Starting phenix.real_space_refine on Thu Feb 15 04:53:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmy_7968/02_2024/6dmy_7968.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmy_7968/02_2024/6dmy_7968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmy_7968/02_2024/6dmy_7968.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmy_7968/02_2024/6dmy_7968.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmy_7968/02_2024/6dmy_7968.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmy_7968/02_2024/6dmy_7968.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1998 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 1 6.06 5 S 47 5.16 5 C 5978 2.51 5 N 1510 2.21 5 O 1673 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 85": "NH1" <-> "NH2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A ARG 138": "NH1" <-> "NH2" Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 536": "NH1" <-> "NH2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "A ARG 772": "NH1" <-> "NH2" Residue "A ARG 893": "NH1" <-> "NH2" Residue "A ARG 906": "NH1" <-> "NH2" Residue "A PHE 974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 982": "NH1" <-> "NH2" Residue "A ARG 1113": "NH1" <-> "NH2" Residue "A ARG 1114": "NH1" <-> "NH2" Residue "A ARG 1150": "NH1" <-> "NH2" Residue "B ASP 129": "OD1" <-> "OD2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 188": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9211 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7821 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 42, 'TRANS': 947} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1213 Classifications: {'peptide': 151} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 145} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Unusual residues: {'NAG': 5, 'Y01': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 9 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Time building chain proxies: 5.38, per 1000 atoms: 0.58 Number of scatterers: 9211 At special positions: 0 Unit cell: (92.735, 86.189, 152.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Ca 2 19.99 S 47 16.00 O 1673 8.00 N 1510 7.00 C 5978 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 226 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 327 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 304 " 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 C 1 " - " NAG C 2 " NAG-ASN " NAG A1801 " - " ASN A 312 " " NAG A1802 " - " ASN A 349 " " NAG A1803 " - " ASN A 414 " " NAG A1804 " - " ASN A 875 " " NAG A1807 " - " ASN A 141 " " NAG C 1 " - " ASN A1000 " Time building additional restraints: 3.40 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 202 " pdb="ZN ZN B 202 " - pdb=" NE2 HIS B 140 " pdb="ZN ZN B 202 " - pdb=" ND1 HIS B 182 " 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 4 sheets defined 53.7% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 74 through 96 removed outlier: 3.727A pdb=" N TRP A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS A 89 " --> pdb=" O ARG A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 115 removed outlier: 3.811A pdb=" N LEU A 102 " --> pdb=" O CYS A 98 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 113 " --> pdb=" O PHE A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 144 Processing helix chain 'A' and resid 171 through 185 Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.675A pdb=" N LEU A 202 " --> pdb=" O LYS A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 223 removed outlier: 3.566A pdb=" N GLN A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 219 " --> pdb=" O TYR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 234 removed outlier: 3.764A pdb=" N ASP A 233 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 267 Processing helix chain 'A' and resid 275 through 285 removed outlier: 3.564A pdb=" N GLU A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 388 through 410 removed outlier: 3.656A pdb=" N SER A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 438 through 457 removed outlier: 3.757A pdb=" N LEU A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N MET A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 489 removed outlier: 3.525A pdb=" N LEU A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 525 Proline residue: A 504 - end of helix removed outlier: 3.636A pdb=" N GLY A 509 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ASP A 513 " --> pdb=" O GLY A 509 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ASP A 514 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 543 Processing helix chain 'A' and resid 544 through 564 removed outlier: 3.611A pdb=" N SER A 552 " --> pdb=" O VAL A 548 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 605 removed outlier: 3.984A pdb=" N GLN A 576 " --> pdb=" O ALA A 572 " (cutoff:3.500A) Proline residue: A 593 - end of