Starting phenix.real_space_refine on Tue Nov 18 04:37:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dmy_7968/11_2025/6dmy_7968.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dmy_7968/11_2025/6dmy_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 { model { file = "/net/cci-nas-00/data/ceres_data/6dmy_7968/11_2025/6dmy_7968.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dmy_7968/11_2025/6dmy_7968.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dmy_7968/11_2025/6dmy_7968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dmy_7968/11_2025/6dmy_7968.map" } 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-2.0-5881/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Unusual residues: {'NAG': 5, 'Y01': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 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: 2.45, per 1000 atoms: 0.27 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: 1.03 Conformation dependent library (CDL) restraints added in 336.9 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: 0.24 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: 1.25 Time building geometry restraints manager: 1.28 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: 5472 24.65 - 49.29: 244 49.29 - 73.94: 43 73.94 - 98.59: 16 98.59 - 123.23: 3 Dihedral angle restraints: 5778 sinusoidal: 2443 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 5775 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: 0.940 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: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.370 Find NCS groups from input model: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 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 : 15.160 123.235 3622 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 covalent geometry : bond 0.00912 ( 9432) covalent geometry : angle 1.44008 (12825) SS BOND : bond 0.00309 ( 3) SS BOND : angle 2.33325 ( 6) hydrogen bonds : bond 0.16075 ( 423) hydrogen bonds : angle 10.28640 ( 1236) metal coordination : bond 0.46410 ( 2) link_BETA1-4 : bond 0.01219 ( 1) link_BETA1-4 : angle 5.63780 ( 3) link_NAG-ASN : bond 0.00601 ( 6) link_NAG-ASN : angle 4.32800 ( 18) link_TRANS : bond 0.00227 ( 1) link_TRANS : angle 0.75485 ( 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 : 0.286 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: 0.7653 (m-10) REVERT: A 1046 PHE cc_start: 0.7700 (m-10) cc_final: 0.7498 (m-80) REVERT: A 1051 TRP cc_start: 0.6439 (t-100) cc_final: 0.5356 (m-10) REVERT: A 1055 ILE cc_start: 0.7874 (mm) cc_final: 0.7659 (mt) outliers start: 36 outliers final: 16 residues processed: 340 average time/residue: 0.1210 time to fit residues: 54.1049 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 : 0.353 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 124 ASN 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 B 81 ASN B 180 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.144764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.129452 restraints weight = 18648.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.132067 restraints weight = 10434.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.133708 restraints weight = 7102.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.134669 restraints weight = 5476.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.135495 restraints weight = 4642.010| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9445 Z= 0.178 Angle : 0.925 19.819 12855 Z= 0.455 Chirality : 0.051 0.323 1471 Planarity : 0.006 0.058 1601 Dihedral : 12.251 97.965 1575 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.85 % Favored : 89.80 % Rotamer: Outliers : 5.60 % Allowed : 15.66 % Favored : 78.73 % 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: -3.05 (0.23), residues: 1137 helix: -1.33 (0.19), residues: 629 sheet: -1.99 (0.59), residues: 68 loop : -2.99 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 80 TYR 0.038 0.002 TYR A1181 PHE 0.016 0.002 PHE A 974 TRP 0.010 0.002 TRP A 460 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 9432) covalent geometry : angle 0.91025 (12825) SS BOND : bond 0.00092 ( 3) SS BOND : angle 1.33887 ( 6) hydrogen bonds : bond 0.05492 ( 423) hydrogen bonds : angle 5.82963 ( 1236) metal coordination : bond 0.02284 ( 2) link_BETA1-4 : bond 0.00033 ( 1) link_BETA1-4 : angle 3.06958 ( 3) link_NAG-ASN : bond 0.00291 ( 6) link_NAG-ASN : angle 4.35179 ( 18) link_TRANS : bond 0.00055 ( 1) link_TRANS : angle 0.43382 ( 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 243 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 189 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.6557 (OUTLIER) cc_final: 0.6293 (pt) REVERT: A 101 PHE cc_start: 0.3835 (OUTLIER) cc_final: 0.2667 (t80) REVERT: A 128 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7295 (mp) REVERT: A 135 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7573 (ttp-110) REVERT: A 152 MET cc_start: 0.7625 (mpp) cc_final: 0.7402 (tpt) REVERT: A 422 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7414 (p90) REVERT: A 471 