Starting phenix.real_space_refine on Fri Sep 11 18:58:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6dmy_7968/09_2026/6dmy_7968.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dmy_7968/09_2026/6dmy_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6dmy_7968/09_2026/6dmy_7968.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6dmy_7968/09_2026/6dmy_7968.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dmy_7968/09_2026/6dmy_7968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dmy_7968/09_2026/6dmy_7968.map" model { file = "/net/cci-nas-00/data/ceres_data/6dmy_7968/09_2026/6dmy_7968.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dmy_7968/09_2026/6dmy_7968.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9211 Number of models: 1 Model: "" Number of chains: 6 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: {'ARG:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'GLU: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 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 chiralities: 5 Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.98, per 1000 atoms: 0.21 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " 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 " TRANS " SER B 201 " - " ASN B 189 " Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 331.0 milliseconds 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: 0.20 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: 1.31 Time building geometry restraints manager: 1.17 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: 0.00 - 4.63: 12597 4.63 - 9.26: 201 9.26 - 13.89: 21 13.89 - 18.52: 4 18.52 - 23.15: 2 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: 5256 24.65 - 49.29: 221 49.29 - 73.94: 32 73.94 - 98.59: 5 98.59 - 123.23: 1 Dihedral angle restraints: 5515 sinusoidal: 2180 harmonic: 3335 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 5512 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: 1608 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 1605 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 34 2.35 - 2.99: 4483 2.99 - 3.63: 13813 3.63 - 4.26: 20110 4.26 - 4.90: 33236 Nonbonded interactions: 71676 Sorted by model distance: 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 3.120 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 nonbonded pdb=" OD2 ASP B 147 " pdb="ZN ZN B 202 " model vdw 2.084 2.230 ... (remaining 71671 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.030 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 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 : 0.011 0.645 9445 Z= 0.467 Angle : 1.451 23.146 12855 Z= 0.771 Chirality : 0.074 0.517 1471 Planarity : 0.009 0.135 1601 Dihedral : 13.712 123.235 3359 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 15.90 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.009 0.001 ARG B 163 TYR 0.026 0.004 TYR A 224 PHE 0.033 0.004 PHE A 422 TRP 0.028 0.004 TRP A 399 HIS 0.015 0.004 HIS A 739 Details of bonding type rmsd/Z covalent geometry : bond 0.00912 / 0.41 ( 9432) covalent geometry : angle 1.44008 / 0.77 (12825) SS BOND : bond 0.00309 / 0.15 ( 3) SS BOND : angle 2.33325 / 1.22 ( 6) hydrogen bonds : bond 0.16075 / 10.65 ( 423) hydrogen bonds : angle 10.28640 / 7.24 ( 1236) metal coordination : bond 0.46410 / 22.18 ( 2) link_BETA1-4 : bond 0.01219 / 0.64 ( 1) link_BETA1-4 : angle 5.63780 / 2.70 ( 3) link_NAG-ASN : bond 0.00601 / 0.30 ( 6) link_NAG-ASN : angle 4.32800 / 2.81 ( 18) link_TRANS : bond 0.00227 / 0.12 ( 1) link_TRANS : angle 0.75485 / 0.39 ( 3) *********************** 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 to be fit. rotamer outliers: 36 poor density : 319 time to evaluate : 0.349 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: 0.8395 (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: 0.7061 (t80) REVERT: A 777 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6510 (mt) REVERT: A 956 MET cc_start: 0.7044 (ppp) cc_final: 0.6717 (ppp) REVERT: A 960 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.6640 (ttt180) REVERT: A 1013 TYR cc_start: 0.7886 (m-10) cc_final: 0.7654 (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: 0.7659 (mt) outliers start: 36 outliers final: 16 residues processed: 340 average time/residue: 0.1135 time to fit residues: 51.4932 Evaluate side-chains 182 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 108 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 GLN A 160 GLN A 274 GLN A 324 ASN A 328 HIS A 336 HIS A 384 HIS A 802 ASN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.144925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.129597 restraints weight = 18608.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.132223 restraints weight = 10431.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.133874 restraints weight = 7093.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.134787 restraints weight = 5458.