00e-02 2.78e+01 dihedral pdb=" CB CYS A 567 " pdb=" SG CYS A 567 " pdb=" SG CYS B 820 " pdb=" CB CYS B 820 " ideal model delta sinusoidal sigma weight residual 93.00 49.23 43.77 1 1.00e+01 1.00e-02 2.67e+01 ... (remaining 11143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1660 0.073 - 0.146: 186 0.146 - 0.219: 2 0.219 - 0.292: 0 0.292 - 0.365: 1 Chirality restraints: 1849 Sorted by residual: chirality pdb=" C1 NAG B1803 " pdb=" ND2 ASN B1391 " pdb=" C2 NAG B1803 " pdb=" O5 NAG B1803 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" C1 NAG B1801 " pdb=" ND2 ASN B 862 " pdb=" C2 NAG B1801 " pdb=" O5 NAG B1801 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 226 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.77e-01 ... (remaining 1846 not shown) Planarity restraints: 3522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 47 " -0.024 2.00e-02 2.50e+03 1.25e-02 6.20e+00 pdb=" CG TRP D 47 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP D 47 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP D 47 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 47 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 47 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 47 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 47 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 47 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 47 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 TRP D 47 " -0.007 2.00e-02 2.50e+03 pdb=" HE1 TRP D 47 " -0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP D 47 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP D 47 " -0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP D 47 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP D 47 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 465 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.80e+00 pdb=" N PRO A 466 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 466 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 466 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 778 " -0.028 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO B 779 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 779 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 779 " -0.023 5.00e-02 4.00e+02 ... (remaining 3519 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 1320 2.19 - 2.79: 47448 2.79 - 3.39: 62521 3.39 - 4.00: 83347 4.00 - 4.60: 127226 Nonbonded interactions: 321862 Sorted by model distance: nonbonded pdb=" O LEU A 58 " pdb=" H CYS A 68 " model vdw 1.583 1.850 nonbonded pdb=" O LYS A 53 " pdb=" HG SER A 114 " model vdw 1.590 1.850 nonbonded pdb=" OE1 GLN B1398 " pdb=" HE1 TRP C1473 " model vdw 1.600 1.850 nonbonded pdb=" OH TYR D 60 " pdb=" H ILE D 70 " model vdw 1.617 1.850 nonbonded pdb=" O THR C1489 " pdb=" HH TYR C1570 " model vdw 1.622 1.850 ... (remaining 321857 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: 2.220 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: 0.320 Extract box with map and model: 6.790 Check model and map are aligned: 0.300 Set scattering table: 0.200 Process input model: 71.120 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11942 Z= 0.217 Angle : 0.529 5.026 16218 Z= 0.283 Chirality : 0.043 0.365 1849 Planarity : 0.003 0.049 2096 Dihedral : 13.608 110.809 4438 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.22), residues: 1495 helix: 1.49 (0.34), residues: 257 sheet: -0.28 (0.23), residues: 524 loop : -0.61 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP D 47 HIS 0.003 0.001 HIS B1150 PHE 0.027 0.001 PHE A 74 TYR 0.008 0.001 TYR A 272 ARG 0.014 0.001 ARG B 979 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 423 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 SER cc_start: 0.7254 (m) cc_final: 0.6882 (p) REVERT: A 107 GLU cc_start: 0.7269 (mm-30) cc_final: 0.7065 (mm-30) REVERT: A 352 MET cc_start: 0.6756 (ptp) cc_final: 0.6496 (ptp) REVERT: A 353 GLU cc_start: 0.7044 (mp0) cc_final: 0.6843 (mp0) REVERT: A 404 LYS cc_start: 0.7710 (mmmt) cc_final: 0.7444 (mmmt) REVERT: A 422 GLN cc_start: 0.7701 (tm-30) cc_final: 0.7111 (tm-30) REVERT: A 433 ILE cc_start: 0.8646 (tt) cc_final: 0.8376 (pt) REVERT: A 642 SER cc_start: 0.8318 (m) cc_final: 0.8044 (p) REVERT: B 815 LYS cc_start: 0.7993 (mttp) cc_final: 0.7715 (mttp) REVERT: B 817 LYS cc_start: 0.7982 (mmtt) cc_final: 0.7716 (mmtp) REVERT: B 910 SER cc_start: 0.7449 (t) cc_final: 0.7212 (p) REVERT: B 968 MET cc_start: 0.7845 (tmm) cc_final: 0.7525 (tmm) REVERT: B 969 ILE cc_start: 0.8831 (mt) cc_final: 0.8359 (mt) REVERT: B 974 PHE cc_start: 0.7611 (t80) cc_final: 0.7377 (t80) REVERT: B 1085 VAL