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7399 (mt) REVERT: A 476 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.8000 (tt) REVERT: A 487 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8244 (tp) REVERT: A 584 ASN cc_start: 0.8596 (t0) cc_final: 0.8383 (t0) REVERT: A 740 TYR cc_start: 0.7301 (t80) cc_final: 0.6893 (t80) REVERT: A 777 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6838 (mt) REVERT: A 804 TYR cc_start: 0.8261 (m-80) cc_final: 0.8037 (m-80) REVERT: A 843 MET cc_start: 0.7635 (ttm) cc_final: 0.7402 (ttm) REVERT: A 942 ARG cc_start: 0.7746 (mmt-90) cc_final: 0.7414 (mmt90) REVERT: A 1051 TRP cc_start: 0.6482 (t-100) cc_final: 0.5635 (m-10) REVERT: A 1055 ILE cc_start: 0.8197 (mm) cc_final: 0.7837 (mt) REVERT: A 1070 MET cc_start: 0.8010 (tpp) cc_final: 0.7736 (tpp) REVERT: A 1183 GLU cc_start: 0.6132 (pt0) cc_final: 0.5789 (pt0) outliers start: 54 outliers final: 19 residues processed: 225 average time/residue: 0.1004 time to fit residues: 31.4484 Evaluate side-chains 176 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 595 ILE Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 805 ILE 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: 2.9990 chunk 106 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN A 328 HIS ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 940 ASN ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.138763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.123156 restraints weight = 18979.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.125699 restraints weight = 10756.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.127365 restraints weight = 7356.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.128358 restraints weight = 5677.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.129096 restraints weight = 4808.402| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.4271 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= 0.174 Angle : 0.858 18.987 12855 Z= 0.420 Chirality : 0.049 0.270 1471 Planarity : 0.006 0.052 1601 Dihedral : 9.678 59.574 1560 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.03 % Favored : 89.53 % Rotamer: Outliers : 5.91 % Allowed : 18.15 % 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: -2.07 (0.24), residues: 1137 helix: -0.40 (0.20), residues: 631 sheet: -1.28 (0.60), residues: 70 loop : -2.84 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 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 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 9432) covalent geometry : angle 0.84550 (12825) SS BOND : bond 0.00160 ( 3) SS BOND : angle 1.24106 ( 6) hydrogen bonds : bond 0.04898 ( 423) hydrogen bonds : angle 5.00160 ( 1236) metal coordination : bond 0.00797 ( 2) link_BETA1-4 : bond 0.00159 ( 1) link_BETA1-4 : angle 3.26366 ( 3) link_NAG-ASN : bond 0.00679 ( 6) link_NAG-ASN : angle 3.68375 ( 18) link_TRANS : bond 0.00005 ( 1) link_TRANS : angle 0.48873 ( 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 223 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 166 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 PHE cc_start: 0.4616 (OUTLIER) cc_final: 0.3179 (t80) REVERT: A 128 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7161 (mt) REVERT: A 135 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7497 (ttp-110) REVERT: A 422 PHE cc_start: 0.7886 (OUTLIER) cc_final: 0.7448 (p90) REVERT: A 471 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7233 (mt) REVERT: A 476 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7973 (tt) REVERT: A 777 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7036 (mt) REVERT: A 804 TYR cc_start: 0.8406 (m-80) cc_final: 0.8169 (m-80) REVERT: A 940 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7855 (p0) REVERT: A 942 ARG cc_start: 0.7801 (mmt-90) cc_final: 0.7583 (mmt90) REVERT: A 981 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.6527 (pp) REVERT: A 1011 ASN cc_start: 0.7750 (m-40) cc_final: 0.7529 (m-40) REVERT: A 1051 TRP cc_start: 0.6473 (t-100) cc_final: 0.5559 (m-10) REVERT: A 1055 ILE cc_start: 0.8211 (mm) cc_final: 0.7925 (mt) outliers start: 57 outliers final: 30 residues processed: 212 average time/residue: 0.0993 time to fit residues: 29.1678 Evaluate side-chains 177 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 138 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 192 MET Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 HIS 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 458 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 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 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 1029 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 A residue 1134 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 101 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3860 r_free = 0.3860 target = 0.138655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.123100 restraints weight = 18930.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.125708 restraints weight = 10672.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.127420 restraints weight = 7231.