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.135613 restraints weight = 4649.894| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9445 Z= 0.169 Angle : 0.915 19.884 12855 Z= 0.449 Chirality : 0.051 0.370 1471 Planarity : 0.006 0.058 1601 Dihedral : 11.058 119.878 1312 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.76 % Favored : 89.71 % Rotamer: Outliers : 5.71 % Allowed : 15.35 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.09 % Twisted Proline : 2.08 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.23), residues: 1137 helix: -1.19 (0.19), residues: 627 sheet: -1.96 (0.59), residues: 68 loop : -2.98 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 942 TYR 0.039 0.002 TYR A1181 PHE 0.017 0.002 PHE A 795 TRP 0.010 0.001 TRP A 844 HIS 0.006 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 ( 9432) covalent geometry : angle 0.90308 / 0.45 (12825) SS BOND : bond 0.00063 / 0.03 ( 3) SS BOND : angle 1.33991 / 0.71 ( 6) hydrogen bonds : bond 0.05270 / 3.43 ( 423) hydrogen bonds : angle 5.60461 / 4.08 ( 1236) metal coordination : bond 0.01049 / 0.52 ( 2) link_BETA1-4 : bond 0.00049 / 0.03 ( 1) link_BETA1-4 : angle 2.51178 / 1.14 ( 3) link_NAG-ASN : bond 0.00968 / 0.49 ( 6) link_NAG-ASN : angle 3.88461 / 3.04 ( 18) link_TRANS : bond 0.00049 / 0.03 ( 1) link_TRANS : angle 0.40880 / 0.19 ( 3) *********************** 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 244 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 189 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.6602 (OUTLIER) cc_final: 0.6374 (pt) REVERT: A 101 PHE cc_start: 0.3851 (OUTLIER) cc_final: 0.2620 (t80) REVERT: A 128 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7372 (mp) REVERT: A 135 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7553 (ttp-110) REVERT: A 422 PHE cc_start: 0.7852 (OUTLIER) cc_final: 0.7411 (p90) REVERT: A 471 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7336 (mt) REVERT: A 476 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7982 (tt) REVERT: A 487 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8268 (tp) REVERT: A 584 ASN cc_start: 0.8580 (t0) cc_final: 0.8239 (t0) REVERT: A 740 TYR cc_start: 0.7275 (t80) cc_final: 0.6857 (t80) REVERT: A 777 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6816 (mt) REVERT: A 804 TYR cc_start: 0.8250 (m-80) cc_final: 0.7999 (m-80) REVERT: A 942 ARG cc_start: 0.7728 (mmt-90) cc_final: 0.7415 (mmt90) REVERT: A 1051 TRP cc_start: 0.6501 (t-100) cc_final: 0.5638 (m-10) REVERT: A 1055 ILE cc_start: 0.8175 (mm) cc_final: 0.7847 (mt) REVERT: A 1070 MET cc_start: 0.8008 (tpp) cc_final: 0.7758 (tpp) REVERT: A 1183 GLU cc_start: 0.6109 (pt0) cc_final: 0.5826 (pt0) outliers start: 55 outliers final: 22 residues processed: 227 average time/residue: 0.1002 time to fit residues: 31.6993 Evaluate side-chains 179 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 135 ARG 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 471 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 777 LEU 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 48 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 105 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 0.0070 chunk 20 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 HIS A 940 ASN A 950 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.141235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.125997 restraints weight = 18776.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.128575 restraints weight = 10554.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.130223 restraints weight = 7210.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.131136 restraints weight = 5564.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.131882 restraints weight = 4738.472| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9445 Z= 0.170 Angle : 0.846 19.130 12855 Z= 0.412 Chirality : 0.049 0.273 1471 Planarity : 0.005 0.058 1601 Dihedral : 9.511 120.877 1297 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.03 % Favored : 89.53 % Rotamer: Outliers : 5.71 % Allowed : 18.36 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.09 % Twisted Proline : 2.08 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.24), residues: 1137 helix: -0.34 (0.20), residues: 631 sheet: -1.25 (0.60), residues: 67 loop : -2.84 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 942 TYR 0.036 0.002 TYR A 224 PHE 0.020 0.002 PHE A 848 TRP 0.012 0.001 TRP A 844 HIS 0.005 0.001 HIS A 846 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 9432) covalent geometry : angle 0.83563 / 0.41 (12825) SS BOND : bond 0.00161 / 0.08 ( 3) SS BOND : angle 1.27639 / 0.67 ( 6) hydrogen bonds : bond 0.04775 / 3.13 ( 423) hydrogen bonds : angle 4.89658 / 3.55 ( 1236) metal coordination : bond 0.00604 / 0.31 ( 2) link_BETA1-4 : bond 0.00201 / 0.11 ( 1) link_BETA1-4 : angle 2.77031 / 1.29 ( 3) link_NAG-ASN : bond 0.00430 / 0.22 ( 6) link_NAG-ASN : angle 