cc_start: 0.8700 (t) cc_final: 0.8426 (p) REVERT: B 1229 TYR cc_start: 0.6102 (m-80) cc_final: 0.5712 (m-80) REVERT: B 1288 TRP cc_start: 0.8076 (t60) cc_final: 0.7855 (t60) REVERT: B 1306 VAL cc_start: 0.7821 (p) cc_final: 0.6868 (p) REVERT: B 1310 ASP cc_start: 0.7123 (m-30) cc_final: 0.6692 (m-30) REVERT: C 1483 MET cc_start: 0.6924 (ptp) cc_final: 0.6238 (ptp) REVERT: C 1527 ASP cc_start: 0.7438 (p0) cc_final: 0.6939 (p0) REVERT: D 78 THR cc_start: 0.8236 (m) cc_final: 0.7918 (p) REVERT: D 102 PHE cc_start: 0.8340 (t80) cc_final: 0.8132 (t80) outliers start: 0 outliers final: 0 residues processed: 423 average time/residue: 0.6160 time to fit residues: 358.6811 Evaluate side-chains 370 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN ** B 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 ASN ** B1214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1256 GLN D 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 11942 Z= 0.370 Angle : 0.635 7.935 16218 Z= 0.333 Chirality : 0.045 0.268 1849 Planarity : 0.005 0.044 2096 Dihedral : 7.325 97.675 1729 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.49 % Allowed : 11.08 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -0.55 (0.21), residues: 1495 helix: 0.94 (0.32), residues: 267 sheet: -0.35 (0.22), residues: 529 loop : -0.81 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 47 HIS 0.008 0.001 HIS B1150 PHE 0.024 0.002 PHE A 74 TYR 0.020 0.002 TYR D 105 ARG 0.005 0.001 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 396 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 SER cc_start: 0.8003 (m) cc_final: 0.7787 (p) REVERT: A 42 GLN cc_start: 0.7135 (pp30) cc_final: 0.6813 (pp30) REVERT: A 62 SER cc_start: 0.7375 (m) cc_final: 0.6973 (p) REVERT: A 116 TRP cc_start: 0.8124 (t60) cc_final: 0.7896 (t60) REVERT: A 304 LYS cc_start: 0.8346 (ttpp) cc_final: 0.7981 (ttpp) REVERT: A 404 LYS cc_start: 0.7788 (mmmt) cc_final: 0.7478 (mttp) REVERT: A 433 ILE cc_start: 0.8546 (tt) cc_final: 0.8188 (pt) REVERT: A 642 SER cc_start: 0.8156 (m) cc_final: 0.7830 (p) REVERT: B 815 LYS cc_start: 0.8093 (mttp) cc_final: 0.7802 (mttp) REVERT: B 817 LYS cc_start: 0.8047 (mmtt) cc_final: 0.7832 (mmtm) REVERT: B 910 SER cc_start: 0.7523 (t) cc_final: 0.7283 (p) REVERT: B 942 GLU cc_start: 0.7272 (mm-30) cc_final: 0.7023 (mm-30) REVERT: B 968 MET cc_start: 0.7793 (tmm) cc_final: 0.7432 (tmm) REVERT: B 969 ILE cc_start: 0.8846 (mt) cc_final: 0.8413 (mt) REVERT: B 974 PHE cc_start: 0.7674 (t80) cc_final: 0.7411 (t80) REVERT: B 1005 ARG cc_start: 0.7596 (mtm180) cc_final: 0.7248 (mtt90) REVERT: B 1085 VAL cc_start: 0.8574 (t) cc_final: 0.8204 (m) REVERT: B 1129 GLN cc_start: 0.8216 (mm-40) cc_final: 0.7688 (tp40) REVERT: B 1229 TYR cc_start: 0.6165 (m-80) cc_final: 0.5910 (m-80) REVERT: B 1288 TRP cc_start: 0.8097 (t60) cc_final: 0.7839 (t60) REVERT: B 1306 VAL cc_start: 0.8133 (p) cc_final: 0.7418 (p) REVERT: B 1310 ASP cc_start: 0.7188 (m-30) cc_final: 0.6853 (m-30) REVERT: B 1384 TYR cc_start: 0.8102 (p90) cc_final: 0.7866 (p90) REVERT: C 1483 MET cc_start: 0.6958 (ptp) cc_final: 0.6329 (ptp) REVERT: C 1523 LEU cc_start: 0.8176 (mt) cc_final: 0.7903 (mp) REVERT: C 1527 ASP cc_start: 0.7418 (p0) cc_final: 0.6985 (p0) REVERT: D 78 THR cc_start: 0.8237 (m) cc_final: 0.7881 (p) outliers start: 19 outliers final: 12 residues processed: 398 average time/residue: 0.6125 time to fit residues: 332.1848 Evaluate side-chains 410 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 398 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 648 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1329 VAL Chi-restraints excluded: chain B residue 1389 MET Chi-restraints excluded: chain C residue 1505 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 135 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1227 ASN B1256 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 11942 Z= 0.371 Angle : 0.601 7.167 16218 Z= 0.316 Chirality : 0.044 0.262 1849 Planarity : 0.004 0.043 2096 Dihedral : 7.212 95.682 1729 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.28 % Allowed : 14.15 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -0.74 (0.21), residues: 1495 helix: 0.76 (0.32), residues: 266 sheet: -0.43 (0.22), residues: 536 loop : -0.96 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 47 HIS 0.008 0.001 HIS B1214 PHE 0.020 0.002 PHE A 74 TYR 0.021 0.001 TYR D 105 ARG 0.005 0.000 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 418 time to evaluate : 2.