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.128482 restraints weight = 5533.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.129259 restraints weight = 4620.476| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9445 Z= 0.142 Angle : 0.791 18.806 12855 Z= 0.384 Chirality : 0.046 0.255 1471 Planarity : 0.005 0.062 1601 Dihedral : 8.948 59.691 1553 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.03 % Favored : 89.62 % Rotamer: Outliers : 4.88 % Allowed : 20.64 % Favored : 74.48 % 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: -1.61 (0.25), residues: 1137 helix: 0.11 (0.21), residues: 627 sheet: -1.47 (0.56), residues: 77 loop : -2.79 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 942 TYR 0.033 0.002 TYR A 224 PHE 0.018 0.001 PHE A 795 TRP 0.012 0.001 TRP A 844 HIS 0.014 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9432) covalent geometry : angle 0.78035 (12825) SS BOND : bond 0.00247 ( 3) SS BOND : angle 1.58306 ( 6) hydrogen bonds : bond 0.04321 ( 423) hydrogen bonds : angle 4.69345 ( 1236) metal coordination : bond 0.00267 ( 2) link_BETA1-4 : bond 0.00180 ( 1) link_BETA1-4 : angle 2.88897 ( 3) link_NAG-ASN : bond 0.00505 ( 6) link_NAG-ASN : angle 3.30653 ( 18) link_TRANS : bond 0.00029 ( 1) link_TRANS : angle 0.33769 ( 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 207 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 160 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.6620 (OUTLIER) cc_final: 0.6376 (pt) REVERT: A 135 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7698 (ttp-110) REVERT: A 422 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7412 (p90) REVERT: A 471 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7204 (mp) REVERT: A 587 MET cc_start: 0.7997 (tmm) cc_final: 0.7408 (tmm) REVERT: A 804 TYR cc_start: 0.8457 (m-80) cc_final: 0.8204 (m-80) REVERT: A 981 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6806 (pp) REVERT: A 1051 TRP cc_start: 0.6442 (t-100) cc_final: 0.5500 (m-10) REVERT: A 1055 ILE cc_start: 0.8168 (mm) cc_final: 0.7910 (mt) REVERT: A 1078 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8250 (mm) outliers start: 47 outliers final: 23 residues processed: 200 average time/residue: 0.0936 time to fit residues: 26.6904 Evaluate side-chains 171 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 135 ARG Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 343 VAL 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 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 947 GLU 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 1078 LEU Chi-restraints excluded: chain B residue 146 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.138187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.122266 restraints weight = 18947.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.124785 restraints weight = 10689.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.126396 restraints weight = 7352.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.127339 restraints weight = 5718.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.128095 restraints weight = 4868.027| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9445 Z= 0.139 Angle : 0.786 13.516 12855 Z= 0.378 Chirality : 0.046 0.251 1471 Planarity : 0.005 0.060 1601 Dihedral : 8.323 59.762 1547 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.38 % Favored : 89.45 % Rotamer: Outliers : 4.67 % Allowed : 22.30 % Favored : 73.03 % 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: -1.24 (0.25), residues: 1137 helix: 0.41 (0.21), residues: 629 sheet: -1.34 (0.57), residues: 77 loop : -2.64 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1114 TYR 0.036 0.002 TYR A1181 PHE 0.017 0.001 PHE A 848 TRP 0.011 0.001 TRP A 844 HIS 0.006 0.001 HIS A 846 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9432) covalent geometry : angle 0.77617 (12825) SS BOND : bond 0.00135 ( 3) SS BOND : angle 1.31091 ( 6) hydrogen bonds : bond 0.04102 ( 423) hydrogen bonds : angle 4.43719 ( 1236) metal coordination : bond 0.00262 ( 2) link_BETA1-4 : bond 0.00132 ( 1) link_BETA1-4 : angle 2.74914 ( 3) link_NAG-ASN : bond 0.00459 ( 6) link_NAG-ASN : angle 3.24530 ( 18) link_TRANS : bond 0.00251 ( 1) link_TRANS : angle 0.41709 ( 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 191 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 146 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 THR cc_start: 0.9105 (OUTLIER) cc_final: 0.8860 (m) REVERT: A 319 MET cc_start: 0.6291 (mmm) cc_final: 0.6048 (mmm) REVERT: A 422 PHE cc_start: 0.7778 (OUTLIER) cc_final: 0.7364 (p90) REVERT: A 471 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7153 (mp) REVERT: A 981 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.7011 (pp) REVERT: A 1051 TRP cc_start: 0.6526 (t-100) cc_final: 0.5547 (m-10) REVERT: A 1055 ILE cc_start: 0.8207 (mm) cc_final: 0.7950 (mt) REVERT: A 1077 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7712 (mmmm) REVERT: A 1078 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8556 (mm) outliers start: 45 outliers final: 33 residues processed: 181 average time/residue: 0.0845 time to fit residues: 22.4793 Evaluate side-chains 168 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 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 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 771 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 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 981 LEU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1077 LYS Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain B residue 146 VAL 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: 1.9990 chunk 71 optimal weight: 0.7980 chunk 14 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** A 584 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.138988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.123604 restraints weight = 18877.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.126056 restraints weight = 10787.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.127628 restraints weight = 7432.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.128696 restraints weight = 5784.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.129258 restraints weight = 4865.552| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 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 0.027 9445 Z= 0.129 Angle : 0.760 11.990 12855 Z= 0.364 Chirality : 0.045 0.246 1471 Planarity : 0.005 0.057 1601 Dihedral : 7.980 59.235 1547 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.55 % Favored : 89.18 % Rotamer: Outliers : 5.39 % Allowed : 22.10 % Favored : 72.51 % 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: -0.91 (0.25), residues: 1137 helix: 0.66 (0.21), residues: 626 sheet: -0.71 (0.62), residues: 67 loop : -2.50 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1114 TYR 0.032 0.001 TYR A 224 PHE 0.017 0.001 PHE A1068 TRP 0.014 0.001 TRP A 844 HIS 0.005 0.001 HIS A 846 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9432) covalent geometry : angle 0.74994 (12825) SS BOND : bond 0.00158 ( 3) SS BOND : angle 1.22917 ( 6) hydrogen bonds : bond 0.03875 ( 423) hydrogen bonds : angle 4.24561 ( 1236) metal coordination : bond 0.00205 ( 2) link_BETA1-4 : bond 0.00086 ( 1) link_BETA1-4 : angle 2.63722 ( 3) link_NAG-ASN : bond 0.00444 ( 6) link_NAG-ASN : angle 3.16892 ( 18) link_TRANS : bond 0.00025 ( 1) link_TRANS : angle 0.62546 ( 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 199 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 147 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6487 (pt) REVERT: A 124 ASN cc_start: 0.5349 (m110) cc_final: 0.4875 (m-40) REVERT: A 135 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7863 (ttp-110) REVERT: A 230 THR cc_start: 0.9068 (OUTLIER) cc_final: 0.8843 (m) REVERT: A 422 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.7390 (p90) REVERT: A 471 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7142 (mp) REVERT: A 740 TYR cc_start: 0.7309 (t80) cc_final: 0.7108 (t80) REVERT: A 750 LYS cc_start: 0.6446 (mmpt) cc_final: 0.6041 (pttt) REVERT: A 874 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7457 (ptmm) REVERT: A 981 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7157 (pp) REVERT: A 1051 TRP cc_start: 0.6463 (t-100) cc_final: 0.5543 (m-10) REVERT: A 1055 ILE cc_start: 0.8121 (mm) cc_final: 0.7867 (mt) REVERT: A 1077 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7912 (mmtt) outliers start: 52 outliers final: 32 residues processed: 185 average time/residue: 0.0853 time to fit residues: 22.9751 Evaluate side-chains 172 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 135 ARG 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 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 771 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 867 LYS Chi-restraints excluded: chain A residue 874 LYS Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 986 ASP Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1077 LYS Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain B residue 146 VAL 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: 1.9990 chunk 82 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 38 optimal weight: 0.0570 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN A 371 GLN ** A 979 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.138095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.122495 restraints weight = 18990.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.125006 restraints weight = 10730.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.126627 restraints weight = 7348.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.127672 restraints weight = 5709.