3.41890 / 2.81 ( 18) link_TRANS : bond 0.00012 / 0.01 ( 1) link_TRANS : angle 0.46311 / 0.21 ( 3) *********************** 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 225 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 170 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 PHE cc_start: 0.4601 (OUTLIER) cc_final: 0.3171 (t80) REVERT: A 128 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7070 (mt) REVERT: A 135 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7707 (ttp-110) REVERT: A 152 MET cc_start: 0.5925 (tpt) cc_final: 0.5711 (tpp) REVERT: A 422 PHE cc_start: 0.7826 (OUTLIER) cc_final: 0.7425 (p90) REVERT: A 471 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7164 (mt) REVERT: A 777 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7051 (mt) REVERT: A 804 TYR cc_start: 0.8443 (m-80) cc_final: 0.8161 (m-80) REVERT: A 940 ASN cc_start: 0.8144 (OUTLIER) cc_final: 0.7790 (p0) REVERT: A 981 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6773 (pp) REVERT: A 1051 TRP cc_start: 0.6485 (t-100) cc_final: 0.5568 (m-10) REVERT: A 1055 ILE cc_start: 0.8199 (mm) cc_final: 0.7916 (mt) outliers start: 55 outliers final: 27 residues processed: 214 average time/residue: 0.0960 time to fit residues: 29.0304 Evaluate side-chains 175 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 125 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 777 LEU 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 940 ASN Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 981 LEU 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 98 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 101 optimal weight: 8.9990 chunk 61 optimal weight: 0.7980 chunk 103 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 110 optimal weight: 0.2980 chunk 92 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 GLN ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 944 HIS ** B 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.136906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.121412 restraints weight = 19077.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.123951 restraints weight = 10627.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.125540 restraints weight = 7239.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.126627 restraints weight = 5606.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.127210 restraints weight = 4712.512| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9445 Z= 0.160 Angle : 0.788 13.841 12855 Z= 0.388 Chirality : 0.047 0.264 1471 Planarity : 0.005 0.064 1601 Dihedral : 8.898 120.516 1288 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.20 % Favored : 89.45 % Rotamer: Outliers : 5.50 % Allowed : 20.23 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.09 % Twisted Proline : 2.08 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.25), residues: 1137 helix: 0.21 (0.21), residues: 621 sheet: -0.97 (0.60), residues: 67 loop : -2.68 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 72 TYR 0.034 0.002 TYR A 224 PHE 0.020 0.002 PHE A 848 TRP 0.011 0.001 TRP A 844 HIS 0.004 0.001 HIS A 846 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 ( 9432) covalent geometry : angle 0.77939 / 0.39 (12825) SS BOND : bond 0.00140 / 0.07 ( 3) SS BOND : angle 1.50259 / 0.79 ( 6) hydrogen bonds : bond 0.04389 / 2.88 ( 423) hydrogen bonds : angle 4.64347 / 3.34 ( 1236) metal coordination : bond 0.00380 / 0.20 ( 2) link_BETA1-4 : bond 0.00086 / 0.05 ( 1) link_BETA1-4 : angle 2.55881 / 1.17 ( 3) link_NAG-ASN : bond 0.00412 / 0.21 ( 6) link_NAG-ASN : angle 2.91197 / 2.42 ( 18) link_TRANS : bond 0.00002 / 0.00 ( 1) link_TRANS : angle 0.41913 / 0.19 ( 3) *********************** 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 202 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 149 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7762 (ttp-110) REVERT: A 397 GLU cc_start: 0.7422 (pp20) cc_final: 0.7200 (pp20) REVERT: A 422 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7421 (p90) REVERT: A 471 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7282 (mp) REVERT: A 501 GLN cc_start: 0.8201 (mp10) cc_final: 0.7897 (mp10) REVERT: A 974 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.8502 (p90) REVERT: A 981 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6911 (pp) REVERT: A 1051 TRP cc_start: 0.6550 (t-100) cc_final: 0.5558 (m-10) REVERT: A 1055 ILE cc_start: 0.8201 (mm) cc_final: 0.7939 (mt) REVERT: A 1077 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7559 (mmmm) REVERT: A 1078 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8458 (mm) outliers start: 53 outliers final: 33 residues processed: 192 average time/residue: 0.0808 time to fit residues: 22.8463 Evaluate side-chains 175 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 230 THR 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 297 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 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 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 974 PHE Chi-restraints excluded: chain A residue 981 LEU 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 1084 VAL Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain B residue 166 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 chunk 110 optimal weight: 0.9980 chunk 71 optimal weight: 0.2980 chunk 96 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 GLN ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** B 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.138084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.122186 restraints weight = 18907.