Starting phenix.real_space_refine on Thu Jul 2 23:52:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ruc_24702/07_2026/7ruc_24702.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ruc_24702/07_2026/7ruc_24702.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ruc_24702/07_2026/7ruc_24702.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ruc_24702/07_2026/7ruc_24702.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ruc_24702/07_2026/7ruc_24702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ruc_24702/07_2026/7ruc_24702.map" model { file = "/net/cci-nas-00/data/ceres_data/7ruc_24702/07_2026/7ruc_24702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ruc_24702/07_2026/7ruc_24702.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 6 5.49 5 Mg 2 5.21 5 S 64 5.16 5 C 6835 2.51 5 N 1832 2.21 5 O 2026 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10766 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2417 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 18, 'TRANS': 287} Chain breaks: 1 Chain: "B" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2412 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 18, 'TRANS': 286} Chain breaks: 1 Chain: "C" Number of atoms: 2175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2175 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 11, 'TRANS': 259} Chain: "D" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 340 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 8, 'TRANS': 34} Chain: "F" Number of atoms: 2175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2175 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 11, 'TRANS': 259} Chain: "G" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 790 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 12, 'TRANS': 87} Chain breaks: 1 Chain: "H" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 392 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 47} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1952 SG CYS A 283 54.155 67.467 98.552 1.00142.37 S ATOM 1975 SG CYS A 286 55.590 69.741 96.078 1.00127.85 S ATOM 4364 SG CYS B 283 53.181 71.227 98.454 1.00138.48 S ATOM 4387 SG CYS B 286 51.745 68.778 96.011 1.00126.91 S Time building chain proxies: 1.92, per 1000 atoms: 0.18 Number of scatterers: 10766 At special positions: 0 Unit cell: (108.9, 125.4, 113.025, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 64 16.00 P 6 15.00 Mg 2 11.99 O 2026 8.00 N 1832 7.00 C 6835 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 281.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" SG CYS A 283 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 283 " pdb="ZN ZN B 401 " - pdb=" SG CYS A 286 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 286 " Number of angles added : 6 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2554 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 2 sheets defined 70.2% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 22 through 28 Processing helix chain 'A' and resid 43 through 57 removed outlier: 3.592A pdb=" N ALA A 57 " --> pdb=" O VAL A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 78 Processing helix chain 'A' and resid 116 through 132 removed outlier: 4.296A pdb=" N ALA A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 152 Processing helix chain 'A' and resid 163 through 187 Proline residue: A 174 - end of helix Processing helix chain 'A' and resid 210 through 232 removed outlier: 3.686A pdb=" N LEU A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 245 through 263 Processing helix chain 'A' and resid 283 through 304 Processing helix chain 'A' and resid 321 through 334 removed outlier: 3.897A pdb=" N GLN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 332 " --> pdb=" O PHE A 328 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 28 Processing helix chain 'B' and resid 43 through 57 removed outlier: 3.517A pdb=" N ALA B 57 " --> pdb=" O VAL B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 78 Processing helix chain 'B' and resid 116 through 131 removed outlier: 4.975A pdb=" N GLY B 122 " --> pdb=" O MET B 118 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 135 through 152 Processing helix chain 'B' and resid 163 through 190 removed outlier: 3.531A pdb=" N THR B 167 " --> pdb=" O PRO B 163 " (cutoff:3.500A) Proline residue: B 174 - end of helix Processing helix chain 'B' and resid 211 through 232 removed outlier: 4.251A pdb=" N LYS B 215 " --> pdb=" O GLN B 211 " (cutoff:3.500A) Proline residue: B 221 - end of helix Processing helix chain 'B' and resid 245 through 263 Processing helix chain 'B' and resid 283 through 304 Processing helix chain 'B' and resid 321 through 334 removed outlier: 4.003A pdb=" N GLN B 331 " --> pdb=" O THR B 327 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 332 " --> pdb=" O PHE B 328 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 37 removed outlier: 3.941A pdb=" N GLN C 24 " --> pdb=" O ARG C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 56 Processing helix chain 'C' and resid 58 through 76 Processing helix chain 'C' and resid 78 through 96 Processing helix chain 'C' and resid 101 through 115 Processing helix chain 'C' and resid 120 through 133 Processing helix chain 'C' and resid 142 through 156 Processing helix chain 'C' and resid 158 through 169 Processing helix chain 'C' and resid 171 through 186 Processing helix chain 'C' and resid 188 through 190 No H-bonds generated for 'chain 'C' and resid 188 through 190' Processing helix chain 'C' and resid 191 through 