helix removed outlier: 4.723A pdb=" N ASP A 605 " --> pdb=" O TYR A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 735 Processing helix chain 'A' and resid 740 through 745 Processing helix chain 'A' and resid 750 through 769 removed outlier: 3.828A pdb=" N ILE A 754 " --> pdb=" O LYS A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 795 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.568A pdb=" N TYR A 820 " --> pdb=" O GLN A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 830 removed outlier: 3.847A pdb=" N LYS A 830 " --> pdb=" O SER A 827 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 827 through 830' Processing helix chain 'A' and resid 843 through 863 Processing helix chain 'A' and resid 881 through 889 removed outlier: 3.790A pdb=" N VAL A 888 " --> pdb=" O TYR A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 904 removed outlier: 3.695A pdb=" N GLN A 901 " --> pdb=" O ASP A 898 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS A 904 " --> pdb=" O GLN A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 930 Processing helix chain 'A' and resid 930 through 937 Processing helix chain 'A' and resid 983 through 1002 removed outlier: 3.825A pdb=" N PHE A 987 " --> pdb=" O ASP A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1018 Processing helix chain 'A' and resid 1026 through 1046 removed outlier: 3.771A pdb=" N PHE A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1075 removed outlier: 3.910A pdb=" N ILE A1055 " --> pdb=" O TRP A1051 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE A1056 " --> pdb=" O THR A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1107 removed outlier: 3.558A pdb=" N ILE A1085 " --> pdb=" O VAL A1081 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLU A1095 " --> pdb=" O GLY A1091 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N PHE A1096 " --> pdb=" O ILE A1092 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR A1097 " --> pdb=" O GLY A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1122 removed outlier: 3.541A pdb=" N LEU A1117 " --> pdb=" O ARG A1113 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N MET A1122 " --> pdb=" O ALA A1118 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1141 removed outlier: 4.747A pdb=" N THR A1133 " --> pdb=" O GLY A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1152 removed outlier: 3.934A pdb=" N VAL A1149 " --> pdb=" O PHE A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1178 removed outlier: 4.306A pdb=" N ILE A1158 " --> pdb=" O ALA A1154 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE A1161 " --> pdb=" O ALA A1157 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A1162 " --> pdb=" O ILE A1158 " (cutoff:3.500A) Proline residue: A1172 - end of helix removed outlier: 3.596A pdb=" N PHE A1177 " --> pdb=" O VAL A1173 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 removed outlier: 3.586A pdb=" N PHE B 73 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS B 74 " --> pdb=" O GLU B 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 70 through 74' Processing helix chain 'B' and resid 99 through 115 Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 157 through 167 Processing sheet with id=AA1, first strand: chain 'A' and resid 228 through 229 removed outlier: 3.612A pdb=" N LEU A 360 " --> pdb=" O GLN A 160 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU A 157 " --> pdb=" O PHE A 422 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE A 422 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 326 through 328 Processing sheet with id=AA3, first strand: chain 'A' and resid 972 through 978 removed outlier: 3.593A pdb=" N ALA A 972 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR A 804 " --> pdb=" O ASN A1011 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER A1007 " --> pdb=" O GLN A 808 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 48 removed outlier: 3.693A pdb=" N ILE B 48 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL B 173 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASP B 147 " --> pdb=" O THR B 125 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE B 85 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N GLU B 126 " --> pdb=" O ILE B 85 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1236 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: 2.75 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2653 1.34 - 1.46: 2402 1.46 - 1.59: 4300 1.59 - 1.71: 0 1.71 - 1.84: 77 Bond restraints: 9432 Sorted by residual: bond pdb=" CAY Y01 A1809 " pdb=" OAW Y01 A1809 " ideal model delta sigma weight residual 1.332 1.457 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" CAY Y01 A1808 " pdb=" OAW Y01 A1808 " ideal model delta sigma weight residual 1.332 1.445 -0.113 2.00e-02 2.50e+03 3.20e+01 bond pdb=" C ASN A 915 " pdb=" N PRO A 916 " ideal model