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.124724 restraints weight = 10579.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.126207 restraints weight = 7214.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.127273 restraints weight = 5671.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.128025 restraints weight = 4770.897| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9445 Z= 0.134 Angle : 0.771 12.585 12855 Z= 0.371 Chirality : 0.046 0.255 1471 Planarity : 0.005 0.058 1601 Dihedral : 8.419 117.675 1284 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.38 % Favored : 89.45 % Rotamer: Outliers : 4.77 % Allowed : 21.89 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.09 % Twisted Proline : 2.08 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.25), residues: 1137 helix: 0.40 (0.21), residues: 631 sheet: -0.73 (0.62), residues: 67 loop : -2.61 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 195 TYR 0.036 0.001 TYR A1181 PHE 0.018 0.001 PHE A 757 TRP 0.013 0.001 TRP A 844 HIS 0.004 0.001 HIS A 846 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 9432) covalent geometry : angle 0.76429 / 0.37 (12825) SS BOND : bond 0.00103 / 0.05 ( 3) SS BOND : angle 1.25950 / 0.69 ( 6) hydrogen bonds : bond 0.04046 / 2.66 ( 423) hydrogen bonds : angle 4.34664 / 3.12 ( 1236) metal coordination : bond 0.00222 / 0.12 ( 2) link_BETA1-4 : bond 0.00247 / 0.13 ( 1) link_BETA1-4 : angle 2.47146 / 1.16 ( 3) link_NAG-ASN : bond 0.00410 / 0.21 ( 6) link_NAG-ASN : angle 2.56420 / 2.14 ( 18) link_TRANS : bond 0.00297 / 0.16 ( 1) link_TRANS : angle 0.49978 / 0.22 ( 3) *********************** 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 189 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 143 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6508 (pt) REVERT: A 230 THR cc_start: 0.9126 (OUTLIER) cc_final: 0.8883 (m) REVERT: A 397 GLU cc_start: 0.7485 (pp20) cc_final: 0.7164 (pp20) REVERT: A 422 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.7397 (p90) REVERT: A 471 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7109 (mm) REVERT: A 501 GLN cc_start: 0.8164 (mp10) cc_final: 0.7866 (mp10) REVERT: A 740 TYR cc_start: 0.7398 (t80) cc_final: 0.7171 (t80) REVERT: A 974 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.8344 (p90) REVERT: A 981 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6946 (pp) REVERT: A 1051 TRP cc_start: 0.6493 (t-100) cc_final: 0.5489 (m-10) REVERT: A 1055 ILE cc_start: 0.8192 (mm) cc_final: 0.7929 (mt) REVERT: A 1077 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7827 (mmmm) outliers start: 46 outliers final: 30 residues processed: 180 average time/residue: 0.0806 time to fit residues: 21.5681 Evaluate side-chains 165 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 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 297 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 564 LEU 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 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 974 PHE Chi-restraints excluded: chain A residue 981 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 A residue 1183 GLU 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: 6.9990 chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 70 optimal weight: 0.0040 chunk 19 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 GLN ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 HIS ** B 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.138682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.123082 restraints weight = 18920.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.125606 restraints weight = 10620.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.127258 restraints weight = 7266.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.128333 restraints weight = 5629.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.129030 restraints weight = 4739.078| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.5449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9445 Z= 0.129 Angle : 0.749 12.185 12855 Z= 0.364 Chirality : 0.045 0.254 1471 Planarity : 0.005 0.054 1601 Dihedral : 8.231 116.904 1282 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.55 % Favored : 89.27 % Rotamer: Outliers : 4.67 % Allowed : 22.61 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.09 % Twisted Proline : 2.