Starting phenix.real_space_refine on Tue Jul 29 04:14:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ruc_24702/07_2025/7ruc_24702.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ruc_24702/07_2025/7ruc_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ruc_24702/07_2025/7ruc_24702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ruc_24702/07_2025/7ruc_24702.map" model { file = "/net/cci-nas-00/data/ceres_data/7ruc_24702/07_2025/7ruc_24702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ruc_24702/07_2025/7ruc_24702.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.37, per 1000 atoms: 0.78 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: 3.20 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.10 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: 3.11 Time building geometry restraints manager: 3.72 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: 6045 17.61 - 35.21: 567 35.21 - 52.82: 114 52.82 - 70.43: 28 70.43 - 88.04: 12 Dihedral angle restraints: 6766 sinusoidal: 2838 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 6763 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: 4.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 32.350 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:4.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 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 : 14.647 88.037 4212 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (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 TRP 0.014 0.001 TRP H 96 HIS 0.005 0.001 HIS B 71 PHE 0.018 0.001 PHE B 173 TYR 0.024 0.001 TYR G1098 ARG 0.014 0.001 ARG C 122 Details of bonding type rmsd hydrogen bonds : bond 0.13371 ( 651) hydrogen bonds : angle 6.01354 ( 1947) metal coordination : bond 0.01379 ( 4) metal coordination : angle 4.71418 ( 6) covalent geometry : bond 0.00358 (10998) covalent geometry : angle 0.53281 (14882) Misc. bond : bond 0.83728 ( 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 : 1.254 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 130 MET cc_start: 0.6357 (mmp) cc_final: 0.5529 (mtp) REVERT: A 140 MET cc_start: 0.6098 (mtm) cc_final: 0.5893 (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: 0.7427 (t0) REVERT: B 140 MET cc_start: 0.6634 (mmp) cc_final: 0.6322 (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: 0.7803 (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: 0.7820 (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: 0.2863 time to fit residues: 80.5255 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 : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 34 optimal weight: 0.3980 chunk 67 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 119 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 326 ASN B 54 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.140648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.099247 restraints weight = 20169.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.102039 restraints weight = 10728.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.103981 restraints weight = 7564.746| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11003 Z= 0.155 Angle : 0.592 6.552 14888 Z= 0.308 Chirality : 0.042 0.149 1637 Planarity : 0.005 0.050 1922 Dihedral : 8.472 87.535 1513 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.01 % Allowed : 5.57 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.24), residues: 1324 helix: 2.02 (0.18), residues: 884 sheet: 0.63 (0.63), residues: 67 loop : 0.17 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 132 HIS 0.004 0.001 HIS B 71 PHE 0.016 0.002 PHE C 255 TYR 0.014 0.002 TYR G1042 ARG 0.010 0.001 ARG C 122 Details of bonding type rmsd hydrogen bonds : bond 0.04508 ( 651) hydrogen bonds : angle 4.51872 ( 1947) metal coordination : bond 0.00814 ( 4) metal coordination : angle 3.53103 ( 6) covalent geometry : bond 0.00352 (10998) covalent geometry : angle 0.58832 (14882) Misc. bond : bond 0.01215 ( 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 170 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.2242 (tpp) cc_final: 0.1010 (tmm) REVERT: B 125 MET cc_start: 0.6045 (mmt) cc_final: 0.5813 (tpp) REVERT: C 158 ASN cc_start: 0.8469 (t0) cc_final: 0.8098 (t0) REVERT: C 208 ASN cc_start: 0.8947 (t0) cc_final: 0.8557 (t0) REVERT: C 226 ILE cc_start: 0.8172 (mm) cc_final: 0.7790 (mt) REVERT: D 1027 GLN cc_start: 0.8241 (mm110) cc_final: 0.7678 (tm-30) REVERT: D 1038 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7187 (mt) REVERT: D 1042 TYR cc_start: 0.7574 (t80) cc_final: 0.7309 (t80) REVERT: D 1043 LEU cc_start: 0.8192 (mm) cc_final: 0.7793 (tt) REVERT: F 271 MET cc_start: 0.8165 (mpp) cc_final: 0.7937 (mpp) REVERT: G 1030 ARG cc_start: 0.7520 (mpp80) cc_final: 0.7229 (ptm160) outliers start: 12 outliers final: 7 residues processed: 165 average time/residue: 0.1960 time to fit residues: 48.7887 Evaluate side-chains 141 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 1038 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 78 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 31 optimal weight: 0.1980 chunk 83 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.140555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.102306 restraints weight = 20500.