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 SER cc_start: 0.8060 (m) cc_final: 0.7848 (p) REVERT: A 62 SER cc_start: 0.7485 (m) cc_final: 0.7093 (p) REVERT: A 104 ARG cc_start: 0.7572 (ttm170) cc_final: 0.7360 (ttm170) REVERT: A 116 TRP cc_start: 0.8130 (t60) cc_final: 0.7795 (t60) REVERT: A 121 LEU cc_start: 0.8366 (mt) cc_final: 0.8143 (mp) REVERT: A 146 ASP cc_start: 0.6398 (t0) cc_final: 0.6182 (t0) REVERT: A 282 VAL cc_start: 0.8678 (t) cc_final: 0.8226 (m) REVERT: A 318 GLU cc_start: 0.7827 (pp20) cc_final: 0.7556 (tm-30) REVERT: A 404 LYS cc_start: 0.7816 (mmmt) cc_final: 0.7601 (mmmt) REVERT: A 421 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8462 (mm) REVERT: A 433 ILE cc_start: 0.8525 (tt) cc_final: 0.8162 (pt) REVERT: A 642 SER cc_start: 0.8185 (m) cc_final: 0.7873 (p) REVERT: B 815 LYS cc_start: 0.8160 (mttp) cc_final: 0.7864 (mttp) REVERT: B 889 VAL cc_start: 0.8563 (p) cc_final: 0.8216 (t) REVERT: B 910 SER cc_start: 0.7591 (t) cc_final: 0.7320 (p) REVERT: B 942 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7086 (mm-30) REVERT: B 968 MET cc_start: 0.7788 (tmm) cc_final: 0.7311 (tmm) REVERT: B 969 ILE cc_start: 0.8819 (mt) cc_final: 0.8394 (mt) REVERT: B 974 PHE cc_start: 0.7670 (t80) cc_final: 0.7369 (t80) REVERT: B 1005 ARG cc_start: 0.7609 (mtm180) cc_final: 0.7272 (mtt180) REVERT: B 1032 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6937 (mt-10) REVERT: B 1085 VAL cc_start: 0.8656 (t) cc_final: 0.8291 (m) REVERT: B 1229 TYR cc_start: 0.6215 (m-80) cc_final: 0.5873 (m-80) REVERT: B 1288 TRP cc_start: 0.8078 (t60) cc_final: 0.7732 (t60) REVERT: B 1310 ASP cc_start: 0.7225 (m-30) cc_final: 0.6891 (m-30) REVERT: B 1384 TYR cc_start: 0.8149 (p90) cc_final: 0.7842 (p90) REVERT: C 1483 MET cc_start: 0.7035 (ptp) cc_final: 0.6485 (ptp) REVERT: C 1523 LEU cc_start: 0.8222 (mt) cc_final: 0.7863 (mp) REVERT: C 1527 ASP cc_start: 0.7396 (p0) cc_final: 0.7037 (p0) REVERT: D 78 THR cc_start: 0.8315 (m) cc_final: 0.7759 (p) outliers start: 29 outliers final: 24 residues processed: 425 average time/residue: 0.6276 time to fit residues: 366.8164 Evaluate side-chains 426 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 401 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 1016 ILE Chi-restraints excluded: chain B residue 1079 THR Chi-restraints excluded: chain B residue 1109 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1329 VAL Chi-restraints excluded: chain B residue 1331 LEU Chi-restraints excluded: chain B residue 1389 MET Chi-restraints excluded: chain B residue 1402 THR Chi-restraints excluded: chain C residue 1505 THR Chi-restraints excluded: chain C residue 1565 ARG Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 73 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.3980 chunk 102 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 136 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN B1348 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11942 Z= 0.242 Angle : 0.562 5.946 16218 Z= 0.289 Chirality : 0.043 0.264 1849 Planarity : 0.004 0.049 2096 Dihedral : 6.973 93.378 1729 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.12 % Allowed : 16.04 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -0.60 (0.21), residues: 1495 helix: 1.02 (0.33), residues: 266 sheet: -0.39 (0.22), residues: 546 loop : -0.89 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 47 HIS 0.005 0.001 HIS B1150 PHE 0.017 0.001 PHE C1494 TYR 0.017 0.001 TYR D 105 ARG 0.006 0.000 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 403 time to evaluate : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 SER cc_start: 0.8061 (m) cc_final: 0.7851 (p) REVERT: A 62 SER cc_start: 0.7410 (m) cc_final: 0.6962 (p) REVERT: A 116 TRP cc_start: 0.8046 (t60) cc_final: 0.7693 (t60) REVERT: A 121 LEU cc_start: 0.8365 (mt) cc_final: 0.8138 (mp) REVERT: A 146 ASP cc_start: 0.6484 (t0) cc_final: 0.6197 (t0) REVERT: A 282 VAL cc_start: 0.8640 (OUTLIER) cc_final: 0.8209 (m) REVERT: A 404 LYS cc_start: 0.7780 (mmmt) cc_final: 0.7573 (mmmt) REVERT: A 421 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8461 (mm) REVERT: A 433 ILE cc_start: 0.8509 (tt) cc_final: 0.8151 (pt) REVERT: A 604 LEU cc_start: 0.8236 (tp) cc_final: 0.8012 (tp) REVERT: A 642 SER cc_start: 0.8168 (m) cc_final: 0.7853 (p) REVERT: A 667 LEU cc_start: 0.8092 (mp) cc_final: 0.7887 (tp) REVERT: B 815 LYS cc_start: 0.8117 (mttp) cc_final: 0.7848 (mttp) REVERT: B 889 VAL cc_start: 0.8539 (p) cc_final: 0.8221 (t) REVERT: B 910 SER cc_start: 0.7667 (t) cc_final: 0.7411 (p) REVERT: B 942 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7004 (mm-30) REVERT: B 968 MET cc_start: 0.7769 (tmm) cc_final: 0.7295 (tmm) REVERT: B 969 ILE cc_start: 0.8877 (mt) cc_final: 0.8433 (mt) REVERT: B 974 