delta sigma weight residual 1.334 1.220 0.114 2.34e-02 1.83e+03 2.36e+01 bond pdb=" CA ASN A1011 " pdb=" C ASN A1011 " ideal model delta sigma weight residual 1.521 1.575 -0.054 1.20e-02 6.94e+03 2.01e+01 bond pdb=" CAX Y01 A1809 " pdb=" OAH Y01 A1809 " ideal model delta sigma weight residual 1.248 1.329 -0.081 2.00e-02 2.50e+03 1.65e+01 ... (remaining 9427 not shown) Histogram of bond angle deviations from ideal: 96.40 - 105.72: 223 105.72 - 115.03: 5637 115.03 - 124.35: 6681 124.35 - 133.67: 255 133.67 - 142.99: 29 Bond angle restraints: 12825 Sorted by residual: angle pdb=" C TYR A1181 " pdb=" N PRO A1182 " pdb=" CA PRO A1182 " ideal model delta sigma weight residual 119.84 142.99 -23.15 1.25e+00 6.40e-01 3.43e+02 angle pdb=" C GLY A1179 " pdb=" N PRO A1180 " pdb=" CA PRO A1180 " ideal model delta sigma weight residual 119.05 133.69 -14.64 1.11e+00 8.12e-01 1.74e+02 angle pdb=" N TYR A 873 " pdb=" CA TYR A 873 " pdb=" C TYR A 873 " ideal model delta sigma weight residual 111.36 123.86 -12.50 1.09e+00 8.42e-01 1.32e+02 angle pdb=" CA PRO A 896 " pdb=" N PRO A 896 " pdb=" CD PRO A 896 " ideal model delta sigma weight residual 112.00 99.49 12.51 1.40e+00 5.10e-01 7.98e+01 angle pdb=" N LEU A 777 " pdb=" CA LEU A 777 " pdb=" C LEU A 777 " ideal model delta sigma weight residual 111.28 119.15 -7.87 1.09e+00 8.42e-01 5.22e+01 ... (remaining 12820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.65: 5471 24.65 - 49.29: 242 49.29 - 73.94: 43 73.94 - 98.59: 16 98.59 - 123.23: 3 Dihedral angle restraints: 5775 sinusoidal: 2441 harmonic: 3334 Sorted by residual: dihedral pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " pdb=" SG CYS A 304 " pdb=" CB CYS A 304 " ideal model delta sinusoidal sigma weight residual 93.00 -179.64 -87.36 1 1.00e+01 1.00e-02 9.16e+01 dihedral pdb=" CA PRO A 316 " pdb=" C PRO A 316 " pdb=" N LEU A 317 " pdb=" CA LEU A 317 " ideal model delta harmonic sigma weight residual 180.00 139.22 40.78 0 5.00e+00 4.00e-02 6.65e+01 dihedral pdb=" CA TYR A 224 " pdb=" C TYR A 224 " pdb=" N PRO A 225 " pdb=" CA PRO A 225 " ideal model delta harmonic sigma weight residual -180.00 -139.31 -40.69 0 5.00e+00 4.00e-02 6.62e+01 ... (remaining 5772 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1301 0.104 - 0.207: 150 0.207 - 0.310: 15 0.310 - 0.414: 2 0.414 - 0.517: 3 Chirality restraints: 1471 Sorted by residual: chirality pdb=" CG LEU A 476 " pdb=" CB LEU A 476 " pdb=" CD1 LEU A 476 " pdb=" CD2 LEU A 476 " both_signs ideal model delta sigma weight residual False -2.59 -2.07 -0.52 2.00e-01 2.50e+01 6.69e+00 chirality pdb=" CA TYR A 873 " pdb=" N TYR A 873 " pdb=" C TYR A 873 " pdb=" CB TYR A 873 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" CB ILE A 531 " pdb=" CA ILE A 531 " pdb=" CG1 ILE A 531 " pdb=" CG2 ILE A 531 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.39e+00 ... (remaining 1468 not shown) Planarity restraints: 1607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 895 " -0.096 5.00e-02 4.00e+02 1.35e-01 2.90e+01 pdb=" N PRO A 896 " 0.232 5.00e-02 4.00e+02 pdb=" CA PRO A 896 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 896 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 774 " 0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C GLY A 774 " -0.059 2.00e-02 2.50e+03 pdb=" O GLY A 774 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU A 775 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 317 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C LEU A 317 " -0.055 2.00e-02 2.50e+03 pdb=" O LEU A 317 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP A 318 " 0.019 2.00e-02 2.50e+03 ... (remaining 1604 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 4 2.04 - 2.76: 1507 2.76 - 3.47: 12758 3.47 - 4.19: 20804 4.19 - 4.90: 36607 Nonbonded interactions: 71680 Sorted by model distance: nonbonded pdb=" C ASN B 189 " pdb=" N SER B 201 " model vdw 1.327 3.350 nonbonded pdb=" CB ARG A 906 " pdb=" OD2 ASP A 909 " model vdw 1.716 3.440 nonbonded pdb=" O GLU A 122 " pdb=" ND2 ASN A 124 " model vdw 1.799 2.520 nonbonded pdb=" O GLY A 866 " pdb=" CD1 ILE A 868 " model vdw 2.006 3.460 nonbonded pdb=" O LEU A 317 " pdb=" OD1 ASP A 318 " model vdw 2.046 3.040 ... (remaining 71675 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 2.960 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 29.450 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 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 : 0.009 0.125 9432 Z= 0.595 Angle : 1.440 23.146 12825 Z= 0.770 Chirality : 0.074 0.517 1471 Planarity : 0.009 0.135 1601 Dihedral : 15.160 123.235 3622 Min Nonbonded Distance : 1.327 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 1.06 % Allowed : 11.61 % Favored : 87.34 % Rotamer: Outliers : 3.73 % Allowed : 8.61 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.09 % Twisted Proline : 4.17 % Twisted General : 0.73 