206 removed outlier: 4.126A pdb=" N VAL C 196 " --> pdb=" O VAL C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 223 Processing helix chain 'C' and resid 234 through 250 Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 262 through 267 Processing helix chain 'C' and resid 270 through 285 removed outlier: 3.902A pdb=" N GLU C 274 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY C 285 " --> pdb=" O GLN C 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 1009 through 1014 removed outlier: 4.370A pdb=" N ALA D1013 " --> pdb=" O PRO D1009 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL D1014 " --> pdb=" O TRP D1010 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1009 through 1014' Processing helix chain 'D' and resid 1015 through 1017 No H-bonds generated for 'chain 'D' and resid 1015 through 1017' Processing helix chain 'D' and resid 1018 through 1030 removed outlier: 3.745A pdb=" N ILE D1022 " --> pdb=" O TRP D1018 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN D1023 " --> pdb=" O VAL D1019 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN D1024 " --> pdb=" O PRO D1020 " (cutoff:3.500A) Processing helix chain 'D' and resid 1039 through 1044 Processing helix chain 'F' and resid 21 through 37 Processing helix chain 'F' and resid 38 through 57 Processing helix chain 'F' and resid 58 through 77 Processing helix chain 'F' and resid 78 through 97 Processing helix chain 'F' and resid 101 through 115 Processing helix chain 'F' and resid 119 through 133 removed outlier: 4.081A pdb=" N VAL F 123 " --> pdb=" O SER F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 156 removed outlier: 3.535A pdb=" N HIS F 146 " --> pdb=" O HIS F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 169 Processing helix chain 'F' and resid 172 through 187 Processing helix chain 'F' and resid 188 through 190 No H-bonds generated for 'chain 'F' and resid 188 through 190' Processing helix chain 'F' and resid 191 through 206 removed outlier: 3.798A pdb=" N VAL F 196 " --> pdb=" O VAL F 192 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU F 206 " --> pdb=" O GLN F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 223 removed outlier: 3.586A pdb=" N ALA F 212 " --> pdb=" O ASN F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 248 Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 262 through 267 Processing helix chain 'F' and resid 269 through 284 removed outlier: 4.289A pdb=" N ASN F 273 " --> pdb=" O ASP F 269 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU F 274 " --> pdb=" O PRO F 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 1017 through 1032 removed outlier: 4.732A pdb=" N ILE G1021 " --> pdb=" O GLU G1017 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG G1030 " --> pdb=" O ILE G1026 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS G1031 " --> pdb=" O GLN G1027 " (cutoff:3.500A) Processing helix chain 'G' and resid 1039 through 1044 Processing helix chain 'G' and resid 1062 through 1075 Processing helix chain 'G' and resid 1081 through 1089 removed outlier: 3.841A pdb=" N LEU G1085 " --> pdb=" O SER G1081 " (cutoff:3.500A) Processing helix chain 'G' and resid 1092 through 1111 removed outlier: 4.357A pdb=" N TYR G1098 " --> pdb=" O VAL G1094 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG G1099 " --> pdb=" O GLN G1095 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN G1111 " --> pdb=" O GLN G1107 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 107 removed outlier: 4.329A pdb=" N VAL H 102 " --> pdb=" O LEU H 98 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG H 105 " --> pdb=" O LYS H 101 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N HIS H 106 " --> pdb=" O VAL H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 130 Processing helix chain 'H' and resid 133 through 140 removed outlier: 3.551A pdb=" N ARG H 137 " --> pdb=" O ASP H 133 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87 removed outlier: 6.470A pdb=" N VAL A 62 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N MET A 97 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE A 64 " --> pdb=" O MET A 97 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A 63 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ASP A 160 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ILE A 65 " --> pdb=" O ASP A 160 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TRP A 33 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE A 239 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE A 35 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL A 241 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLY A 37 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N ILE A 243 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N ASN A 268 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE A 238 " --> pdb=" O ASN A 268 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ILE A 270 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N CYS A 240 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASN A 272 " --> pdb=" O CYS A 240 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N CYS A 242 " --> pdb=" O ASN A 272 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU A 274 " --> pdb=" O CYS A 242 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE A 269 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU A 312 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL A 271 " --> pdb=" O LEU A 312 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 86 through 87 removed outlier: 