PHE cc_start: 0.7642 (t80) cc_final: 0.7416 (t80) REVERT: B 1005 ARG cc_start: 0.7530 (mtm180) cc_final: 0.7259 (mtt180) REVERT: B 1085 VAL cc_start: 0.8574 (t) cc_final: 0.8216 (m) REVERT: B 1229 TYR cc_start: 0.6229 (m-80) cc_final: 0.5881 (m-80) REVERT: B 1288 TRP cc_start: 0.7985 (t60) cc_final: 0.7702 (t60) REVERT: B 1310 ASP cc_start: 0.7215 (m-30) cc_final: 0.6880 (m-30) REVERT: B 1348 ASN cc_start: 0.6218 (t0) cc_final: 0.6009 (t0) REVERT: B 1384 TYR cc_start: 0.8162 (p90) cc_final: 0.7819 (p90) REVERT: C 1483 MET cc_start: 0.7025 (ptp) cc_final: 0.6492 (ptp) REVERT: C 1523 LEU cc_start: 0.8192 (mt) cc_final: 0.7807 (mp) REVERT: C 1527 ASP cc_start: 0.7406 (p0) cc_final: 0.7060 (p0) REVERT: D 78 THR cc_start: 0.8273 (m) cc_final: 0.7713 (p) REVERT: D 83 MET cc_start: 0.7271 (mpp) cc_final: 0.7043 (mpp) outliers start: 27 outliers final: 21 residues processed: 414 average time/residue: 0.6161 time to fit residues: 347.9975 Evaluate side-chains 421 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 398 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain B residue 1016 ILE Chi-restraints excluded: chain B residue 1031 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1165 LYS Chi-restraints excluded: chain B residue 1331 LEU Chi-restraints excluded: chain B residue 1389 MET Chi-restraints excluded: chain B residue 1402 THR Chi-restraints excluded: chain C residue 1505 THR Chi-restraints excluded: chain C residue 1565 ARG Chi-restraints excluded: chain D residue 22 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 2 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 0 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 11942 Z= 0.409 Angle : 0.604 6.801 16218 Z= 0.317 Chirality : 0.044 0.271 1849 Planarity : 0.004 0.053 2096 Dihedral : 7.047 92.538 1729 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.67 % Allowed : 16.59 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -0.80 (0.21), residues: 1495 helix: 0.74 (0.33), residues: 264 sheet: -0.43 (0.22), residues: 552 loop : -1.05 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 47 HIS 0.009 0.001 HIS B1214 PHE 0.026 0.002 PHE C1494 TYR 0.024 0.002 TYR D 105 ARG 0.005 0.000 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 411 time to evaluate : 1.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLN cc_start: 0.6999 (pp30) cc_final: 0.6781 (pp30) REVERT: A 62 SER cc_start: 0.7552 (m) cc_final: 0.7132 (p) REVERT: A 116 TRP cc_start: 0.8112 (t60) cc_final: 0.7717 (t60) REVERT: A 146 ASP cc_start: 0.6491 (t0) cc_final: 0.6204 (t0) REVERT: A 262 MET cc_start: 0.7578 (mpp) cc_final: 0.7341 (mpp) REVERT: A 282 VAL cc_start: 0.8656 (OUTLIER) cc_final: 0.8237 (m) REVERT: A 318 GLU cc_start: 0.7853 (pp20) cc_final: 0.7562 (tm-30) REVERT: A 346 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.6440 (tt0) REVERT: A 379 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.7658 (t) REVERT: A 421 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8487 (mm) REVERT: A 433 ILE cc_start: 0.8523 (tt) cc_final: 0.8170 (pt) REVERT: A 604 LEU cc_start: 0.8234 (tp) cc_final: 0.8018 (tp) REVERT: A 623 LYS cc_start: 0.8255 (tppt) cc_final: 0.8048 (tppt) REVERT: A 642 SER cc_start: 0.8213 (m) cc_final: 0.7901 (p) REVERT: B 815 LYS cc_start: 0.8187 (mttp) cc_final: 0.7908 (mttp) REVERT: B 889 VAL cc_start: 0.8622 (p) cc_final: 0.8275 (t) REVERT: B 910 SER cc_start: 0.7695 (t) cc_final: 0.7416 (p) REVERT: B 942 GLU cc_start: 0.7357 (mm-30) cc_final: 0.7013 (mm-30) REVERT: B 968 MET cc_start: 0.7722 (tmm) cc_final: 0.7158 (tmm) REVERT: B 969 ILE cc_start: 0.8876 (mt) cc_final: 0.8448 (mt) REVERT: B 974 PHE cc_start: 0.7639 (t80) cc_final: 0.7407 (t80) REVERT: B 1032 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6885 (mt-10) REVERT: B 1085 VAL cc_start: 0.8660 (t) cc_final: 0.8277 (m) REVERT: B 1229 TYR cc_start: 0.6191 (m-80) cc_final: 0.5839 (m-80) REVERT: B 1288 TRP cc_start: 0.8124 (t60) cc_final: 0.7805 (t60) REVERT: B 1310 ASP cc_start: 0.7303 (m-30) cc_final: 0.6898 (m-30) REVERT: B 1384 TYR cc_start: 0.8202 (p90) cc_final: 0.7860 (p90) REVERT: C 1483 MET cc_start: 0.7148 (ptp) cc_final: 0.6689 (ptp) REVERT: C 1523 LEU cc_start: 0.8158 (mt) cc_final: 0.7837 (mp) REVERT: C 1527 ASP cc_start: 0.7431 (p0) cc_final: 0.7120 (p0) REVERT: C 1541 VAL cc_start: 0.7883 (t) cc_final: 0.7611 (m) REVERT: D 78 THR cc_start: 0.8179 (m) cc_final: 0.7597 (p) outliers start: 34 outliers final: 27 residues processed: 423 average time/residue: 0.6247 time to fit residues: 360.2006 Evaluate side-chains 435 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 404 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 