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.80 (0.19), residues: 1137 helix: -3.04 (0.14), residues: 607 sheet: -2.67 (0.61), residues: 65 loop : -3.30 (0.25), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP A 399 HIS 0.015 0.004 HIS A 739 PHE 0.033 0.004 PHE A 422 TYR 0.026 0.004 TYR A 224 ARG 0.009 0.001 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 319 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6708 (mp) REVERT: A 422 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.8397 (p90) REVERT: A 487 LEU cc_start: 0.8397 (tm) cc_final: 0.8160 (tp) REVERT: A 740 TYR cc_start: 0.7498 (t80) cc_final: 0.7063 (t80) REVERT: A 777 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6511 (mt) REVERT: A 956 MET cc_start: 0.7044 (ppp) cc_final: 0.6719 (ppp) REVERT: A 960 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.6641 (ttt180) REVERT: A 1013 TYR cc_start: 0.7886 (m-10) cc_final: 0.7653 (m-10) REVERT: A 1046 PHE cc_start: 0.7700 (m-10) cc_final: 0.7498 (m-80) REVERT: A 1051 TRP cc_start: 0.6439 (t-100) cc_final: 0.5356 (m-10) REVERT: A 1055 ILE cc_start: 0.7874 (mm) cc_final: 0.7660 (mt) outliers start: 36 outliers final: 16 residues processed: 340 average time/residue: 0.2600 time to fit residues: 115.6621 Evaluate side-chains 184 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 164 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 867 LYS Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 874 LYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 960 ARG Chi-restraints excluded: chain A residue 1077 LYS Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 201 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 89 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 GLN A 324 ASN A 328 HIS A 336 HIS A 384 HIS A 802 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 929 ASN ** A 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1121 HIS ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9432 Z= 0.248 Angle : 0.886 19.819 12825 Z= 0.438 Chirality : 0.050 0.305 1471 Planarity : 0.006 0.054 1601 Dihedral : 12.020 83.823 1575 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.62 % Allowed : 9.85 % Favored : 89.53 % Rotamer: Outliers : 5.71 % Allowed : 15.25 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.09 % Twisted Proline : 2.08 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.23), residues: 1137 helix: -1.17 (0.19), residues: 628 sheet: -1.97 (0.59), residues: 68 loop : -2.95 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 460 HIS 0.007 0.001 HIS A 289 PHE 0.018 0.002 PHE A 795 TYR 0.041 0.002 TYR A1181 ARG 0.005 0.001 ARG A 906 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 182 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.6631 (OUTLIER) cc_final: 0.6347 (pt) REVERT: A 101 PHE cc_start: 0.3778 (OUTLIER) cc_final: 0.2602 (t80) REVERT: A 128 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7194 (mp) REVERT: A 152 MET cc_start: 0.7812 (mpp) cc_final: 0.7299 (tpt) REVERT: A 422 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.8151 (p90) REVERT: A 487 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8117 (tp) REVERT: A 584 ASN cc_start: 0.8475 (t0) cc_final: 0.8133 (t0) REVERT: A 740 TYR cc_start: 0.7403 (t80) cc_final: 0.6932 (t80) REVERT: A 777 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6485 (mt) REVERT: A 1051 TRP cc_start: 0.6556 (t-100) cc_final: 0.5617 (m-10) REVERT: A 1055 ILE cc_start: 0.8204 (mm) cc_final: 0.7878 (mt) REVERT: A 1070 MET cc_start: 0.7993 (tpp) cc_final: 0.7736 (tpp) REVERT: A 1183 GLU cc_start: 0.6211 (pt0) cc_final: 0.5917 (pt0) REVERT: B 103 LYS cc_start: 0.7878 (ttmt) cc_final: 0.7513 (ttmt) outliers start: 55 outliers final: 21 residues processed: 223 average time/residue: 0.2186 time to fit residues: 66.9920 Evaluate side-chains 171 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 144 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 867 LYS Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 874 LYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1077 LYS Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain B residue 188 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 70 optimal weight: 0.3980 chunk 28 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 HIS A 371 GLN A 501 GLN A 940 ASN ** A1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9432 Z= 0.201 Angle : 0.796 14.275 12825 Z= 0.389 Chirality : 0.047 0.258 1471 Planarity : 0.005 0.060 1601 Dihedral : 9.507 71.527 1561 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.29 % Favored : 89.36 % Rotamer: Outliers : 5.60 % Allowed : 18.05 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.09 % Twisted Proline : 2.08 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.24), residues: 1137 helix: -0.24 (0.21), residues: 630 sheet: -1.14 (0.61), residues: 65 loop : -2.90 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 844 HIS 0.006 0.001 HIS A 846 PHE 0.023 0.002 PHE A 795 TYR 0.032 0.002 TYR A 224 ARG 0.004 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 173 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 PHE cc_start: 0.4298 (OUTLIER) cc_final: 0.3024 (t80) REVERT: A 128 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6960 (mt) REVERT: A 135 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7460 (ttp-110) REVERT: A 152 MET cc_start: 0.7639 (mpp) cc_final: 0.7208 (tpp) REVERT: A 371 GLN cc_start: 0.7346 (mt0) cc_final: 0.6690 (mt0) REVERT: A 422 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.8203 (p90) REVERT: A 487 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8119 (tp) REVERT: A 777 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.6826 (mt) REVERT: A 824 ARG cc_start: 0.6543 (ptt180) cc_final: 0.6285 (mtp180) REVERT: A 1011 ASN cc_start: 0.8173 (m-40) cc_final: 0.7896 (m-40) REVERT: A 1051 TRP cc_start: 0.6411 (t-100) cc_final: 0.5491 (m-10) REVERT: A 1055 ILE cc_start: 0.8220 (mm) cc_final: 0.7947 (mt) outliers start: 54 outliers final: 30 residues processed: 216 average time/residue: 0.2232 time to fit residues: 67.4284 Evaluate side-chains 174 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 138 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 867 LYS Chi-restraints excluded: chain A residue 874 LYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1077 LYS Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 188 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.0870 chunk 77 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 11 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 110 optimal weight: 0.4980 chunk 54 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 overall best weight: 1.0560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 940 ASN A 944 HIS A 950 HIS ** A1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9432 Z= 0.197 Angle : 0.750 13.426 12825 Z= 0.368 Chirality : 0.046 0.252 1471 Planarity : 0.005 0.063 1601 Dihedral : 8.663 59.807 1554 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.47 % Favored : 89.27 % Rotamer: Outliers : 5.29 % Allowed : 20.64 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.09 % Twisted Proline : 2.08 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.25), residues: 1137 helix: 0.27 (0.21), residues: 622 sheet: -0.94 (0.62), residues: 67 loop : -2.82 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 844 HIS 0.004 0.001 HIS A 846 PHE 0.017 0.002 PHE A 848 TYR 0.031 0.001 TYR A 224 ARG 0.003 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 146 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.7003 (mp) REVERT: A 152 MET cc_start: 0.7698 (mpp) cc_final: 0.7231 (tpp) REVERT: A 237 GLU cc_start: 0.7497 (mp0) cc_final: 0.7188 (mp0) REVERT: A 319 MET cc_start: 0.6287 (mmm) cc_final: 0.6071 (mmm) REVERT: A 371 GLN cc_start: 0.7430 (mt0) cc_final: 0.6869 (mt0) REVERT: A 397 GLU cc_start: 0.8463 (pp20) cc_final: 0.8159 (pp20) REVERT: A 422 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8204 (p90) REVERT: A 487 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8134 (tp) REVERT: A 974 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.8050 (p90) REVERT: A 1011 ASN cc_start: 0.8161 (m-40) cc_final: 0.7887 (m-40) REVERT: A 1051 TRP cc_start: 0.6451 (t-100) cc_final: 0.5476 (m-10) REVERT: A 1055 ILE cc_start: 0.8187 (mm) cc_final: 0.7984 (mt) outliers start: 51 outliers final: 32 residues processed: 188 average time/residue: 0.2016 time to fit residues: 53.6454 Evaluate side-chains 171 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 135 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 867 LYS Chi-restraints excluded: chain A residue 874 LYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 974 PHE Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1077 LYS Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain B residue 149 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.0010 chunk 62 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 940 ASN A1099 HIS ** B 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9432 Z= 0.172 Angle : 0.732 13.105 12825 Z= 0.353 Chirality : 0.045 0.247 1471 Planarity : 0.005 0.059 1601 Dihedral : 8.085 58.212 1549 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.64 % Favored : 89.18 % Rotamer: Outliers : 5.71 % Allowed : 21.27 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.09 % Twisted Proline : 2.