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.103002 restraints weight = 13058.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.102990 restraints weight = 9479.773| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1828 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= 0.145 Angle : 0.547 6.770 14888 Z= 0.283 Chirality : 0.041 0.173 1637 Planarity : 0.005 0.055 1922 Dihedral : 8.006 88.064 1513 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.43 % Allowed : 7.17 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.24), residues: 1324 helix: 1.99 (0.18), residues: 886 sheet: 0.42 (0.60), residues: 72 loop : 0.26 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 132 HIS 0.004 0.001 HIS B 166 PHE 0.013 0.002 PHE C 188 TYR 0.025 0.002 TYR C 275 ARG 0.006 0.000 ARG C 122 Details of bonding type rmsd hydrogen bonds : bond 0.04060 ( 651) hydrogen bonds : angle 4.31471 ( 1947) metal coordination : bond 0.00743 ( 4) metal coordination : angle 3.88739 ( 6) covalent geometry : bond 0.00332 (10998) covalent geometry : angle 0.54155 (14882) Misc. bond : bond 0.00257 ( 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 163 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.2075 (tpp) cc_final: 0.0809 (tmm) REVERT: A 147 ARG cc_start: 0.7112 (ttm110) cc_final: 0.6813 (mtt-85) REVERT: A 297 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9133 (mp) REVERT: B 264 ILE cc_start: 0.9477 (mm) cc_final: 0.9238 (mt) REVERT: C 158 ASN cc_start: 0.8448 (t0) cc_final: 0.8066 (t0) REVERT: C 208 ASN cc_start: 0.8917 (t0) cc_final: 0.8609 (t0) REVERT: C 226 ILE cc_start: 0.8068 (mm) cc_final: 0.7705 (mt) REVERT: C 239 PHE cc_start: 0.8351 (t80) cc_final: 0.8127 (t80) REVERT: C 255 PHE cc_start: 0.8390 (t80) cc_final: 0.7946 (t80) REVERT: D 1038 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7109 (mt) REVERT: D 1043 LEU cc_start: 0.8238 (mm) cc_final: 0.7845 (tt) REVERT: F 208 ASN cc_start: 0.8164 (t0) cc_final: 0.7923 (t0) REVERT: F 269 ASP cc_start: 0.7843 (t0) cc_final: 0.7612 (t0) REVERT: G 1030 ARG cc_start: 0.7769 (mpp80) cc_final: 0.7213 (ptp-170) REVERT: G 1042 TYR cc_start: 0.7498 (t80) cc_final: 0.7188 (t80) outliers start: 17 outliers final: 9 residues processed: 160 average time/residue: 0.2343 time to fit residues: 57.4384 Evaluate side-chains 155 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 1.286 ------------------------------------------------------------------------------- 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 D residue 1038 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 326 ASN F 198 GLN ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.140393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.104532 restraints weight = 20222.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.102689 restraints weight = 13032.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.103209 restraints weight = 10154.164| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2036 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= 0.151 Angle : 0.553 11.139 14888 Z= 0.283 Chirality : 0.041 0.159 1637 Planarity : 0.005 0.048 1922 Dihedral : 7.601 84.217 1513 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.77 % Allowed : 8.95 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.23), residues: 1324 helix: 1.93 (0.18), residues: 882 sheet: 0.40 (0.59), residues: 72 loop : 0.23 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 241 HIS 0.004 0.001 HIS H 106 PHE 0.016 0.001 PHE C 188 TYR 0.013 0.001 TYR A 250 ARG 0.005 0.000 ARG B 179 Details of bonding type rmsd hydrogen bonds : bond 0.03990 ( 651) hydrogen bonds : angle 4.25504 ( 1947) metal coordination : bond 0.00869 ( 4) metal coordination : angle 3.72421 ( 6) covalent geometry : bond 0.00350 (10998) covalent geometry : angle 0.54785 (14882) Misc. bond : bond 0.00121 ( 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: 21 poor density : 152 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.2121 (tpp) cc_final: 0.0833 (tmm) REVERT: A 147 ARG cc_start: 0.7030 (ttm110) cc_final: 0.6820 (mtt-85) REVERT: C 158 ASN cc_start: 0.8451 (t0) cc_final: 0.8076 (t0) REVERT: C 208 ASN cc_start: 0.8867 (t0) cc_final: 0.8621 (t0) REVERT: C 226 ILE cc_start: 0.8124 (mm) cc_final: 0.7743 (mt) REVERT: C 239 PHE cc_start: 0.8397 (t80) cc_final: 0.8185 (t80) REVERT: D 1043 LEU cc_start: 0.8259 (mm) cc_final: 0.7823 (tt) REVERT: F 269 ASP cc_start: 0.7759 (t0) cc_final: 0.6691 (t0) REVERT: F 271 MET cc_start: 0.8128 (mpp) cc_final: 0.7675 (mpp) outliers start: 21 outliers final: 14 residues processed: 167 average time/residue: 0.2027 time to fit residues: 50.6987 Evaluate side-chains 156 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 1.321 ------------------------------------------------------------------------------- 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 157 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 285 MET 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 49 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 16 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 326 ASN B 68 ASN B 331 GLN ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1027 GLN H 106 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.141039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.105088 restraints weight = 20112.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.103555 restraints weight = 12550.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.103593 restraints weight = 11114.000| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11003 Z= 0.139 Angle : 0.552 13.337 14888 Z= 0.283 Chirality : 0.040 0.140 1637 Planarity : 0.005 0.049 1922 Dihedral : 7.195 75.000 1513 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.28 % Allowed : 9.45 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.24), residues: 1324 helix: 1.89 (0.18), residues: 887 sheet: -0.01 (0.54), residues: 83 loop : 0.35 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP F 241 HIS 0.004 0.001 HIS B 166 PHE 0.015 0.001 PHE C 188 TYR 0.013 0.001 TYR A 250 ARG 0.006 0.000 ARG B 179 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 651) hydrogen bonds : angle 4.22259 ( 1947) metal coordination : bond 0.00840 ( 4) metal coordination : angle 3.95585 ( 6) covalent geometry : bond 0.00318 (10998) covalent geometry : angle 0.54651 (14882) Misc. bond : bond 0.00090 ( 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 180 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 1.559 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: 0.0665 (tmm) REVERT: B 71 HIS cc_start: 0.7660 (m-70) cc_final: 0.7351 (m-70) REVERT: B 179 ARG cc_start: 0.7857 (mtm110) cc_final: 0.7503 (ptp90) REVERT: B 264 ILE cc_start: 0.9482 (mm) cc_final: 0.9196 (mm) REVERT: C 158 ASN cc_start: 0.8426 (t0) cc_final: 0.8041 (t0) REVERT: C 208 ASN cc_start: 0.8847 (t0) cc_final: 0.8572 (t0) REVERT: C 226 ILE cc_start: 0.8049 (mm) cc_final: 0.7658 (mt) REVERT: C 239 PHE cc_start: 0.8384 (t80) cc_final: 0.8170 (t80) REVERT: D 1043 LEU cc_start: 0.8264 (mm) cc_final: 0.7828 (tt) outliers start: 27 outliers final: 20 residues processed: 171 average time/residue: 0.1960 time to fit residues: 50.3251 Evaluate side-chains 163 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 F residue 233 VAL Chi-restraints excluded: chain G residue 1089 LEU Chi-restraints excluded: chain G residue 1100 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 121 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 101 optimal weight: 0.0770 chunk 26 optimal weight: 0.5980 chunk 125 optimal weight: 0.3980 chunk 59 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 6 optimal weight: 0.0980 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 0.0870 chunk 63 optimal weight: 1.9990 overall best weight: 0.2516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 326 ASN F 198 GLN ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.142230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.106655 restraints weight = 20356.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.104497 restraints weight = 12855.