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.26), residues: 1137 helix: 0.57 (0.21), residues: 631 sheet: -0.58 (0.62), residues: 67 loop : -2.48 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1114 TYR 0.031 0.001 TYR A 224 PHE 0.015 0.001 PHE A1068 TRP 0.011 0.001 TRP A 844 HIS 0.005 0.001 HIS A1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 9432) covalent geometry : angle 0.74307 / 0.36 (12825) SS BOND : bond 0.00139 / 0.07 ( 3) SS BOND : angle 1.16348 / 0.64 ( 6) hydrogen bonds : bond 0.03877 / 2.55 ( 423) hydrogen bonds : angle 4.28458 / 3.07 ( 1236) metal coordination : bond 0.00198 / 0.10 ( 2) link_BETA1-4 : bond 0.00078 / 0.04 ( 1) link_BETA1-4 : angle 2.28331 / 1.04 ( 3) link_NAG-ASN : bond 0.00397 / 0.20 ( 6) link_NAG-ASN : angle 2.49496 / 2.09 ( 18) link_TRANS : bond 0.00011 / 0.01 ( 1) link_TRANS : angle 0.35207 / 0.15 ( 3) *********************** 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 182 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 137 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6490 (pt) REVERT: A 230 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8851 (m) REVERT: A 397 GLU cc_start: 0.7451 (pp20) cc_final: 0.7119 (pp20) REVERT: A 422 PHE cc_start: 0.7771 (OUTLIER) cc_final: 0.7422 (p90) REVERT: A 471 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7106 (mm) REVERT: A 974 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.8327 (p90) REVERT: A 981 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.7022 (pp) REVERT: A 1051 TRP cc_start: 0.6447 (t-100) cc_final: 0.5480 (m-10) REVERT: A 1055 ILE cc_start: 0.8156 (mm) cc_final: 0.7907 (mt) REVERT: A 1087 ILE cc_start: 0.7840 (mm) cc_final: 0.7635 (mp) outliers start: 45 outliers final: 31 residues processed: 170 average time/residue: 0.0769 time to fit residues: 19.6665 Evaluate side-chains 167 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 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 297 LEU 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 431 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 488 CYS 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 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 981 LEU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1183 GLU 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 47 optimal weight: 3.9990 chunk 82 optimal weight: 0.0000 chunk 58 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 28 optimal weight: 0.0670 chunk 20 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 GLN A 361 GLN ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1099 HIS ** B 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.138656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.123047 restraints weight = 18955.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.125590 restraints weight = 10619.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.127156 restraints weight = 7240.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.128260 restraints weight = 5634.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.128854 restraints weight = 4723.997| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.5624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9445 Z= 0.132 Angle : 0.750 11.825 12855 Z= 0.362 Chirality : 0.045 0.254 1471 Planarity : 0.005 0.053 1601 Dihedral : 7.940 116.006 1277 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.03 % Favored : 89.80 % Rotamer: Outliers : 5.08 % Allowed : 22.93 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.09 % Twisted Proline : 2.08 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.26), residues: 1137 helix: 0.66 (0.21), residues: 629 sheet: -0.63 (0.61), residues: 67 loop : -2.40 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1114 TYR 0.031 0.001 TYR A 224 PHE 0.015 0.001 PHE A 848 TRP 0.011 0.001 TRP A 844 HIS 0.004 0.001 HIS A1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 9432) covalent geometry : angle 0.74372 / 0.36 (12825) SS BOND : bond 0.00121 / 0.06 ( 3) SS BOND : angle 1.11598 / 0.61 ( 6) hydrogen bonds : bond 0.03811 / 2.50 ( 423) hydrogen bonds : angle 4.23085 / 3.02 ( 1236) metal coordination : bond 0.00221 / 0.12 ( 2) link_BETA1-4 : bond 0.00018 / 0.01 ( 1) link_BETA1-4 : angle 2.27853 / 1.04 ( 3) link_NAG-ASN : bond 0.00385 / 0.19 ( 6) link_NAG-ASN : angle 2.42573 / 2.04 ( 18) link_TRANS : bond 0.00013 / 0.01 ( 1) link_TRANS : angle 0.34278 / 0.15 ( 3) *********************** 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 190 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 141 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6464 (pt) REVERT: A 230 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8860 (m) REVERT: A 397 GLU cc_start: 0.7417 (pp20) cc_final: 0.7089 (pp20) REVERT: A 422 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.7401 (p90) REVERT: A 471 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7093 (mm) REVERT: A 501 GLN cc_start: 0.8093 (mp10) cc_final: 0.7879 (mp10) REVERT: A 760 LEU cc_start: 0.7869 (tt) cc_final: 0.7600 (tt) REVERT: A 974 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8329 (p90) REVERT: A 981 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7069 (pp) REVERT: A 1051 TRP cc_start: 0.6415 (t-100) cc_final: 0.5474 (m-10) REVERT: A 1055 ILE cc_start: 0.8104 (mm) cc_final: 0.7861 (mt) REVERT: A 1078 LEU cc_start: 0.8787 (mm) cc_final: 0.8563 (mm) REVERT: B 172 TRP cc_start: 0.8714 (OUTLIER) cc_final: 0.8362 (t60) outliers start: 49 outliers final: 35 residues processed: 177 average time/residue: 0.0765 time to fit residues: 20.5450 Evaluate side-chains 174 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 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 328 HIS Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 488 CYS 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 740 TYR 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 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 1029 LEU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1058 MET Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 172 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 23 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 7 optimal weight: 0.0050 chunk 108 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 GLN A 371 GLN A1099 HIS ** B 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.138131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.122549 restraints weight = 18670.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.125080 restraints weight = 10557.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.126701 restraints weight = 7229.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.127750 restraints weight = 5609.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.128470 restraints weight = 4716.424| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.5761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9445 Z= 0.133 Angle : 0.755 11.516 12855 Z= 0.364 Chirality : 0.045 0.255 1471 Planarity : 0.005 0.052 1601 Dihedral : 7.749 115.308 1275 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.64 % Favored : 89.27 % Rotamer: Outliers : 5.39 % Allowed : 22.30 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.09 % Twisted Proline : 2.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.26), residues: 1137 helix: 0.70 (0.21), residues: 633 sheet: -0.66 (0.61), residues: 67 loop : -2.37 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1114 TYR 0.037 0.001 TYR A1181 PHE 0.016 0.001 PHE A 848 TRP 0.011 0.001 TRP A 844 HIS 0.004 0.001 HIS A1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 9432) covalent geometry : angle 0.74930 / 0.36 (12825) SS BOND : bond 0.00137 / 0.07 ( 3) SS BOND : angle 1.11738 / 0.61 ( 6) hydrogen bonds : bond 0.03777 / 2.49 ( 423) hydrogen bonds : angle 4.18222 / 2.99 ( 1236) metal coordination : bond 0.00255 / 0.13 ( 2) link_BETA1-4 : bond 0.00015 / 0.01 ( 1) link_BETA1-4 : angle 2.32259 / 1.06 ( 3) link_NAG-ASN : bond 0.00382 / 0.19 ( 6) link_NAG-ASN : angle 2.42025 / 2.04 ( 18) link_TRANS : bond 0.00007 / 0.00 ( 1) link_TRANS : angle 0.24285 / 0.10 ( 3) *********************** 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 to be fit. rotamer outliers: 52 poor density : 137 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.6693 (OUTLIER) cc_final: 0.6466 (pt) REVERT: A 124 ASN cc_start: 0.5712 (m-40) cc_final: 0.5305 (m-40) REVERT: A 230 THR cc_start: 0.9118 (OUTLIER) cc_final: 0.8888 (m) REVERT: A 397 GLU cc_start: 0.7427 (pp20) cc_final: 0.7084 (pp20) REVERT: A 422 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.7457 (p90) REVERT: A 471 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7139 (mm) REVERT: A 750 LYS cc_start: 0.6606 (mmpt) cc_final: 0.6115 (pttt) REVERT: A 974 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.8276 (p90) REVERT: A 981 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7148 (pp) REVERT: A 1020 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8245 (pt0) REVERT: A 1051 TRP cc_start: 0.6429 (t-100) cc_final: 0.5452 (m-10) REVERT: A 1055 ILE cc_start: 0.8105 (mm) cc_final: 0.7863 (mt) REVERT: A 1078 LEU cc_start: 0.8801 (mm) cc_final: 0.8546 (mm) REVERT: B 172 TRP cc_start: 0.8734 (OUTLIER) cc_final: 0.8341 (t60) outliers start: 52 outliers final: 35 residues processed: 174 average time/residue: 0.0798 time to fit residues: 20.8823 Evaluate side-chains 174 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 131 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 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 297 LEU 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 431 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 488 CYS 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 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 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 1020 GLN 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 1058 MET Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 172 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 38 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 2 optimal weight: 0.0870 chunk 111 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 GLN A1099 HIS ** B 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.139089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.123827 restraints weight = 18768.