1031 THR Chi-restraints excluded: chain B residue 1109 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1329 VAL Chi-restraints excluded: chain B residue 1331 LEU Chi-restraints excluded: chain B residue 1389 MET Chi-restraints excluded: chain B residue 1402 THR Chi-restraints excluded: chain C residue 1505 THR Chi-restraints excluded: chain C residue 1565 ARG Chi-restraints excluded: chain D residue 22 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 28 optimal weight: 0.1980 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11942 Z= 0.334 Angle : 0.587 6.072 16218 Z= 0.305 Chirality : 0.043 0.270 1849 Planarity : 0.004 0.058 2096 Dihedral : 6.940 92.116 1729 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.52 % Allowed : 18.87 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -0.73 (0.21), residues: 1495 helix: 0.82 (0.33), residues: 265 sheet: -0.34 (0.22), residues: 529 loop : -1.04 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 47 HIS 0.006 0.001 HIS B1150 PHE 0.021 0.002 PHE C1494 TYR 0.021 0.002 TYR D 105 ARG 0.006 0.000 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 403 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLN cc_start: 0.6919 (pp30) cc_final: 0.6707 (pp30) REVERT: A 62 SER cc_start: 0.7569 (m) cc_final: 0.7140 (p) REVERT: A 116 TRP cc_start: 0.8077 (t60) cc_final: 0.7656 (t60) REVERT: A 146 ASP cc_start: 0.6522 (t0) cc_final: 0.6185 (t0) REVERT: A 262 MET cc_start: 0.7511 (mpp) cc_final: 0.7262 (mpp) REVERT: A 282 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8230 (m) REVERT: A 304 LYS cc_start: 0.8303 (ttpp) cc_final: 0.7967 (ttmm) REVERT: A 346 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.6331 (tt0) REVERT: A 404 LYS cc_start: 0.7848 (mmmt) cc_final: 0.7429 (mttm) REVERT: A 433 ILE cc_start: 0.8515 (tt) cc_final: 0.8175 (pt) REVERT: A 604 LEU cc_start: 0.8235 (tp) cc_final: 0.8014 (tp) REVERT: A 642 SER cc_start: 0.8202 (m) cc_final: 0.7917 (p) REVERT: B 815 LYS cc_start: 0.8175 (mttp) cc_final: 0.7899 (mttp) REVERT: B 888 LEU cc_start: 0.7374 (mt) cc_final: 0.7102 (mp) REVERT: B 889 VAL cc_start: 0.8659 (p) cc_final: 0.8326 (t) REVERT: B 910 SER cc_start: 0.7716 (t) cc_final: 0.7443 (p) REVERT: B 942 GLU cc_start: 0.7309 (mm-30) cc_final: 0.6940 (mm-30) REVERT: B 968 MET cc_start: 0.7689 (tmm) cc_final: 0.7157 (tmm) REVERT: B 969 ILE cc_start: 0.8870 (mt) cc_final: 0.8447 (mt) REVERT: B 974 PHE cc_start: 0.7614 (t80) cc_final: 0.7398 (t80) REVERT: B 1085 VAL cc_start: 0.8582 (t) cc_final: 0.8206 (m) REVERT: B 1129 GLN cc_start: 0.8251 (mm-40) cc_final: 0.8040 (tp40) REVERT: B 1162 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7185 (mm-30) REVERT: B 1229 TYR cc_start: 0.6211 (m-80) cc_final: 0.5809 (m-80) REVERT: B 1288 TRP cc_start: 0.8064 (t60) cc_final: 0.7777 (t60) REVERT: B 1310 ASP cc_start: 0.7273 (m-30) cc_final: 0.6900 (m-30) REVERT: B 1358 LEU cc_start: 0.8090 (tt) cc_final: 0.7867 (tt) REVERT: B 1384 TYR cc_start: 0.8216 (p90) cc_final: 0.7783 (p90) REVERT: C 1483 MET cc_start: 0.7138 (ptp) cc_final: 0.6729 (ptp) REVERT: C 1503 LYS cc_start: 0.8442 (ptpt) cc_final: 0.7989 (ptpt) REVERT: C 1523 LEU cc_start: 0.8149 (mt) cc_final: 0.7836 (mp) REVERT: C 1527 ASP cc_start: 0.7413 (p0) cc_final: 0.7115 (p0) REVERT: D 78 THR cc_start: 0.8014 (m) cc_final: 0.7418 (p) outliers start: 32 outliers final: 27 residues processed: 412 average time/residue: 0.6117 time to fit residues: 343.9386 Evaluate side-chains 425 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 396 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 801 ASP Chi-restraints excluded: chain B residue 1031 THR Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain B residue 1109 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1165 LYS Chi-restraints excluded: chain B residue 1215 ASN Chi-restraints excluded: chain B residue 1331 LEU Chi-restraints excluded: chain B residue 1389 MET Chi-restraints excluded: chain B residue 1402 THR Chi-restraints excluded: chain C residue 1505 THR Chi-restraints excluded: chain C residue 1565 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 88 optimal weight: 0.0470 chunk 66 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11942 Z= 0.258 Angle : 0.570 6.326 16218 Z= 0.293 Chirality : 0.043 0.277 1849 Planarity : 0.004 0.061 2096 Dihedral : 6.792 91.951 1729 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.20 % Allowed : 19.65 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 1495 helix: 1.10 (0.33), residues: 265 sheet: -0.35 (0.22), residues: 530 loop : -0.97 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 47 