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.105620 restraints weight = 10306.569| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2411 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= 0.117 Angle : 0.546 12.517 14888 Z= 0.277 Chirality : 0.039 0.138 1637 Planarity : 0.005 0.055 1922 Dihedral : 6.751 65.620 1513 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.60 % Allowed : 10.97 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.24), residues: 1324 helix: 1.92 (0.18), residues: 887 sheet: 0.03 (0.55), residues: 83 loop : 0.40 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP F 241 HIS 0.003 0.001 HIS A 166 PHE 0.015 0.001 PHE C 188 TYR 0.013 0.001 TYR A 250 ARG 0.004 0.000 ARG B 179 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 651) hydrogen bonds : angle 4.15545 ( 1947) metal coordination : bond 0.00429 ( 4) metal coordination : angle 4.10098 ( 6) covalent geometry : bond 0.00252 (10998) covalent geometry : angle 0.53961 (14882) Misc. bond : bond 0.00061 ( 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 177 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.1930 (tpp) cc_final: 0.0702 (tmm) REVERT: A 127 GLN cc_start: 0.5999 (pt0) cc_final: 0.5599 (mm-40) REVERT: B 71 HIS cc_start: 0.7577 (m-70) cc_final: 0.7264 (m-70) REVERT: B 171 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8521 (mp) REVERT: B 179 ARG cc_start: 0.7839 (mtm110) cc_final: 0.7506 (ptp90) REVERT: B 264 ILE cc_start: 0.9464 (mm) cc_final: 0.9182 (mt) REVERT: C 158 ASN cc_start: 0.8419 (t0) cc_final: 0.8040 (t0) REVERT: C 203 PHE cc_start: 0.8127 (m-80) cc_final: 0.7908 (m-80) REVERT: C 208 ASN cc_start: 0.8797 (t0) cc_final: 0.8583 (t0) REVERT: C 226 ILE cc_start: 0.8082 (mm) cc_final: 0.7695 (mt) REVERT: D 1043 LEU cc_start: 0.8247 (mm) cc_final: 0.7838 (tt) outliers start: 19 outliers final: 14 residues processed: 170 average time/residue: 0.2175 time to fit residues: 56.8107 Evaluate side-chains 160 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 1.416 ------------------------------------------------------------------------------- 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 310 VAL Chi-restraints excluded: chain A residue 326 ASN 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 1019 VAL Chi-restraints excluded: chain G residue 1089 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 117 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 308 HIS ** 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 = 0.3914 r_free = 0.3914 target = 0.137722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.094920 restraints weight = 20565.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.097980 restraints weight = 10946.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.099816 restraints weight = 7547.025| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 11003 Z= 0.266 Angle : 0.640 13.379 14888 Z= 0.330 Chirality : 0.044 0.145 1637 Planarity : 0.005 0.075 1922 Dihedral : 7.242 74.776 1513 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.36 % Allowed : 11.81 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.23), residues: 1324 helix: 1.67 (0.17), residues: 883 sheet: -0.30 (0.54), residues: 80 loop : 0.19 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP F 241 HIS 0.007 0.002 HIS F 165 PHE 0.018 0.002 PHE F 232 TYR 0.016 0.002 TYR A 250 ARG 0.006 0.001 ARG C 122 Details of bonding type rmsd hydrogen bonds : bond 0.04384 ( 651) hydrogen bonds : angle 4.41211 ( 1947) metal coordination : bond 0.01461 ( 4) metal coordination : angle 3.60351 ( 6) covalent geometry : bond 0.00635 (10998) covalent geometry : angle 0.63599 (14882) Misc. bond : bond 0.00185 ( 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 176 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.2027 (tpp) cc_final: 0.0822 (tmm) REVERT: A 127 GLN cc_start: 0.6153 (pt0) cc_final: 0.5674 (mm110) REVERT: B 171 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8730 (mp) REVERT: B 264 ILE cc_start: 0.9480 (mm) cc_final: 0.9253 (mm) REVERT: C 158 ASN cc_start: 0.8485 (t0) cc_final: 0.8132 (t0) REVERT: C 226 ILE cc_start: 0.8170 (mm) cc_final: 0.7792 (mt) REVERT: D 1043 LEU cc_start: 0.8218 (mm) cc_final: 0.7833 (tt) outliers start: 28 outliers final: 23 residues processed: 166 average time/residue: 0.1875 time to fit residues: 47.9034 Evaluate side-chains 164 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 1.303 ------------------------------------------------------------------------------- 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 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 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 C residue 60 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 282 LEU 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 17 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN A 331 GLN F 238 ASN ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.140405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.098216 restraints weight = 20308.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.101312 restraints weight = 10726.