6.555A pdb=" N VAL B 62 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N MET B 97 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE B 64 " --> pdb=" O MET B 97 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TRP B 33 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILE B 239 " --> pdb=" O TRP B 33 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE B 35 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL B 241 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLY B 37 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ASN B 268 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS B 240 " --> pdb=" O ASN B 268 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE B 269 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU B 312 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL B 271 " --> pdb=" O LEU B 312 " (cutoff:3.500A) 651 hydrogen bonds defined for protein. 1947 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: 1.38 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3527 1.34 - 1.46: 1966 1.46 - 1.58: 5393 1.58 - 1.69: 6 1.69 - 1.81: 106 Bond restraints: 10998 Sorted by residual: bond pdb=" C LEU A 314 " pdb=" N LEU A 315 " ideal model delta sigma weight residual 1.330 1.303 0.027 1.47e-02 4.63e+03 3.26e+00 bond pdb=" CA PRO B 163 " pdb=" C PRO B 163 " ideal model delta sigma weight residual 1.525 1.514 0.012 9.70e-03 1.06e+04 1.49e+00 bond pdb=" O3B ATP B 402 " pdb=" PB ATP B 402 " ideal model delta sigma weight residual 1.592 1.562 0.030 3.00e-02 1.11e+03 1.01e+00 bond pdb=" C1' ATP B 402 " pdb=" C2' ATP B 402 " ideal model delta sigma weight residual 1.531 1.520 0.011 1.20e-02 6.94e+03 8.73e-01 bond pdb=" C1' ATP A 401 " pdb=" C2' ATP A 401 " ideal model delta sigma weight residual 1.531 1.520 0.011 1.20e-02 6.94e+03 8.51e-01 ... (remaining 10993 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 14537 1.40 - 2.79: 248 2.79 - 4.19: 83 4.19 - 5.59: 6 5.59 - 6.98: 8 Bond angle restraints: 14882 Sorted by residual: angle pdb=" N ASP B 116 " pdb=" CA ASP B 116 " pdb=" C ASP B 116 " ideal model delta sigma weight residual 112.97 110.05 2.92 1.06e+00 8.90e-01 7.61e+00 angle pdb=" N SER G1097 " pdb=" CA SER G1097 " pdb=" C SER G1097 " ideal model delta sigma weight residual 111.75 108.44 3.31 1.28e+00 6.10e-01 6.68e+00 angle pdb=" C2' ATP A 401 " pdb=" C3' ATP A 401 " pdb=" O3' ATP A 401 " ideal model delta sigma weight residual 111.83 105.10 6.73 2.67e+00 1.40e-01 6.35e+00 angle pdb=" C1' ATP A 401 " pdb=" C2' ATP A 401 " pdb=" O2' ATP A 401 " ideal model delta sigma weight residual 110.58 103.60 6.98 2.79e+00 1.28e-01 6.25e+00 angle pdb=" C2' ATP B 402 " pdb=" C3' ATP B 402 " pdb=" O3' ATP B 402 " ideal model delta sigma weight residual 111.83 105.29 6.54 2.67e+00 1.40e-01 6.01e+00 ... (remaining 14877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 6027 17.61 - 35.21: 556 35.21 - 52.82: 90 52.82 - 70.43: 21 70.43 - 88.04: 10 Dihedral angle restraints: 6704 sinusoidal: 2776 harmonic: 3928 Sorted by residual: dihedral pdb=" CA LEU A 303 " pdb=" C LEU A 303 " pdb=" N TYR A 304 " pdb=" CA TYR A 304 " ideal model delta harmonic sigma weight residual -180.00 -163.63 -16.37 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CB GLU F 181 " pdb=" CG GLU F 181 " pdb=" CD GLU F 181 " pdb=" OE1 GLU F 181 " ideal model delta sinusoidal sigma weight residual 0.00 88.04 -88.04 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CG ARG B 263 " pdb=" CD ARG B 263 " pdb=" NE ARG B 263 " pdb=" CZ ARG B 263 " ideal model delta sinusoidal sigma weight residual 180.00 135.99 44.01 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 6701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1462 0.060 - 0.120: 157 0.120 - 0.180: 12 0.180 - 0.240: 2 0.240 - 0.300: 4 Chirality restraints: 1637 Sorted by residual: chirality pdb=" C2' ATP A 401 " pdb=" C1' ATP A 401 " pdb=" C3' ATP A 401 " pdb=" O2' ATP A 401 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" C2' ATP B 402 " pdb=" C1' ATP B 402 " pdb=" C3' ATP B 402 " pdb=" O2' ATP B 402 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C3' ATP A 401 " pdb=" C2' ATP A 401 " pdb=" C4' ATP A 401 " pdb=" O3' ATP A 401 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 1634 not shown) Planarity restraints: 1922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO F 230 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO F 231 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO F 231 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 231 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 122 " -0.132 9.50e-02 1.11e+02 5.95e-02 2.76e+00 pdb=" NE ARG C 122 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG C 122 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 122 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG C 122 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 197 " 0.008 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" C ALA C 197 " -0.026 2.00e-02 2.50e+03 pdb=" O ALA C 197 " 0.010 2.00e-02 2.50e+03 pdb=" N GLN C 198 " 0.009 2.00e-02 2.50e+03 ... (remaining 1919 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 48 2.40 - 3.02: 7471 3.02 - 3.65: 17099 3.65 - 4.27: 24908 4.27 - 4.90: 41551 Nonbonded interactions: 91077 Sorted by model distance: nonbonded pdb=" O2B ATP A 401 " pdb="MG MG A 402 " model vdw 1.772 2.170 nonbonded pdb=" O2G ATP A 401 " pdb="MG MG A 402 " model vdw 1.780 2.170 nonbonded pdb=" O2G ATP B 402 " pdb="MG MG B 403 " model vdw 1.856 2.170 nonbonded pdb=" O2B ATP B 402 " pdb="MG MG B 403 " model vdw 1.858 2.170 nonbonded pdb=" OG1 THR B 45 " pdb="MG MG B 403 " model vdw 1.962 2.170 ... (remaining 91072 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 190 or resid 210 through 339)) selection = (chain 'B' and resid 16 through 339) } ncs_group { reference = chain 'C' selection = chain 'F' } 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: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.560 Find NCS groups from input model: 0.130 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:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.837 11003 Z= 0.817 Angle : 0.541 8.052 14888 Z= 0.283 Chirality : 0.040 0.300 1637 Planarity : 0.004 0.060 1922 Dihedral : 14.002 88.037 4150 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.89 (0.24), residues: 1324 helix: 1.87 (0.18), residues: 861 sheet: 0.70 (0.63), residues: 67 loop : 0.08 (0.34), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 122 TYR 0.024 0.001 TYR G1098 PHE 0.018 0.001 PHE B 173 TRP 0.014 0.001 TRP H 96 HIS 0.005 0.001 HIS B 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (10998) covalent geometry : angle 0.53281 / 0.28 (14882) hydrogen bonds : bond 0.13371 / 9.03 ( 651) hydrogen bonds : angle 6.01354 / 4.36 ( 1947) metal coordination : bond 0.01379 / 0.69 ( 4) metal coordination : angle 4.71418 / 2.34 ( 6) Misc. bond : bond 0.83728 / 44.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.8683 (ttmm) cc_final: 0.8479 (tppt) REVERT: A 91 TYR cc_start: 0.8539 (m-80) cc_final: 0.7911 (m-80) REVERT: A 118 MET cc_start: 0.1844 (tpp) cc_final: 0.0711 (tmm) REVERT: A 140 MET cc_start: 0.6098 (mtm) cc_final: 0.5891 (mtm) REVERT: A 258 GLU cc_start: 0.7352 (tp30) cc_final: 0.7030 (tp30) REVERT: A 323 ASP cc_start: 0.7994 (p0) cc_final: 0.7428 (t0) REVERT: B 140 MET cc_start: 0.6634 (mmp) cc_final: 0.6324 (mmm) REVERT: B 146 MET cc_start: 0.8080 (mtp) cc_final: 0.7871 (mtm) REVERT: C 91 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7913 (mm-30) REVERT: C 102 ASP cc_start: 0.7543 (t70) cc_final: 0.7095 (t0) REVERT: C 156 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7596 (mt-10) REVERT: C 158 ASN cc_start: 0.7802 (t0) cc_final: 0.6970 (t0) REVERT: C 208 ASN cc_start: 0.8714 (t0) cc_final: 0.8273 (t0) REVERT: C 209 LYS cc_start: 0.8882 (ptpt) cc_final: 0.8203 (ttpp) REVERT: C 226 ILE cc_start: 0.7488 (mm) cc_final: 0.7169 (mt) REVERT: C 228 ASP cc_start: 0.7013 (t0) cc_final: 0.6802 (t0) REVERT: D 1043 LEU cc_start: 0.8196 (mm) cc_final: 0.7879 (mm) REVERT: F 208 ASN cc_start: 0.8184 (t0) cc_final: 0.7886 (t0) REVERT: G 1026 ILE cc_start: 0.7819 (mt) cc_final: 0.7008 (mt) REVERT: G 1030 ARG cc_start: 0.7784 (mpp80) cc_final: 0.7498 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.0845 time to fit residues: 23.4853 Evaluate side-chains 141 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 GLN A 68 ASN A 326 ASN B 54 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.140486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.098713 restraints weight = 20400.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.101807 restraints weight = 10703.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.103544 restraints weight = 7376.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.104614 restraints weight = 6077.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.105013 restraints weight = 5457.869| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11003 Z= 0.157 Angle : 0.594 6.651 14888 Z= 0.308 Chirality : 0.042 0.149 1637 Planarity : 0.005 0.051 1922 Dihedral : 5.492 81.145 1451 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.01 % Allowed : 5.91 % Favored : 93.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 2.08 (0.24), residues: 1324 helix: 1.99 (0.18), residues: 882 sheet: 0.63 (0.62), residues: 67 loop : 0.14 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 122 TYR 0.015 0.002 TYR G1042 PHE 0.017 0.002 PHE C 255 TRP 0.008 0.001 TRP F 132 HIS 0.005 0.001 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (10998) covalent geometry : angle 0.58971 / 0.31 (14882) hydrogen bonds : bond 0.04506 / 3.01 ( 651) hydrogen bonds : angle 4.50323 / 3.26 ( 1947) metal coordination : bond 0.00652 / 0.33 ( 4) metal coordination : angle 3.48848 / 1.70 ( 6) Misc. bond : bond 0.00458 / 0.24 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.2303 (tpp) cc_final: 0.1057 (tmm) REVERT: B 125 MET cc_start: 0.6077 (mmt) cc_final: 0.5841 (tpp) REVERT: B 264 ILE cc_start: 0.9451 (mm) cc_final: 0.9166 (mt) REVERT: C 158 ASN cc_start: 0.8468 (t0) cc_final: 0.8109 (t0) REVERT: C 208 ASN cc_start: 0.8938 (t0) cc_final: 0.8588 (t0) REVERT: C 226 ILE cc_start: 0.8190 (mm) cc_final: 0.7807 (mt) REVERT: D 1027 GLN cc_start: 0.8222 (mm110) cc_final: 0.7677 (tm-30) REVERT: D 1042 TYR cc_start: 0.7604 (t80) cc_final: 0.7371 (t80) REVERT: D 1043 LEU cc_start: 0.8179 (mm) cc_final: 0.7794 (tt) REVERT: F 271 MET cc_start: 0.8156 (mpp) cc_final: 0.7934 (mpp) REVERT: G 1030 ARG cc_start: 0.7478 (mpp80) cc_final: 0.7192 (ptm160) outliers start: 12 outliers final: 7 residues processed: 164 average time/residue: 0.0671 time to fit residues: 16.8354 Evaluate side-chains 139 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 132 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 60 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 2 optimal weight: 0.4980 chunk 32 optimal weight: 0.0980 chunk 11 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 24 optimal weight: 0.0020 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 ASN ** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 GLN ** 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 = 0.3968 r_free = 0.3968 target = 0.141581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.103125 restraints weight = 20363.