HIS 0.006 0.001 HIS B1150 PHE 0.019 0.001 PHE C1494 TYR 0.018 0.001 TYR D 105 ARG 0.008 0.000 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 397 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 SER cc_start: 0.7560 (m) cc_final: 0.7133 (p) REVERT: A 116 TRP cc_start: 0.8033 (t60) cc_final: 0.7570 (t60) REVERT: A 146 ASP cc_start: 0.6542 (t0) cc_final: 0.6254 (t0) REVERT: A 233 VAL cc_start: 0.7888 (p) cc_final: 0.7650 (t) REVERT: A 262 MET cc_start: 0.7444 (mpp) cc_final: 0.7176 (mpp) REVERT: A 282 VAL cc_start: 0.8620 (OUTLIER) cc_final: 0.8216 (m) REVERT: A 304 LYS cc_start: 0.8287 (ttpp) cc_final: 0.7965 (ttmm) REVERT: A 346 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.6417 (tt0) REVERT: A 379 VAL cc_start: 0.8318 (OUTLIER) cc_final: 0.7594 (t) REVERT: A 404 LYS cc_start: 0.7852 (mmmt) cc_final: 0.7430 (mttm) REVERT: A 642 SER cc_start: 0.8203 (m) cc_final: 0.7916 (p) REVERT: B 815 LYS cc_start: 0.8245 (mttp) cc_final: 0.7976 (mttp) REVERT: B 888 LEU cc_start: 0.7352 (mt) cc_final: 0.7083 (mp) REVERT: B 889 VAL cc_start: 0.8647 (p) cc_final: 0.8319 (t) REVERT: B 910 SER cc_start: 0.7715 (t) cc_final: 0.7441 (p) REVERT: B 941 ARG cc_start: 0.7461 (ptp-110) cc_final: 0.7210 (ptp90) REVERT: B 947 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7022 (mm-30) REVERT: B 968 MET cc_start: 0.7678 (tmm) cc_final: 0.7122 (tmm) REVERT: B 969 ILE cc_start: 0.8840 (mt) cc_final: 0.8415 (mt) REVERT: B 974 PHE cc_start: 0.7595 (t80) cc_final: 0.7375 (t80) REVERT: B 1085 VAL cc_start: 0.8559 (t) cc_final: 0.8187 (m) REVERT: B 1162 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7188 (mm-30) REVERT: B 1229 TYR cc_start: 0.6205 (m-80) cc_final: 0.5795 (m-80) REVERT: B 1288 TRP cc_start: 0.8027 (t60) cc_final: 0.7755 (t60) REVERT: B 1310 ASP cc_start: 0.7277 (m-30) cc_final: 0.6883 (m-30) REVERT: B 1384 TYR cc_start: 0.8251 (p90) cc_final: 0.7909 (p90) REVERT: C 1483 MET cc_start: 0.7121 (ptp) cc_final: 0.6702 (ptp) REVERT: C 1503 LYS cc_start: 0.8409 (ptpt) cc_final: 0.7939 (ptpt) REVERT: C 1527 ASP cc_start: 0.7410 (p0) cc_final: 0.7132 (p0) REVERT: C 1541 VAL cc_start: 0.7814 (t) cc_final: 0.7586 (m) REVERT: D 78 THR cc_start: 0.7922 (m) cc_final: 0.7326 (p) outliers start: 28 outliers final: 19 residues processed: 408 average time/residue: 0.6302 time to fit residues: 353.0393 Evaluate side-chains 415 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 393 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain B residue 801 ASP Chi-restraints excluded: chain B residue 1031 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1389 MET Chi-restraints excluded: chain B residue 1402 THR Chi-restraints excluded: chain C residue 1505 THR Chi-restraints excluded: chain C residue 1565 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 138 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11942 Z= 0.229 Angle : 0.563 6.907 16218 Z= 0.286 Chirality : 0.043 0.281 1849 Planarity : 0.004 0.062 2096 Dihedral : 6.698 91.387 1729 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.12 % Allowed : 20.60 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -0.51 (0.21), residues: 1495 helix: 1.27 (0.33), residues: 264 sheet: -0.31 (0.22), residues: 528 loop : -0.92 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 47 HIS 0.005 0.001 HIS B1150 PHE 0.018 0.001 PHE C1494 TYR 0.017 0.001 TYR D 105 ARG 0.008 0.000 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 399 time to evaluate : 1.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 SER cc_start: 0.7564 (m) cc_final: 0.7138 (p) REVERT: A 116 TRP cc_start: 0.8007 (t60) cc_final: 0.7606 (t60) REVERT: A 146 ASP cc_start: 0.6560 (t0) cc_final: 0.6266 (t0) REVERT: A 233 VAL cc_start: 0.7853 (p) cc_final: 0.7627 (t) REVERT: A 262 MET cc_start: 0.7429 (mpp) cc_final: 0.7197 (mpp) REVERT: A 282 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8225 (m) REVERT: A 304 LYS cc_start: 0.8294 (ttpp) cc_final: 0.7947 (ttmm) REVERT: A 346 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.6411 (tt0) REVERT: A 379 VAL cc_start: 0.8286 (OUTLIER) cc_final: 0.7562 (t) REVERT: A 404 LYS cc_start: 0.7839 (mmmt) cc_final: 0.7419 (mttm) REVERT: A 433 ILE cc_start: 0.8490 (tt) cc_final: 0.8144 (pt) REVERT: A 642 SER cc_start: 0.8200 (m) cc_final: 0.7921 (p) REVERT: B 815 LYS cc_start: 0.8242 (mttp) cc_final: 0.7977 (mttp) REVERT: B 888 LEU cc_start: 0.7351 (mt) cc_final: 0.7092 (mp) REVERT: B 889 VAL cc_start: 0.8652 (p) cc_final: 0.8314 (t) REVERT: B 910 SER cc_start: 0.7718 (t) cc_final: 0.7443 (p) REVERT: B 947 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7038 (mm-30) REVERT: B 968 MET