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.103151 restraints weight = 7346.886| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2625 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= 0.143 Angle : 0.583 14.448 14888 Z= 0.298 Chirality : 0.041 0.161 1637 Planarity : 0.005 0.070 1922 Dihedral : 6.713 63.321 1513 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.36 % Allowed : 13.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.24), residues: 1324 helix: 1.78 (0.18), residues: 886 sheet: -0.10 (0.55), residues: 78 loop : 0.20 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP F 241 HIS 0.003 0.001 HIS F 168 PHE 0.020 0.001 PHE F 232 TYR 0.014 0.001 TYR A 250 ARG 0.004 0.000 ARG B 179 Details of bonding type rmsd hydrogen bonds : bond 0.03891 ( 651) hydrogen bonds : angle 4.22060 ( 1947) metal coordination : bond 0.00726 ( 4) metal coordination : angle 3.13747 ( 6) covalent geometry : bond 0.00326 (10998) covalent geometry : angle 0.57940 (14882) Misc. bond : bond 0.00122 ( 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 172 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.2063 (tpp) cc_final: 0.0788 (tmm) REVERT: A 125 MET cc_start: 0.4617 (tpt) cc_final: 0.4279 (ptt) REVERT: A 127 GLN cc_start: 0.6134 (pt0) cc_final: 0.5740 (mm110) REVERT: B 71 HIS cc_start: 0.7615 (m-70) cc_final: 0.7285 (m-70) REVERT: B 171 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8683 (mp) REVERT: B 264 ILE cc_start: 0.9475 (mm) cc_final: 0.9225 (mt) REVERT: C 158 ASN cc_start: 0.8475 (t0) cc_final: 0.8116 (t0) REVERT: C 203 PHE cc_start: 0.8195 (m-80) cc_final: 0.7980 (m-80) REVERT: C 226 ILE cc_start: 0.8187 (mm) cc_final: 0.7817 (mt) REVERT: D 1043 LEU cc_start: 0.8163 (mm) cc_final: 0.7635 (tt) REVERT: F 194 MET cc_start: 0.7651 (ttp) cc_final: 0.7397 (ttp) outliers start: 28 outliers final: 22 residues processed: 159 average time/residue: 0.1936 time to fit residues: 47.0629 Evaluate side-chains 160 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 1.272 ------------------------------------------------------------------------------- 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 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 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 F residue 244 LEU Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 282 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 16 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 0.0770 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN ** 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 = 0.3953 r_free = 0.3953 target = 0.140587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.098879 restraints weight = 20422.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.101911 restraints weight = 10872.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.103757 restraints weight = 7448.420| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2763 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= 0.144 Angle : 0.598 12.880 14888 Z= 0.304 Chirality : 0.041 0.140 1637 Planarity : 0.005 0.071 1922 Dihedral : 6.630 62.348 1513 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.36 % Allowed : 13.42 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.24), residues: 1324 helix: 1.77 (0.18), residues: 884 sheet: -0.33 (0.53), residues: 83 loop : 0.20 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP F 241 HIS 0.003 0.001 HIS C 223 PHE 0.025 0.001 PHE F 232 TYR 0.013 0.001 TYR F 272 ARG 0.004 0.000 ARG C 122 Details of bonding type rmsd hydrogen bonds : bond 0.03871 ( 651) hydrogen bonds : angle 4.22163 ( 1947) metal coordination : bond 0.00693 ( 4) metal coordination : angle 3.60687 ( 6) covalent geometry : bond 0.00332 (10998) covalent geometry : angle 0.59414 (14882) Misc. bond : bond 0.00107 ( 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 171 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.2070 (tpp) cc_final: 0.0776 (tmm) REVERT: A 127 GLN cc_start: 0.6180 (pt0) cc_final: 0.5783 (mm110) REVERT: B 71 HIS cc_start: 0.7731 (m-70) cc_final: 0.7362 (m-70) REVERT: B 171 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8728 (mp) REVERT: B 264 ILE cc_start: 0.9471 (mm) cc_final: 0.9227 (mt) REVERT: C 91 GLU cc_start: 0.8323 (mm-30) cc_final: 0.8108 (mm-30) REVERT: C 158 ASN cc_start: 0.8455 (t0) cc_final: 0.8064 (t0) REVERT: C 203 PHE cc_start: 0.8185 (m-80) cc_final: 0.7978 (m-80) REVERT: C 226 ILE cc_start: 0.8174 (mm) cc_final: 0.7819 (mt) REVERT: F 164 TYR cc_start: 0.8751 (t80) cc_final: 0.8334 (t80) outliers start: 28 outliers final: 21 residues processed: 159 average time/residue: 0.1874 time to fit