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.103954 restraints weight = 11634.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.104397 restraints weight = 9067.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.104950 restraints weight = 7786.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.105166 restraints weight = 7433.039| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11003 Z= 0.127 Angle : 0.533 7.078 14888 Z= 0.275 Chirality : 0.040 0.184 1637 Planarity : 0.004 0.056 1922 Dihedral : 5.525 87.124 1451 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.43 % Allowed : 7.09 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 2.14 (0.24), residues: 1324 helix: 2.00 (0.18), residues: 885 sheet: 0.42 (0.60), residues: 72 loop : 0.30 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 122 TYR 0.029 0.001 TYR C 275 PHE 0.015 0.001 PHE C 255 TRP 0.007 0.001 TRP F 132 HIS 0.003 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (10998) covalent geometry : angle 0.52718 / 0.27 (14882) hydrogen bonds : bond 0.03937 / 2.62 ( 651) hydrogen bonds : angle 4.26312 / 3.08 ( 1947) metal coordination : bond 0.00606 / 0.30 ( 4) metal coordination : angle 3.86130 / 1.78 ( 6) Misc. bond : bond 0.00184 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.1965 (tpp) cc_final: 0.0732 (tmm) REVERT: A 147 ARG cc_start: 0.7054 (ttm110) cc_final: 0.6817 (mtt-85) REVERT: A 297 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9137 (mp) REVERT: B 264 ILE cc_start: 0.9439 (mm) cc_final: 0.9194 (mt) REVERT: C 158 ASN cc_start: 0.8479 (t0) cc_final: 0.8052 (t0) REVERT: C 208 ASN cc_start: 0.8923 (t0) cc_final: 0.8567 (t0) REVERT: C 226 ILE cc_start: 0.8018 (mm) cc_final: 0.7655 (mt) REVERT: D 1043 LEU cc_start: 0.8273 (mm) cc_final: 0.7838 (tt) REVERT: G 1030 ARG cc_start: 0.7818 (mpp80) cc_final: 0.7270 (ptp-170) outliers start: 17 outliers final: 10 residues processed: 172 average time/residue: 0.0704 time to fit residues: 18.3905 Evaluate side-chains 154 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain F residue 233 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 99 optimal weight: 0.2980 chunk 61 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 1 optimal weight: 0.0000 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 ASN B 331 GLN ** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.141757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.099522 restraints weight = 20665.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.102599 restraints weight = 10376.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.104639 restraints weight = 7077.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.105714 restraints weight = 5719.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.106192 restraints weight = 5120.204| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11003 Z= 0.124 Angle : 0.530 8.413 14888 Z= 0.272 Chirality : 0.039 0.151 1637 Planarity : 0.004 0.050 1922 Dihedral : 5.573 89.981 1451 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.60 % Allowed : 9.20 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 2.09 (0.23), residues: 1324 helix: 1.98 (0.17), residues: 884 sheet: 0.12 (0.55), residues: 82 loop : 0.31 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 179 TYR 0.013 0.001 TYR A 250 PHE 0.016 0.001 PHE C 188 TRP 0.029 0.002 TRP F 241 HIS 0.003 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (10998) covalent geometry : angle 0.52400 / 0.27 (14882) hydrogen bonds : bond 0.03760 / 2.49 ( 651) hydrogen bonds : angle 4.20441 / 3.03 ( 1947) metal coordination : bond 0.00574 / 0.28 ( 4) metal coordination : angle 3.86591 / 2.02 ( 6) Misc. bond : bond 0.00080 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.2249 (tpp) cc_final: 0.0910 (tmm) REVERT: B 264 ILE cc_start: 0.9437 (mm) cc_final: 0.9216 (mt) REVERT: C 158 ASN cc_start: 0.8497 (t0) cc_final: 0.8074 (t0) REVERT: C 208 ASN cc_start: 0.8891 (t0) cc_final: 0.8637 (t0) REVERT: C 226 ILE cc_start: 0.8120 (mm) cc_final: 0.7736 (mt) REVERT: D 1043 LEU cc_start: 0.8209 (mm) cc_final: 0.7814 (tt) REVERT: F 269 ASP cc_start: 0.7902 (t0) cc_final: 0.6939 (t0) REVERT: F 271 MET cc_start: 0.8092 (mpp) cc_final: 0.7676 (mpp) outliers start: 19 outliers final: 12 residues processed: 170 average time/residue: 0.0703 time to fit residues: 18.2200 Evaluate side-chains 156 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 60 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 ASN A 326 ASN B 68 ASN ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1027 GLN H 106 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.140957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.101481 restraints weight = 20348.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.102927 restraints weight = 11526.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.103523 restraints weight = 8761.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.103755 restraints weight = 7719.