cc_start: 0.7660 (tmm) cc_final: 0.7104 (tmm) REVERT: B 969 ILE cc_start: 0.8863 (mt) cc_final: 0.8419 (mt) REVERT: B 974 PHE cc_start: 0.7602 (t80) cc_final: 0.7381 (t80) REVERT: B 1085 VAL cc_start: 0.8523 (t) cc_final: 0.8154 (m) REVERT: B 1129 GLN cc_start: 0.8285 (tp40) cc_final: 0.8031 (tp40) REVERT: B 1203 THR cc_start: 0.8240 (p) cc_final: 0.7934 (t) REVERT: B 1288 TRP cc_start: 0.8004 (t60) cc_final: 0.7749 (t60) REVERT: B 1310 ASP cc_start: 0.7275 (m-30) cc_final: 0.6886 (m-30) REVERT: B 1384 TYR cc_start: 0.8270 (p90) cc_final: 0.7918 (p90) REVERT: C 1483 MET cc_start: 0.7111 (ptp) cc_final: 0.6694 (ptp) REVERT: C 1503 LYS cc_start: 0.8368 (ptpt) cc_final: 0.7897 (ptpt) REVERT: C 1527 ASP cc_start: 0.7423 (p0) cc_final: 0.7149 (p0) REVERT: C 1541 VAL cc_start: 0.7808 (t) cc_final: 0.7599 (m) REVERT: D 73 ASP cc_start: 0.6542 (p0) cc_final: 0.5739 (p0) REVERT: D 78 THR cc_start: 0.7874 (m) cc_final: 0.7044 (p) outliers start: 27 outliers final: 22 residues processed: 408 average time/residue: 0.6165 time to fit residues: 344.9723 Evaluate side-chains 421 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 396 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain B residue 801 ASP Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 1031 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1402 THR Chi-restraints excluded: chain C residue 1472 ILE Chi-restraints excluded: chain C residue 1505 THR Chi-restraints excluded: chain C residue 1565 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 41 optimal weight: 0.0060 chunk 121 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11942 Z= 0.276 Angle : 0.581 6.994 16218 Z= 0.297 Chirality : 0.043 0.283 1849 Planarity : 0.004 0.073 2096 Dihedral : 6.658 90.424 1729 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.12 % Allowed : 21.38 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -0.55 (0.21), residues: 1495 helix: 1.23 (0.33), residues: 264 sheet: -0.32 (0.22), residues: 528 loop : -0.95 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 47 HIS 0.006 0.001 HIS B1150 PHE 0.020 0.001 PHE C1494 TYR 0.019 0.001 TYR B1315 ARG 0.009 0.000 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 407 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 SER cc_start: 0.7609 (m) cc_final: 0.7159 (p) REVERT: A 116 TRP cc_start: 0.8017 (t60) cc_final: 0.7589 (t60) REVERT: A 146 ASP cc_start: 0.6593 (t0) cc_final: 0.6249 (t0) REVERT: A 233 VAL cc_start: 0.7972 (p) cc_final: 0.7725 (t) REVERT: A 262 MET cc_start: 0.7424 (mpp) cc_final: 0.7206 (mpp) REVERT: A 304 LYS cc_start: 0.8287 (ttpp) cc_final: 0.7952 (ttmm) REVERT: A 346 GLU cc_start: 0.6672 (OUTLIER) cc_final: 0.6436 (tt0) REVERT: A 379 VAL cc_start: 0.8266 (OUTLIER) cc_final: 0.7526 (t) REVERT: A 404 LYS cc_start: 0.7877 (mmmt) cc_final: 0.7431 (mttm) REVERT: A 433 ILE cc_start: 0.8466 (tt) cc_final: 0.8137 (pt) REVERT: A 521 GLU cc_start: 0.6569 (mm-30) cc_final: 0.6319 (mm-30) REVERT: A 604 LEU cc_start: 0.8270 (tp) cc_final: 0.7934 (tp) REVERT: A 642 SER cc_start: 0.8222 (m) cc_final: 0.7949 (p) REVERT: B 815 LYS cc_start: 0.8268 (mttp) cc_final: 0.7995 (mttp) REVERT: B 888 LEU cc_start: 0.7352 (mt) cc_final: 0.7098 (mp) REVERT: B 889 VAL cc_start: 0.8649 (p) cc_final: 0.8320 (t) REVERT: B 910 SER cc_start: 0.7733 (t) cc_final: 0.7444 (p) REVERT: B 947 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7034 (mm-30) REVERT: B 968 MET cc_start: 0.7643 (tmm) cc_final: 0.7079 (tmm) REVERT: B 969 ILE cc_start: 0.8868 (mt) cc_final: 0.8418 (mt) REVERT: B 974 PHE cc_start: 0.7589 (t80) cc_final: 0.7370 (t80) REVERT: B 1085 VAL cc_start: 0.8535 (t) cc_final: 0.8164 (m) REVERT: B 1129 GLN cc_start: 0.8311 (tp40) cc_final: 0.8075 (tp40) REVERT: B 1162 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6993 (mm-30) REVERT: B 1288 TRP cc_start: 0.8012 (t60) cc_final: 0.7765 (t60) REVERT: B 1310 ASP cc_start: 0.7269 (m-30) cc_final: 0.6893 (m-30) REVERT: B 1380 VAL cc_start: 0.8203 (m) cc_final: 0.7892 (t) REVERT: B 1384 TYR cc_start: 0.8284 (p90) cc_final: 0.7921 (p90) REVERT: C 1483 MET cc_start: 0.7112 (ptp) cc_final: 0.6671 (ptp) REVERT: C 1503 LYS cc_start: 0.8342 (ptpt) cc_final: 0.7887 (ptpt) REVERT: C 1527 ASP cc_start: 0.7431 (p0) cc_final: 0.7178 (p0) REVERT: D 73 ASP cc_start: 0.6488 (p0) cc_final: 0.5593 (p0) REVERT: D 78 THR cc_start: 0.7832 (m) cc_final: 0.6995 (p) outliers start: 27 outliers final: 25 residues processed: 417 average time/residue: 0.5964 time to fit residues: 340.6107 Evaluate side-chains 426 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 399 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 801 