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.126292 restraints weight = 10606.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.127918 restraints weight = 7291.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.128957 restraints weight = 5644.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.129535 restraints weight = 4755.006| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.5909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9445 Z= 0.141 Angle : 0.766 11.078 12855 Z= 0.369 Chirality : 0.045 0.257 1471 Planarity : 0.005 0.054 1601 Dihedral : 7.637 114.640 1275 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.73 % Favored : 89.18 % Rotamer: Outliers : 5.19 % Allowed : 22.51 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.09 % Twisted Proline : 2.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.26), residues: 1137 helix: 0.84 (0.21), residues: 626 sheet: -0.55 (0.61), residues: 67 loop : -2.18 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1114 TYR 0.036 0.001 TYR A1181 PHE 0.018 0.001 PHE A 848 TRP 0.009 0.001 TRP A 844 HIS 0.004 0.001 HIS A1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 9432) covalent geometry : angle 0.76054 / 0.37 (12825) SS BOND : bond 0.00139 / 0.07 ( 3) SS BOND : angle 1.10990 / 0.60 ( 6) hydrogen bonds : bond 0.03813 / 2.51 ( 423) hydrogen bonds : angle 4.18123 / 2.98 ( 1236) metal coordination : bond 0.00317 / 0.17 ( 2) link_BETA1-4 : bond 0.00000 / 0.00 ( 1) link_BETA1-4 : angle 2.43952 / 1.11 ( 3) link_NAG-ASN : bond 0.00397 / 0.20 ( 6) link_NAG-ASN : angle 2.44611 / 2.06 ( 18) link_TRANS : bond 0.00010 / 0.01 ( 1) link_TRANS : angle 0.34350 / 0.15 ( 3) *********************** 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 181 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 131 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASN cc_start: 0.5805 (m-40) cc_final: 0.5457 (m-40) REVERT: A 397 GLU cc_start: 0.7378 (pp20) cc_final: 0.7082 (pp20) REVERT: A 422 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7516 (p90) REVERT: A 471 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7213 (mm) REVERT: A 750 LYS cc_start: 0.6625 (mmpt) cc_final: 0.6160 (pttt) REVERT: A 974 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.8316 (p90) REVERT: A 981 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7151 (pp) REVERT: A 1020 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8239 (pt0) REVERT: A 1051 TRP cc_start: 0.6430 (t-100) cc_final: 0.5457 (m-10) REVERT: A 1055 ILE cc_start: 0.8112 (mm) cc_final: 0.7853 (mt) REVERT: A 1078 LEU cc_start: 0.8798 (mm) cc_final: 0.8565 (mm) REVERT: B 172 TRP cc_start: 0.8732 (OUTLIER) cc_final: 0.8364 (t60) outliers start: 50 outliers final: 36 residues processed: 169 average time/residue: 0.0800 time to fit residues: 20.2051 Evaluate side-chains 169 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 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 297 LEU 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 431 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 488 CYS 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 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 1020 GLN 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 A residue 1183 GLU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 135 SER 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 44 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 22 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 GLN A1099 HIS B 182 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.139185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.123855 restraints weight = 18807.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.126386 restraints weight = 10614.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.128030 restraints weight = 7272.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.129053 restraints weight = 5614.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.129651 restraints weight = 4736.086| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.6026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 2.224 9445 Z= 0.775 Angle : 0.768 10.920 12855 Z= 0.369 Chirality : 0.046 0.257 1471 Planarity : 0.005 0.055 1601 Dihedral : 7.434 113.941 1271 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.99 % Favored : 88.92 % Rotamer: Outliers : 4.67 % Allowed : 23.44 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.09 % Twisted Proline : 2.