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.25), residues: 1137 helix: 0.57 (0.21), residues: 622 sheet: -0.66 (0.63), residues: 67 loop : -2.68 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 844 HIS 0.005 0.001 HIS A 846 PHE 0.014 0.001 PHE A 848 TYR 0.035 0.001 TYR A1181 ARG 0.005 0.000 ARG A 195 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 151 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.6660 (OUTLIER) cc_final: 0.6442 (pt) REVERT: A 152 MET cc_start: 0.7567 (mpp) cc_final: 0.7100 (tpp) REVERT: A 154 ASN cc_start: 0.9264 (OUTLIER) cc_final: 0.8728 (p0) REVERT: A 371 GLN cc_start: 0.7427 (mt0) cc_final: 0.6841 (mt0) REVERT: A 422 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.8188 (p90) REVERT: A 487 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8128 (tp) REVERT: A 750 LYS cc_start: 0.6312 (mmpt) cc_final: 0.6011 (pttt) REVERT: A 974 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7969 (p90) REVERT: A 1051 TRP cc_start: 0.6430 (t-100) cc_final: 0.5485 (m-10) REVERT: A 1055 ILE cc_start: 0.8115 (mm) cc_final: 0.7881 (mt) REVERT: A 1070 MET cc_start: 0.7919 (tpp) cc_final: 0.7642 (tpp) REVERT: A 1077 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7515 (mmmm) REVERT: A 1078 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8613 (mm) outliers start: 55 outliers final: 36 residues processed: 191 average time/residue: 0.1835 time to fit residues: 50.7030 Evaluate side-chains 179 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 136 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 867 LYS Chi-restraints excluded: chain A residue 874 LYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 974 PHE Chi-restraints excluded: chain A residue 986 ASP Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1077 LYS Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 166 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 7.9990 chunk 99 optimal weight: 0.0470 chunk 21 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 110 optimal weight: 0.3980 chunk 91 optimal weight: 0.3980 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 0.0670 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN A 496 ASN A 901 GLN A 940 ASN ** B 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.5409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9432 Z= 0.162 Angle : 0.725 12.813 12825 Z= 0.349 Chirality : 0.044 0.244 1471 Planarity : 0.005 0.050 1601 Dihedral : 7.784 59.890 1546 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.20 % Favored : 89.53 % Rotamer: Outliers : 4.98 % Allowed : 23.03 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.09 % Twisted Proline : 2.08 % 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: -0.83 (0.26), residues: 1137 helix: 0.78 (0.21), residues: 622 sheet: -0.50 (0.63), residues: 67 loop : -2.56 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 844 HIS 0.004 0.001 HIS A 846 PHE 0.012 0.001 PHE A1068 TYR 0.029 0.001 TYR A1181 ARG 0.003 0.000 ARG A 195 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 143 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6426 (pt) REVERT: A 152 MET cc_start: 0.7530 (mpp) cc_final: 0.7156 (tpp) REVERT: A 154 ASN cc_start: 0.9245 (OUTLIER) cc_final: 0.8755 (p0) REVERT: A 371 GLN cc_start: 0.7392 (mt0) cc_final: 0.6894 (mt0) REVERT: A 397 GLU cc_start: 0.8409 (pp20) cc_final: 0.8064 (pp20) REVERT: A 422 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.8185 (p90) REVERT: A 487 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8039 (tp) REVERT: A 750 LYS cc_start: 0.6502 (mmpt) cc_final: 0.6090 (pttt) REVERT: A 974 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7908 (p90) REVERT: A 1051 TRP cc_start: 0.6403 (t-100) cc_final: 0.5472 (m-10) REVERT: A 1055 ILE cc_start: 0.8092 (mm) cc_final: 0.7866 (mt) REVERT: A 1070 MET cc_start: 0.7885 (tpp) cc_final: 0.7644 (tpp) REVERT: A 1077 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7569 (mmmm) outliers start: 48 outliers final: 30 residues processed: 176 average time/residue: 0.1893 time to fit residues: 48.8554 Evaluate side-chains 171 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 135 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 867 LYS Chi-restraints excluded: chain A residue 874 LYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 974 PHE Chi-restraints excluded: chain A residue 986 ASP Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1077 LYS Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 166 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN A1099 HIS ** B 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.5578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9432 Z= 0.183 Angle : 0.728 12.051 12825 Z= 0.352 Chirality : 0.044 0.248 1471 Planarity : 0.005 0.056 1601 Dihedral : 7.654 58.994 1544 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.38 % Favored : 89.45 % Rotamer: Outliers : 5.19 % Allowed : 23.76 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.09 % Twisted Proline : 2.08 % 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: -0.71 (0.26), residues: 1137 helix: 0.88 (0.21), residues: 622 sheet: -0.62 (0.61), residues: 67 loop : -2.48 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 