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.128386 restraints weight = 4809.577| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.5654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9445 Z= 0.136 Angle : 0.757 11.610 12855 Z= 0.367 Chirality : 0.045 0.247 1471 Planarity : 0.005 0.054 1601 Dihedral : 7.724 59.294 1542 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.38 % Favored : 89.45 % Rotamer: Outliers : 5.19 % Allowed : 23.34 % Favored : 71.47 % 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: -0.78 (0.26), residues: 1137 helix: 0.76 (0.21), residues: 626 sheet: -0.64 (0.62), residues: 67 loop : -2.44 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1114 TYR 0.031 0.001 TYR A 224 PHE 0.017 0.001 PHE A1068 TRP 0.011 0.001 TRP A 844 HIS 0.004 0.001 HIS A1099 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9432) covalent geometry : angle 0.74752 (12825) SS BOND : bond 0.00139 ( 3) SS BOND : angle 1.13366 ( 6) hydrogen bonds : bond 0.03831 ( 423) hydrogen bonds : angle 4.25723 ( 1236) metal coordination : bond 0.00278 ( 2) link_BETA1-4 : bond 0.00036 ( 1) link_BETA1-4 : angle 2.65526 ( 3) link_NAG-ASN : bond 0.00430 ( 6) link_NAG-ASN : angle 3.14821 ( 18) link_TRANS : bond 0.00058 ( 1) link_TRANS : angle 0.32054 ( 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 187 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 137 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6465 (pt) REVERT: A 124 ASN cc_start: 0.5446 (m110) cc_final: 0.5053 (m-40) REVERT: A 135 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7861 (ttp-110) REVERT: A 361 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.7960 (tt0) REVERT: A 397 GLU cc_start: 0.7448 (pp20) cc_final: 0.7158 (pp20) REVERT: A 422 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.7421 (p90) REVERT: A 471 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7142 (mm) REVERT: A 981 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7049 (pp) REVERT: A 1051 TRP cc_start: 0.6440 (t-100) cc_final: 0.5490 (m-10) REVERT: A 1055 ILE cc_start: 0.8140 (mm) cc_final: 0.7890 (mt) REVERT: A 1087 ILE cc_start: 0.7888 (mm) cc_final: 0.7684 (mp) outliers start: 50 outliers final: 32 residues processed: 175 average time/residue: 0.0810 time to fit residues: 21.1814 Evaluate side-chains 167 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 129 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 135 ARG Chi-restraints excluded: chain A residue 192 MET 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 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 981 LEU Chi-restraints excluded: chain A residue 986 ASP Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 166 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 23 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS A 361 GLN ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 HIS B 182 HIS B 189 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.135263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.119765 restraints weight = 18751.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.122337 restraints weight = 10562.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.123930 restraints weight = 7177.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.124911 restraints weight = 5565.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.125637 restraints weight = 4714.509| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.5921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 2.225 9445 Z= 0.787 Angle : 0.820 10.937 12855 Z= 0.399 Chirality : 0.048 0.255 1471 Planarity : 0.005 0.057 1601 Dihedral : 7.634 58.940 1534 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.73 % Favored : 89.09 % Rotamer: Outliers : 5.71 % Allowed : 22.51 % Favored : 71.78 % 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: -0.82 (0.26), residues: 1137 helix: 0.66 (0.21), residues: 634 sheet: -0.80 (0.61), residues: 67 loop : -2.35 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 942 TYR 0.038 0.002 TYR A1181 PHE 0.025 0.002 PHE A 848 TRP 0.011 0.001 TRP A 460 HIS 0.004 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 9432) covalent geometry : angle 0.80895 (12825) SS BOND : bond 0.00233 ( 3) SS BOND : angle 1.19687 ( 6) hydrogen bonds : bond 0.04383 ( 423) hydrogen bonds : angle 4.45006 ( 1236) metal coordination : bond 1.57356 ( 2) link_BETA1-4 : bond 0.00217 ( 1) link_BETA1-4 : angle 3.46091 ( 3) link_NAG-ASN : bond 0.00486 ( 6) link_NAG-ASN : angle 3.37421 ( 18) link_TRANS : bond 0.00274 ( 1) link_TRANS : angle 0.35933 ( 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 183 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 128 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASN cc_start: 0.5864 (m110) cc_final: 0.5370 (m-40) REVERT: A 135 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7789 (ttp-110) REVERT: A 397 GLU cc_start: 0.7587 (pp20) cc_final: 0.7293 (pp20) REVERT: A 422 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7597 (p90) REVERT: A 471 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7332 (mm) REVERT: A 740 TYR cc_start: 0.7357 (OUTLIER) cc_final: 0.6603 (m-80) REVERT: A 756 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7570 (mt) REVERT: A 940 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7744 (p0) REVERT: A 981 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7341 (pp) REVERT: A 1020 GLN cc_start: 0.9247 (OUTLIER) cc_final: 0.8348 (pt0) REVERT: A 1051 TRP cc_start: 0.6348 (t-100) cc_final: 0.5574 (m-10) REVERT: A 1055 ILE cc_start: 0.8271 (mm) cc_final: 0.8047 (mt) REVERT: B 129 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7378 (m-30) REVERT: B 172 TRP cc_start: 0.8761 (OUTLIER) cc_final: 0.8249 (t60) outliers start: 55 outliers final: 34 residues processed: 171 average time/residue: 0.0818 time to fit residues: 20.6677 Evaluate side-chains 164 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 120 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL 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 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 595 ILE Chi-restraints excluded: chain A residue 740 TYR Chi-restraints excluded: chain A residue 756 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 867 LYS 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 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 1079 SER 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 97 LEU Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 146 VAL 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: 0.0020 chunk 52 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 25 optimal weight: 0.1980 chunk 84 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 111 optimal weight: 0.0060 chunk 68 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN A 371 GLN A 496 ASN A1099 HIS ** B 134 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 = 0.3878 r_free = 0.3878 target = 0.140035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.124981 restraints weight = 18608.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.127534 restraints weight = 10584.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.129146 restraints weight = 7246.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.130167 restraints weight = 5613.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.130867 restraints weight = 4720.294| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.6049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9445 Z= 0.133 Angle : 0.794 14.487 12855 Z= 0.378 Chirality : 0.046 0.246 1471 Planarity : 0.005 0.057 1601 Dihedral : 7.411 58.575 1534 Min Nonbonded Distance : 1.492 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.59 % Favored : 90.33 % Rotamer: Outliers : 4.56 % Allowed : 23.96 % Favored : 71.47 % 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: -0.66 (0.26), residues: 1137 helix: 0.82 (0.21), residues: 636 sheet: -0.59 (0.62), residues: 67 loop : -2.40 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1114 TYR 0.037 0.001 TYR A1181 PHE 0.019 0.001 PHE A1068 TRP 0.018 0.001 TRP A 844 HIS 0.027 0.002 HIS B 182 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9432) covalent geometry : angle 0.78445 (12825) SS BOND : bond 0.00169 ( 3) SS BOND : angle 1.23874 ( 6) hydrogen bonds : bond 0.03845 ( 423) hydrogen bonds : angle 4.28579 ( 1236) metal coordination : bond 0.04680 ( 2) link_BETA1-4 : bond 0.00065 ( 1) link_BETA1-4 : angle 2.77520 ( 3) link_NAG-ASN : bond 0.00475 ( 6) link_NAG-ASN : angle 3.18988 ( 18) link_TRANS : bond 0.00107 ( 1) link_TRANS : angle 0.18857 ( 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 176 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 132 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASN cc_start: 0.5658 (m110) cc_final: 0.5232 (m-40) REVERT: A 135 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7770 (ttp-110) REVERT: A 397 GLU cc_start: 0.7372 (pp20) cc_final: 0.7051 (pp20) REVERT: A 422 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7414 (p90) REVERT: A 471 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7268 (mm) REVERT: A 740 TYR cc_start: 0.7323 (OUTLIER) cc_final: 0.6604 (m-80) REVERT: A 750 LYS cc_start: 0.6555 (mmpt) cc_final: 0.6149 (pttt) REVERT: A 940 ASN cc_start: 0.7998 (OUTLIER) cc_final: 0.7476 (p0) REVERT: A 981 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7175 (pp) REVERT: A 1051 TRP cc_start: 0.6364 (t-100) cc_final: 0.5435 (m-10) REVERT: A 1055 ILE cc_start: 0.8163 (mm) cc_final: 0.7878 (mt) REVERT: B 172 TRP cc_start: 0.8655 (OUTLIER) cc_final: 0.8176 (t60) outliers start: 44 outliers final: 31 residues processed: 165 average time/residue: 0.0838 time to fit residues: 20.3010 Evaluate side-chains 163 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 192 MET 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 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 908 VAL Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 940 ASN Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 986 ASP 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 1079 SER Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain B residue 51 VAL 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: 0.7980 chunk 49 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN A1099 HIS B 189 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.139644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.124570 restraints weight = 18654.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.127068 restraints weight = 10572.