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.104015 restraints weight = 7550.303| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11003 Z= 0.158 Angle : 0.555 7.203 14888 Z= 0.284 Chirality : 0.040 0.153 1637 Planarity : 0.005 0.050 1922 Dihedral : 5.589 89.348 1451 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.86 % Allowed : 10.55 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 2.00 (0.24), residues: 1324 helix: 1.89 (0.17), residues: 888 sheet: -0.01 (0.55), residues: 83 loop : 0.34 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 179 TYR 0.013 0.002 TYR A 250 PHE 0.015 0.002 PHE C 188 TRP 0.049 0.002 TRP F 241 HIS 0.004 0.001 HIS B 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (10998) covalent geometry : angle 0.54875 / 0.28 (14882) hydrogen bonds : bond 0.03828 / 2.52 ( 651) hydrogen bonds : angle 4.21942 / 3.04 ( 1947) metal coordination : bond 0.00936 / 0.46 ( 4) metal coordination : angle 4.02951 / 2.11 ( 6) Misc. bond : bond 0.00119 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.1896 (tpp) cc_final: 0.0652 (tmm) REVERT: A 126 MET cc_start: 0.7147 (ppp) cc_final: 0.6943 (ppp) REVERT: A 127 GLN cc_start: 0.5986 (pt0) cc_final: 0.5460 (mm110) REVERT: B 71 HIS cc_start: 0.7651 (m-70) cc_final: 0.7304 (m-70) REVERT: B 179 ARG cc_start: 0.7820 (mtm110) cc_final: 0.7464 (ptp90) REVERT: B 264 ILE cc_start: 0.9463 (mm) cc_final: 0.9248 (mt) REVERT: C 158 ASN cc_start: 0.8447 (t0) cc_final: 0.8026 (t0) REVERT: C 203 PHE cc_start: 0.8240 (m-80) cc_final: 0.8009 (m-80) REVERT: C 208 ASN cc_start: 0.8926 (t0) cc_final: 0.8582 (t0) REVERT: C 226 ILE cc_start: 0.8051 (mm) cc_final: 0.7671 (mt) REVERT: D 1043 LEU cc_start: 0.8224 (mm) cc_final: 0.7796 (tt) REVERT: F 241 TRP cc_start: 0.8017 (t60) cc_final: 0.7807 (t60) outliers start: 22 outliers final: 18 residues processed: 170 average time/residue: 0.0676 time to fit residues: 17.6125 Evaluate side-chains 162 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain G residue 1089 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 127 optimal weight: 0.0570 chunk 92 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 ASN ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1027 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.140641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.101427 restraints weight = 20447.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.102562 restraints weight = 11165.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.103238 restraints weight = 8179.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.103433 restraints weight = 7605.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.103623 restraints weight = 7268.820| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11003 Z= 0.133 Angle : 0.539 9.252 14888 Z= 0.276 Chirality : 0.040 0.200 1637 Planarity : 0.005 0.069 1922 Dihedral : 5.558 88.043 1451 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.86 % Allowed : 11.31 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 2.02 (0.24), residues: 1324 helix: 1.91 (0.17), residues: 888 sheet: -0.03 (0.55), residues: 83 loop : 0.37 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 179 TYR 0.013 0.001 TYR A 250 PHE 0.014 0.001 PHE C 188 TRP 0.029 0.002 TRP F 241 HIS 0.003 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (10998) covalent geometry : angle 0.53305 / 0.28 (14882) hydrogen bonds : bond 0.03675 / 2.41 ( 651) hydrogen bonds : angle 4.15815 / 3.00 ( 1947) metal coordination : bond 0.00717 / 0.35 ( 4) metal coordination : angle 3.98890 / 2.12 ( 6) Misc. bond : bond 0.00091 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.1853 (tpp) cc_final: 0.0654 (tmm) REVERT: B 71 HIS cc_start: 0.7605 (m-70) cc_final: 0.7336 (m-70) REVERT: B 171 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8569 (mp) REVERT: B 179 ARG cc_start: 0.7828 (mtm110) cc_final: 0.7487 (ptp90) REVERT: B 264 ILE cc_start: 0.9467 (mm) cc_final: 0.9228 (mt) REVERT: C 158 ASN cc_start: 0.8436 (t0) cc_final: 0.8019 (t0) REVERT: C 203 PHE cc_start: 0.8232 (m-80) cc_final: 0.7981 (m-80) REVERT: C 226 ILE cc_start: 0.8035 (mm) cc_final: 0.7647 (mt) REVERT: D 1043 LEU cc_start: 0.8183 (mm) cc_final: 0.7790 (tt) REVERT: F 241 TRP cc_start: 0.7932 (t60) cc_final: 0.7708 (t60) outliers start: 22 outliers final: 17 residues processed: 166 average time/residue: 0.0630 time to fit residues: 16.1911 Evaluate side-chains 161 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain G residue 1019 VAL Chi-restraints excluded: chain G residue 1089 LEU Chi-restraints excluded: chain G residue 1100 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 2 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 308 HIS ** F 261 GLN ** 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 = 0.3944 r_free = 0.3944 target = 0.139575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.097273 restraints weight = 20341.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.100321 restraints weight = 10624.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.102044 restraints weight = 7276.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.103206 restraints weight = 5960.