ASP Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 1031 THR Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain B residue 1109 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1402 THR Chi-restraints excluded: chain C residue 1472 ILE Chi-restraints excluded: chain C residue 1505 THR Chi-restraints excluded: chain C residue 1565 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 72 optimal weight: 0.0980 chunk 94 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11942 Z= 0.229 Angle : 0.573 7.357 16218 Z= 0.290 Chirality : 0.043 0.285 1849 Planarity : 0.004 0.075 2096 Dihedral : 6.567 89.936 1729 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.04 % Allowed : 21.93 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -0.44 (0.22), residues: 1495 helix: 1.30 (0.33), residues: 266 sheet: -0.26 (0.22), residues: 542 loop : -0.89 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 47 HIS 0.005 0.001 HIS B1150 PHE 0.019 0.001 PHE C1494 TYR 0.018 0.001 TYR B1315 ARG 0.011 0.000 ARG A 137 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 404 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 SER cc_start: 0.7592 (m) cc_final: 0.7140 (p) REVERT: A 116 TRP cc_start: 0.7985 (t60) cc_final: 0.7559 (t60) REVERT: A 146 ASP cc_start: 0.6613 (t0) cc_final: 0.6296 (t0) REVERT: A 262 MET cc_start: 0.7403 (mpp) cc_final: 0.7175 (mpp) REVERT: A 304 LYS cc_start: 0.8275 (ttpp) cc_final: 0.7942 (ttmm) REVERT: A 346 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.6430 (tt0) REVERT: A 379 VAL cc_start: 0.8224 (OUTLIER) cc_final: 0.7485 (t) REVERT: A 404 LYS cc_start: 0.7870 (mmmt) cc_final: 0.7427 (mttm) REVERT: A 433 ILE cc_start: 0.8472 (tt) cc_final: 0.8152 (pt) REVERT: A 642 SER cc_start: 0.8231 (m) cc_final: 0.7977 (p) REVERT: B 815 LYS cc_start: 0.8251 (mttp) cc_final: 0.7973 (mttp) REVERT: B 888 LEU cc_start: 0.7335 (mt) cc_final: 0.7090 (mp) REVERT: B 889 VAL cc_start: 0.8649 (p) cc_final: 0.8316 (t) REVERT: B 910 SER cc_start: 0.7735 (t) cc_final: 0.7450 (p) REVERT: B 947 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7040 (mm-30) REVERT: B 968 MET cc_start: 0.7625 (tmm) cc_final: 0.7206 (tmm) REVERT: B 969 ILE cc_start: 0.8871 (mt) cc_final: 0.8433 (mt) REVERT: B 974 PHE cc_start: 0.7567 (t80) cc_final: 0.7179 (t80) REVERT: B 1085 VAL cc_start: 0.8524 (t) cc_final: 0.8155 (m) REVERT: B 1129 GLN cc_start: 0.8303 (tp40) cc_final: 0.8084 (tp40) REVERT: B 1288 TRP cc_start: 0.7973 (t60) cc_final: 0.7748 (t60) REVERT: B 1310 ASP cc_start: 0.7249 (m-30) cc_final: 0.6877 (m-30) REVERT: B 1380 VAL cc_start: 0.8189 (m) cc_final: 0.7888 (t) REVERT: B 1384 TYR cc_start: 0.8270 (p90) cc_final: 0.7889 (p90) REVERT: B 1400 GLU cc_start: 0.7576 (tm-30) cc_final: 0.6866 (mt-10) REVERT: C 1483 MET cc_start: 0.7081 (ptp) cc_final: 0.6645 (ptp) REVERT: C 1503 LYS cc_start: 0.8348 (ptpt) cc_final: 0.7884 (ptpt) REVERT: C 1527 ASP cc_start: 0.7421 (p0) cc_final: 0.7159 (p0) REVERT: D 73 ASP cc_start: 0.6467 (p0) cc_final: 0.5500 (p0) REVERT: D 78 THR cc_start: 0.7788 (m) cc_final: 0.6939 (p) outliers start: 26 outliers final: 23 residues processed: 414 average time/residue: 0.6000 time to fit residues: 339.5439 Evaluate side-chains 419 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 394 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain B residue 801 ASP Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 1031 THR Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1402 THR Chi-restraints excluded: chain C residue 1472 ILE Chi-restraints excluded: chain C residue 1505 THR Chi-restraints excluded: chain C residue 1565 ARG Chi-restraints excluded: chain D residue 47 TRP Chi-restraints excluded: chain D residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.124224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.108972 restraints weight = 53755.745| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.77 r_work: 0.3321 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11942 Z= 0.267 Angle : 0.586 7.455 16218 Z= 0.299 Chirality : 0.043 0.284 1849 Planarity : 0.004 0.080 2096 Dihedral : 6.540 89.125 1729 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.97 % Allowed : 22.25 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -0.48 (0.22), residues: 1495 helix: 1.22 (0.33), residues: 266 sheet: -0.27 (0.22), residues: 541 loop : -0.90 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 47 HIS 0.006 0.001 HIS B1150 PHE 0.019 0.001 PHE C1494 TYR 0.018 0.002 TYR D 105 ARG 0.011 0.000 ARG A 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7370.45 seconds wall clock time: 129 minutes 21.65 seconds (7761.65 seconds total)