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.26), residues: 1137 helix: 0.88 (0.21), residues: 626 sheet: -0.43 (0.61), residues: 67 loop : -2.13 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1114 TYR 0.036 0.001 TYR A1181 PHE 0.017 0.001 PHE A 848 TRP 0.010 0.001 TRP A 844 HIS 0.004 0.001 HIS A1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 9432) covalent geometry : angle 0.76156 / 0.37 (12825) SS BOND : bond 0.00143 / 0.07 ( 3) SS BOND : angle 1.13375 / 0.61 ( 6) hydrogen bonds : bond 0.03794 / 2.50 ( 423) hydrogen bonds : angle 4.16907 / 2.98 ( 1236) metal coordination : bond 1.57284 / 74.90 ( 2) link_BETA1-4 : bond 0.00086 / 0.05 ( 1) link_BETA1-4 : angle 2.46707 / 1.12 ( 3) link_NAG-ASN : bond 0.00403 / 0.20 ( 6) link_NAG-ASN : angle 2.45725 / 2.09 ( 18) link_TRANS : bond 0.00018 / 0.01 ( 1) link_TRANS : angle 0.25352 / 0.10 ( 3) ********************** 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 173 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 128 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASN cc_start: 0.5901 (m-40) cc_final: 0.5504 (m-40) REVERT: A 397 GLU cc_start: 0.7393 (pp20) cc_final: 0.7068 (pp20) REVERT: A 422 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7517 (p90) REVERT: A 471 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7299 (mm) REVERT: A 750 LYS cc_start: 0.6609 (mmpt) cc_final: 0.6170 (pttt) REVERT: A 974 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8331 (p90) REVERT: A 981 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7200 (pp) REVERT: A 1020 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8214 (pt0) REVERT: A 1051 TRP cc_start: 0.6422 (t-100) cc_final: 0.5457 (m-10) REVERT: A 1055 ILE cc_start: 0.8098 (mm) cc_final: 0.7854 (mt) REVERT: A 1078 LEU cc_start: 0.8821 (mm) cc_final: 0.8591 (mm) REVERT: B 172 TRP cc_start: 0.8697 (OUTLIER) cc_final: 0.8350 (t60) outliers start: 45 outliers final: 35 residues processed: 163 average time/residue: 0.0793 time to fit residues: 19.4002 Evaluate side-chains 168 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 127 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 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 297 LEU 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 431 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 488 CYS 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 806 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 867 LYS 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 1020 GLN 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 51 VAL Chi-restraints excluded: chain B residue 135 SER 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 36 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 78 optimal weight: 0.0170 chunk 66 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 GLN A1099 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.140937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.125847 restraints weight = 18432.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.128336 restraints weight = 10590.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.129868 restraints weight = 7299.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.130943 restraints weight = 5696.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.131567 restraints weight = 4782.980| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.6130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9445 Z= 0.130 Angle : 0.752 10.738 12855 Z= 0.361 Chirality : 0.045 0.256 1471 Planarity : 0.005 0.057 1601 Dihedral : 7.336 113.489 1271 Min Nonbonded Distance : 1.413 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.76 % Favored : 90.15 % Rotamer: Outliers : 4.56 % Allowed : 23.55 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.09 % Twisted Proline : 2.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.26), residues: 1137 helix: 1.02 (0.21), residues: 620 sheet: -0.22 (0.61), residues: 67 loop : -2.05 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1114 TYR 0.035 0.001 TYR A1181 PHE 0.013 0.001 PHE A1068 TRP 0.013 0.001 TRP A 844 HIS 0.033 0.002 HIS B 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 9432) covalent geometry : angle 0.74615 / 0.36 (12825) SS BOND : bond 0.00145 / 0.07 ( 3) SS BOND : angle 1.17035 / 0.64 ( 6) hydrogen bonds : bond 0.03652 / 2.42 ( 423) hydrogen bonds : angle 4.08845 / 2.90 ( 1236) metal coordination : bond 0.05495 / 2.72 ( 2) link_BETA1-4 : bond 0.00127 / 0.07 ( 1) link_BETA1-4 : angle 2.25271 / 1.03 ( 3) link_NAG-ASN : bond 0.00386 / 0.19 ( 6) link_NAG-ASN : angle 2.40586 / 2.07 ( 18) link_TRANS : bond 0.00032 / 0.02 ( 1) link_TRANS : angle 0.22148 / 0.09 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1620.53 seconds wall clock time: 28 minutes 45.99 seconds (1725.99 seconds total)