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.103447 restraints weight = 5309.517| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11003 Z= 0.170 Angle : 0.564 9.973 14888 Z= 0.289 Chirality : 0.041 0.145 1637 Planarity : 0.005 0.064 1922 Dihedral : 5.579 89.027 1451 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.19 % Allowed : 11.81 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.96 (0.24), residues: 1324 helix: 1.87 (0.18), residues: 888 sheet: -0.07 (0.55), residues: 83 loop : 0.32 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 179 TYR 0.013 0.002 TYR A 250 PHE 0.015 0.001 PHE F 232 TRP 0.025 0.002 TRP F 241 HIS 0.004 0.001 HIS F 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (10998) covalent geometry : angle 0.55797 / 0.29 (14882) hydrogen bonds : bond 0.03805 / 2.49 ( 651) hydrogen bonds : angle 4.20083 / 3.02 ( 1947) metal coordination : bond 0.00986 / 0.49 ( 4) metal coordination : angle 4.05387 / 2.18 ( 6) Misc. bond : bond 0.00128 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.2153 (tpp) cc_final: 0.0878 (tmm) REVERT: A 127 GLN cc_start: 0.6105 (pt0) cc_final: 0.5756 (mm110) REVERT: B 171 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8533 (mp) REVERT: B 264 ILE cc_start: 0.9457 (mm) cc_final: 0.9238 (mt) REVERT: B 284 LYS cc_start: 0.8107 (mmtm) cc_final: 0.7902 (mmtm) REVERT: C 158 ASN cc_start: 0.8461 (t0) cc_final: 0.8077 (t0) REVERT: C 203 PHE cc_start: 0.8219 (m-80) cc_final: 0.7993 (m-80) REVERT: C 226 ILE cc_start: 0.8178 (mm) cc_final: 0.7802 (mt) REVERT: D 1043 LEU cc_start: 0.8119 (mm) cc_final: 0.7790 (tt) REVERT: F 273 ASN cc_start: 0.8350 (m-40) cc_final: 0.7698 (t0) outliers start: 26 outliers final: 21 residues processed: 168 average time/residue: 0.0686 time to fit residues: 17.7109 Evaluate side-chains 167 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 1014 VAL Chi-restraints excluded: chain G residue 1019 VAL Chi-restraints excluded: chain G residue 1089 LEU Chi-restraints excluded: chain G residue 1100 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 126 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 ASN A 331 GLN F 168 HIS ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1027 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.140236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.101531 restraints weight = 20235.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.102006 restraints weight = 10980.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.102492 restraints weight = 8093.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.102684 restraints weight = 7494.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.102945 restraints weight = 7308.960| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11003 Z= 0.142 Angle : 0.556 11.917 14888 Z= 0.285 Chirality : 0.040 0.145 1637 Planarity : 0.005 0.060 1922 Dihedral : 5.543 87.694 1451 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.36 % Allowed : 12.41 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.97 (0.24), residues: 1324 helix: 1.89 (0.18), residues: 887 sheet: -0.10 (0.56), residues: 83 loop : 0.29 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 179 TYR 0.013 0.001 TYR A 250 PHE 0.032 0.001 PHE F 232 TRP 0.055 0.002 TRP F 241 HIS 0.003 0.001 HIS F 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (10998) covalent geometry : angle 0.55093 / 0.29 (14882) hydrogen bonds : bond 0.03738 / 2.46 ( 651) hydrogen bonds : angle 4.16394 / 2.99 ( 1947) metal coordination : bond 0.00592 / 0.30 ( 4) metal coordination : angle 3.61686 / 1.90 ( 6) Misc. bond : bond 0.00093 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.1789 (tpp) cc_final: 0.0585 (tmm) REVERT: A 127 GLN cc_start: 0.5987 (pt0) cc_final: 0.5583 (mm110) REVERT: B 71 HIS cc_start: 0.7674 (m-70) cc_final: 0.7420 (m-70) REVERT: B 171 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8614 (mp) REVERT: B 264 ILE cc_start: 0.9464 (mm) cc_final: 0.9235 (mt) REVERT: C 158 ASN cc_start: 0.8442 (t0) cc_final: 0.8044 (t0) REVERT: C 203 PHE cc_start: 0.8239 (m-80) cc_final: 0.7994 (m-80) REVERT: C 226 ILE cc_start: 0.8071 (mm) cc_final: 0.7701 (mt) REVERT: D 1043 LEU cc_start: 0.8171 (mm) cc_final: 0.7827 (tt) REVERT: F 273 ASN cc_start: 0.8498 (m-40) cc_final: 0.7811 (t0) outliers start: 28 outliers final: 20 residues processed: 171 average time/residue: 0.0734 time to fit residues: 19.6280 Evaluate side-chains 163 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 1019 VAL Chi-restraints excluded: chain G residue 1089 LEU Chi-restraints excluded: chain G residue 1100 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 HIS A 326 ASN F 168 HIS F 238 ASN F 261 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.139912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.102001 restraints weight = 20186.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.101186 restraints weight = 13356.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.102120 restraints weight = 9144.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.102942 restraints weight = 8691.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.102908 restraints weight = 7412.236| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11003 Z= 0.155 Angle : 0.571 12.851 14888 Z= 0.293 Chirality : 0.041 0.147 1637 Planarity : 0.005 0.075 1922 Dihedral : 5.567 87.375 1451 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.94 % Allowed : 12.91 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.91 (0.24), residues: 1324 helix: 1.86 (0.18), residues: 887 sheet: -0.18 (0.55), residues: 83 loop : 0.27 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 179 TYR 0.015 0.002 TYR G1042 PHE 0.023 0.001 PHE F 232 TRP 0.052 0.002 TRP F 241 HIS 0.004 0.001 HIS F 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (10998) covalent geometry : angle 0.56705 / 0.29 (14882) hydrogen bonds : bond 0.03804 / 2.52 ( 651) hydrogen bonds : angle 4.19869 / 3.01 ( 1947) metal coordination : bond 0.00762 / 0.38 ( 4) metal coordination : angle 3.58367 / 1.93 ( 6) Misc. bond : bond 0.00106 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.1915 (tpp) cc_final: 0.0675 (tmm) REVERT: A 125 MET cc_start: 0.4942 (tpt) cc_final: 0.4511 (ptt) REVERT: A 127 GLN cc_start: 