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.128657 restraints weight = 7282.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.129599 restraints weight = 5677.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.130358 restraints weight = 4817.674| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.6114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9445 Z= 0.137 Angle : 0.776 13.706 12855 Z= 0.371 Chirality : 0.045 0.250 1471 Planarity : 0.005 0.056 1601 Dihedral : 7.295 58.335 1534 Min Nonbonded Distance : 1.404 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.99 % Favored : 88.92 % Rotamer: Outliers : 4.25 % Allowed : 24.38 % Favored : 71.37 % 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: -0.59 (0.26), residues: 1137 helix: 0.90 (0.21), residues: 633 sheet: -0.56 (0.62), residues: 67 loop : -2.38 (0.30), residues: 437 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 A1068 TRP 0.013 0.001 TRP A 844 HIS 0.022 0.002 HIS B 182 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9432) covalent geometry : angle 0.76666 (12825) SS BOND : bond 0.00155 ( 3) SS BOND : angle 1.26692 ( 6) hydrogen bonds : bond 0.03774 ( 423) hydrogen bonds : angle 4.24996 ( 1236) metal coordination : bond 0.05297 ( 2) link_BETA1-4 : bond 0.00095 ( 1) link_BETA1-4 : angle 2.69207 ( 3) link_NAG-ASN : bond 0.00422 ( 6) link_NAG-ASN : angle 3.13633 ( 18) link_TRANS : bond 0.00012 ( 1) link_TRANS : angle 0.27100 ( 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 165 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASN cc_start: 0.5854 (m110) cc_final: 0.5392 (m-40) REVERT: A 135 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7738 (ttp-110) REVERT: A 397 GLU cc_start: 0.7435 (pp20) cc_final: 0.7134 (pp20) REVERT: A 422 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7469 (p90) REVERT: A 471 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7308 (mm) REVERT: A 740 TYR cc_start: 0.7332 (OUTLIER) cc_final: 0.6602 (m-80) REVERT: A 940 ASN cc_start: 0.8069 (OUTLIER) cc_final: 0.7627 (p0) REVERT: A 974 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.8024 (p90) REVERT: A 981 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7185 (pp) REVERT: A 1051 TRP cc_start: 0.6345 (t-100) cc_final: 0.5425 (m-10) REVERT: A 1055 ILE cc_start: 0.8154 (mm) cc_final: 0.7885 (mt) REVERT: B 172 TRP cc_start: 0.8696 (OUTLIER) cc_final: 0.8282 (t60) outliers start: 41 outliers final: 31 residues processed: 158 average time/residue: 0.0873 time to fit residues: 20.2851 Evaluate side-chains 160 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 121 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 192 MET 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 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 908 VAL Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 940 ASN 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 1043 CYS Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain B residue 51 VAL 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: 7.9990 chunk 42 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 103 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3880 r_free = 0.3880 target = 0.140215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.125208 restraints weight = 18456.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.127769 restraints weight = 10508.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.129327 restraints weight = 7195.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.130343 restraints weight = 5606.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.130972 restraints weight = 4724.480| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.6233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9445 Z= 0.131 Angle : 0.769 13.258 12855 Z= 0.367 Chirality : 0.045 0.248 1471 Planarity : 0.005 0.056 1601 Dihedral : 7.253 58.411 1534 Min Nonbonded Distance : 1.428 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.47 % Favored : 89.45 % Rotamer: Outliers : 4.36 % Allowed : 24.59 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.09 % Twisted Proline : 2.08 % Twisted General : 0.00 % Rama-Z 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: -0.51 (0.26), residues: 1137 helix: 0.96 (0.21), residues: 632 sheet: -0.53 (0.62), residues: 67 loop : -2.32 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1114 TYR 0.035 0.001 TYR A1181 PHE 0.018 0.001 PHE A1068 TRP 0.014 0.001 TRP A 844 HIS 0.021 0.001 HIS B 182 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9432) covalent geometry : angle 0.75977 (12825) SS BOND : bond 0.00164 ( 3) SS BOND : angle 1.28040 ( 6) hydrogen bonds : bond 0.03684 ( 423) hydrogen bonds : angle 4.20371 ( 1236) metal coordination : bond 0.04592 ( 2) link_BETA1-4 : bond 0.00097 ( 1) link_BETA1-4 : angle 2.57061 ( 3) link_NAG-ASN : bond 0.00409 ( 6) link_NAG-ASN : angle 3.06065 ( 18) link_TRANS : bond 0.00074 ( 1) link_TRANS : angle 0.22859 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1595.77 seconds wall clock time: 28 minutes 19.51 seconds (1699.51 seconds total)