844 HIS 0.004 0.001 HIS A 846 PHE 0.016 0.001 PHE A 848 TYR 0.030 0.001 TYR A 224 ARG 0.002 0.000 ARG A 195 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 134 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6443 (pt) REVERT: A 152 MET cc_start: 0.7506 (mpp) cc_final: 0.7143 (tpp) REVERT: A 154 ASN cc_start: 0.9285 (OUTLIER) cc_final: 0.8759 (p0) REVERT: A 371 GLN cc_start: 0.7405 (mt0) cc_final: 0.6896 (mt0) REVERT: A 422 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.8248 (p90) REVERT: A 750 LYS cc_start: 0.6574 (mmpt) cc_final: 0.6128 (pttt) REVERT: A 974 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.7931 (p90) REVERT: A 983 ASP cc_start: 0.8131 (m-30) cc_final: 0.7558 (p0) REVERT: A 1051 TRP cc_start: 0.6432 (t-100) cc_final: 0.5456 (m-10) REVERT: A 1055 ILE cc_start: 0.8158 (mm) cc_final: 0.7943 (mt) outliers start: 50 outliers final: 34 residues processed: 170 average time/residue: 0.1910 time to fit residues: 47.6708 Evaluate side-chains 168 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 130 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 867 LYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 974 PHE Chi-restraints excluded: chain A residue 986 ASP Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 166 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 99 optimal weight: 0.0040 chunk 105 optimal weight: 1.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** B 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.5750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9432 Z= 0.179 Angle : 0.717 11.609 12825 Z= 0.348 Chirality : 0.044 0.246 1471 Planarity : 0.005 0.054 1601 Dihedral : 7.239 57.054 1536 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.64 % Favored : 89.27 % Rotamer: Outliers : 5.39 % Allowed : 23.34 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.09 % Twisted Proline : 2.08 % 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: -0.64 (0.26), residues: 1137 helix: 0.93 (0.21), residues: 624 sheet: -0.65 (0.61), residues: 67 loop : -2.44 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 844 HIS 0.004 0.001 HIS A 846 PHE 0.015 0.001 PHE A 848 TYR 0.036 0.001 TYR A1181 ARG 0.003 0.000 ARG A 536 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 137 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.6684 (OUTLIER) cc_final: 0.6448 (pt) REVERT: A 152 MET cc_start: 0.7463 (mpp) cc_final: 0.7079 (tpp) REVERT: A 154 ASN cc_start: 0.9297 (OUTLIER) cc_final: 0.8775 (p0) REVERT: A 371 GLN cc_start: 0.7399 (mt0) cc_final: 0.6503 (mt0) REVERT: A 397 GLU cc_start: 0.8455 (pp20) cc_final: 0.8100 (pp20) REVERT: A 422 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.8210 (p90) REVERT: A 750 LYS cc_start: 0.6530 (mmpt) cc_final: 0.6129 (pttt) REVERT: A 956 MET cc_start: 0.7389 (ppp) cc_final: 0.6541 (mmt) REVERT: A 974 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7879 (p90) REVERT: A 983 ASP cc_start: 0.8202 (m-30) cc_final: 0.7552 (p0) REVERT: A 1051 TRP cc_start: 0.6446 (t-100) cc_final: 0.5458 (m-10) REVERT: A 1055 ILE cc_start: 0.8111 (mm) cc_final: 0.7892 (mt) REVERT: A 1078 LEU cc_start: 0.8908 (mm) cc_final: 0.8707 (mm) outliers start: 52 outliers final: 36 residues processed: 174 average time/residue: 0.1746 time to fit residues: 44.8481 Evaluate side-chains 171 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 131 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 867 LYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 974 PHE Chi-restraints excluded: chain A residue 986 ASP Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 166 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 61 optimal weight: 0.1980 chunk 44 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 108 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN A 940 ASN ** B 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.5863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9432 Z= 0.174 Angle : 0.717 11.386 12825 Z= 0.347 Chirality : 0.044 0.245 1471 Planarity : 0.005 0.054 1601 Dihedral : 7.159 56.989 1536 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.38 % Favored : 89.45 % Rotamer: Outliers : 4.88 % Allowed : 23.96 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.09 % Twisted Proline : 2.08 % 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: -0.42 (0.26), residues: 1137 helix: 1.08 (0.21), residues: 619 sheet: -0.57 (0.62), residues: 67 loop : -2.25 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 844 HIS 0.004 0.001 HIS A 846 PHE 0.014 0.001 PHE A 848 TYR 0.036 0.001 TYR A1181 ARG 0.003 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 137 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.6684 (OUTLIER) cc_final: 0.6448 (pt) REVERT: A 128 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6495 (mp) REVERT: A 152 MET cc_start: 0.7448 (mpp) cc_final: 0.7104 (tpp) REVERT: A 154 ASN cc_start: 0.9306 (OUTLIER) cc_final: 0.8763 (p0) REVERT: A 371 GLN cc_start: 0.7387 (mt0) cc_final: 0.6483 (mt0) REVERT: A 397 GLU cc_start: 0.8417 (pp20) cc_final: 0.8039 (pp20) REVERT: A 422 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.8213 (p90) REVERT: A 750 LYS cc_start: 0.6526 (mmpt) cc_final: 0.6156 (pttt) REVERT: A 974 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7884 (p90) REVERT: A 983 ASP cc_start: 0.8223 (m-30) cc_final: 0.7623 (p0) REVERT: A 1051 TRP cc_start: 0.6357 (t-100) cc_final: 0.5429 (m-10) REVERT: A 1055 ILE cc_start: 0.8119 (mm) cc_final: 0.7913 (mt) REVERT: A 1078 LEU cc_start: 0.8924 (mm) cc_final: 0.8710 (mm) outliers start: 47 outliers final: 34 residues processed: 170 average time/residue: 0.1808 time to fit residues: 44.9989 Evaluate side-chains 169 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 130 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 867 LYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 974 PHE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 986 ASP Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 166 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 0.0970 chunk 96 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN A 940 ASN ** B 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.6001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9432 Z= 0.213 Angle : 0.739 11.046 12825 Z= 0.358 Chirality : 0.045 0.248 1471 Planarity : 0.005 0.057 1601 Dihedral : 7.233 57.254 1536 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.73 % Favored : 89.09 % Rotamer: Outliers : 4.56 % Allowed : 24.38 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.09 % Twisted Proline : 2.08 % 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 (0.26), residues: 1137 helix: 1.09 (0.21), residues: 619 sheet: -0.65 (0.61), residues: 67 loop : -2.30 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 460 HIS 0.004 0.001 HIS B 133 PHE 0.019 0.001 PHE A 848 TYR 0.036 0.002 TYR A1181 ARG 0.003 0.000 ARG A 138 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 131 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6506 (mp) REVERT: A 152 MET cc_start: 0.7501 (mpp) cc_final: 0.7116 (tpp) REVERT: A 154 ASN cc_start: 0.9330 (OUTLIER) cc_final: 0.8763 (p0) REVERT: A 371 GLN cc_start: 0.7385 (mt0) cc_final: 0.6432 (mt0) REVERT: A 397 GLU cc_start: 0.8401 (pp20) cc_final: 0.8036 (pp20) REVERT: A 422 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.8281 (p90) REVERT: A 750 LYS cc_start: 0.6561 (mmpt) cc_final: 0.6227 (pttt) REVERT: A 974 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7932 (p90) REVERT: A 983 ASP cc_start: 0.8270 (m-30) cc_final: 0.7697 (p0) REVERT: A 1051 TRP cc_start: 0.6304 (t-100) cc_final: 0.5375 (m-10) REVERT: A 1055 ILE cc_start: 0.8164 (mm) cc_final: 0.7942 (mt) REVERT: A 1078 LEU cc_start: 0.8941 (mm) cc_final: 0.8738 (mm) REVERT: B 172 TRP cc_start: 0.8617 (OUTLIER) cc_final: 0.7879 (t60) outliers start: 44 outliers final: 33 residues processed: 168 average time/residue: 0.1764 time to fit residues: 44.0133 Evaluate side-chains 165 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 127 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 867 LYS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 974 PHE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 986 ASP Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 172 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 chunk 16 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 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 124 ASN A 361 GLN A1121 HIS ** B 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.138802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.123467 restraints weight = 18780.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.126005 restraints weight = 10634.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.127363 restraints weight = 7240.862| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.6079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9432 Z= 0.201 Angle : 0.736 10.927 12825 Z= 0.356 Chirality : 0.045 0.248 1471 Planarity : 0.005 0.060 1601 Dihedral : 7.255 57.231 1536 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.91 % Favored : 88.92 % Rotamer: Outliers : 4.46 % Allowed : 24.69 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.09 % Twisted Proline : 2.08 % 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: -0.42 (0.26), residues: 1137 helix: 1.05 (0.21), residues: 627 sheet: -0.65 (0.62), residues: 67 loop : -2.25 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 460 HIS 0.003 0.001 HIS A 846 PHE 0.017 0.001 PHE A 848 TYR 0.035 0.002 TYR A1181 ARG 0.004 0.000 ARG A 138 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2014.41 seconds wall clock time: 37 minutes 17.99 seconds (2237.99 seconds total)