residues: 45.8907 Evaluate side-chains 160 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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 241 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 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 310 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain F residue 244 LEU 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 32 optimal weight: 0.0470 chunk 2 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 129 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN F 261 GLN G1027 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.140988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.103199 restraints weight = 20402.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.103654 restraints weight = 10915.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.104088 restraints weight = 8662.598| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2853 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= 0.138 Angle : 0.608 14.548 14888 Z= 0.308 Chirality : 0.041 0.252 1637 Planarity : 0.005 0.086 1922 Dihedral : 6.505 61.872 1513 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.19 % Allowed : 14.18 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.24), residues: 1324 helix: 1.77 (0.18), residues: 883 sheet: -0.35 (0.54), residues: 83 loop : 0.18 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP F 241 HIS 0.003 0.001 HIS C 223 PHE 0.020 0.001 PHE F 232 TYR 0.014 0.001 TYR F 272 ARG 0.020 0.000 ARG G1030 Details of bonding type rmsd hydrogen bonds : bond 0.03794 ( 651) hydrogen bonds : angle 4.21313 ( 1947) metal coordination : bond 0.00605 ( 4) metal coordination : angle 3.47986 ( 6) covalent geometry : bond 0.00316 (10998) covalent geometry : angle 0.60455 (14882) Misc. bond : bond 0.00096 ( 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 166 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.1773 (tpp) cc_final: 0.0581 (tmm) REVERT: A 127 GLN cc_start: 0.6138 (pt0) cc_final: 0.5635 (mm110) REVERT: B 71 HIS cc_start: 0.7723 (m-70) cc_final: 0.7371 (m-70) REVERT: B 171 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8755 (mp) REVERT: B 264 ILE cc_start: 0.9495 (mm) cc_final: 0.9229 (mt) REVERT: C 158 ASN cc_start: 0.8461 (t0) cc_final: 0.8072 (t0) REVERT: C 203 PHE cc_start: 0.8184 (m-80) cc_final: 0.7942 (m-80) REVERT: C 226 ILE cc_start: 0.8055 (mm) cc_final: 0.7713 (mt) REVERT: F 195 PHE cc_start: 0.8087 (m-80) cc_final: 0.7810 (m-80) REVERT: G 1027 GLN cc_start: 0.7948 (mm110) cc_final: 0.7650 (mm110) REVERT: G 1042 TYR cc_start: 0.7712 (t80) cc_final: 0.7202 (t80) outliers start: 26 outliers final: 23 residues processed: 155 average time/residue: 0.2606 time to fit residues: 62.5907 Evaluate side-chains 160 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 1.359 ------------------------------------------------------------------------------- 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 241 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 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 285 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain F residue 276 LEU 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 82 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 60 optimal weight: 0.0470 chunk 47 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.140698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.103776 restraints weight = 20198.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.103643 restraints weight = 13098.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.103664 restraints weight = 10230.526| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11003 Z= 0.144 Angle : 0.604 14.662 14888 Z= 0.306 Chirality : 0.041 0.241 1637 Planarity : 0.005 0.070 1922 Dihedral : 6.452 61.914 1513 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.28 % Allowed : 14.01 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.24), residues: 1324 helix: 1.78 (0.18), residues: 884 sheet: -0.35 (0.54), residues: 83 loop : 0.17 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP F 241 HIS 0.004 0.001 HIS C 223 PHE 0.018 0.001 PHE F 232 TYR 0.015 0.001 TYR G1042 ARG 0.003 0.000 ARG C 122 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 651) hydrogen bonds : angle 4.20115 ( 1947) metal coordination : bond 0.00691 ( 4) metal coordination : angle 3.45477 ( 6) covalent geometry : bond 0.00334 (10998) covalent geometry : angle 0.59996 (14882) Misc. bond : bond 0.00108 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3916.64 seconds wall clock time: 70 minutes 37.15 seconds (4237.15 seconds total)