0.6099 (pt0) cc_final: 0.5574 (mm110) REVERT: B 171 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8778 (mp) REVERT: B 264 ILE cc_start: 0.9480 (mm) cc_final: 0.9243 (mm) REVERT: B 284 LYS cc_start: 0.8160 (mmtm) cc_final: 0.7919 (mmtm) REVERT: C 158 ASN cc_start: 0.8441 (t0) cc_final: 0.8082 (t0) REVERT: C 203 PHE cc_start: 0.8194 (m-80) cc_final: 0.7957 (m-80) REVERT: C 226 ILE cc_start: 0.8126 (mm) cc_final: 0.7783 (mt) REVERT: D 1043 LEU cc_start: 0.8158 (mm) cc_final: 0.7639 (tt) REVERT: F 195 PHE cc_start: 0.8150 (m-80) cc_final: 0.7928 (m-80) REVERT: F 273 ASN cc_start: 0.8335 (m-40) cc_final: 0.7762 (t0) outliers start: 23 outliers final: 20 residues processed: 158 average time/residue: 0.0796 time to fit residues: 19.6085 Evaluate side-chains 162 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain G residue 1019 VAL Chi-restraints excluded: chain G residue 1089 LEU Chi-restraints excluded: chain G residue 1100 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 15 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 121 optimal weight: 8.9990 chunk 47 optimal weight: 0.0670 chunk 20 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 131 optimal weight: 20.0000 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 HIS A 326 ASN F 168 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.140296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.102077 restraints weight = 20127.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.101546 restraints weight = 13361.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.102120 restraints weight = 9386.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.102629 restraints weight = 8574.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.102806 restraints weight = 7695.941| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11003 Z= 0.140 Angle : 0.592 13.823 14888 Z= 0.301 Chirality : 0.041 0.156 1637 Planarity : 0.006 0.117 1922 Dihedral : 5.595 86.346 1451 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.03 % Allowed : 13.50 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.89 (0.24), residues: 1324 helix: 1.86 (0.18), residues: 884 sheet: -0.15 (0.54), residues: 83 loop : 0.20 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG G1030 TYR 0.018 0.001 TYR G1042 PHE 0.023 0.001 PHE F 232 TRP 0.064 0.002 TRP F 241 HIS 0.003 0.001 HIS C 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (10998) covalent geometry : angle 0.58831 / 0.30 (14882) hydrogen bonds : bond 0.03723 / 2.47 ( 651) hydrogen bonds : angle 4.20036 / 3.01 ( 1947) metal coordination : bond 0.00653 / 0.33 ( 4) metal coordination : angle 3.50169 / 1.88 ( 6) Misc. bond : bond 0.00089 / 0.05 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.1860 (tpp) cc_final: 0.0609 (tmm) REVERT: A 125 MET cc_start: 0.5012 (tpt) cc_final: 0.4495 (ptt) REVERT: A 127 GLN cc_start: 0.6094 (pt0) cc_final: 0.5602 (mm-40) REVERT: B 71 HIS cc_start: 0.7701 (m-70) cc_final: 0.7443 (m-70) REVERT: B 171 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8714 (mp) REVERT: B 264 ILE cc_start: 0.9485 (mm) cc_final: 0.9255 (mt) REVERT: C 158 ASN cc_start: 0.8439 (t0) cc_final: 0.8068 (t0) REVERT: C 226 ILE cc_start: 0.8079 (mm) cc_final: 0.7731 (mt) REVERT: F 195 PHE cc_start: 0.8057 (m-80) cc_final: 0.7839 (m-80) REVERT: F 272 TYR cc_start: 0.8422 (m-80) cc_final: 0.8100 (m-80) REVERT: F 273 ASN cc_start: 0.8345 (m-40) cc_final: 0.7792 (t0) outliers start: 24 outliers final: 21 residues processed: 158 average time/residue: 0.0704 time to fit residues: 17.4561 Evaluate side-chains 162 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 1014 VAL Chi-restraints excluded: chain G residue 1019 VAL Chi-restraints excluded: chain G residue 1089 LEU Chi-restraints excluded: chain G residue 1100 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 42 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 60 optimal weight: 0.0980 chunk 123 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 HIS A 326 ASN F 168 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.140373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.102181 restraints weight = 20332.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.101928 restraints weight = 13248.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.103011 restraints weight = 9333.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.103281 restraints weight = 8220.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.103457 restraints weight = 7454.507| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11003 Z= 0.143 Angle : 0.588 14.782 14888 Z= 0.300 Chirality : 0.041 0.143 1637 Planarity : 0.005 0.072 1922 Dihedral : 5.549 85.725 1451 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.19 % Allowed : 13.42 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.87 (0.24), residues: 1324 helix: 1.84 (0.18), residues: 885 sheet: -0.15 (0.55), residues: 83 loop : 0.19 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 179 TYR 0.013 0.001 TYR A 250 PHE 0.027 0.002 PHE C 112 TRP 0.052 0.002 TRP F 241 HIS 0.004 0.001 HIS C 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (10998) covalent geometry : angle 0.58366 / 0.30 (14882) hydrogen bonds : bond 0.03734 / 2.46 ( 651) hydrogen bonds : angle 4.18563 / 3.00 ( 1947) metal coordination : bond 0.00690 / 0.34 ( 4) metal coordination : angle 3.49941 / 1.89 ( 6) Misc. bond : bond 0.00097 / 0.05 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1646.35 seconds wall clock time: 29 minutes 17.08 seconds (1757.08 seconds total)