Starting phenix.real_space_refine on Fri Jul 3 02:51:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rua_24701/07_2026/7rua_24701.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rua_24701/07_2026/7rua_24701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rua_24701/07_2026/7rua_24701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rua_24701/07_2026/7rua_24701.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7rua_24701/07_2026/7rua_24701.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rua_24701/07_2026/7rua_24701.cif" model { file = "/net/cci-nas-00/data/ceres_data/7rua_24701/07_2026/7rua_24701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rua_24701/07_2026/7rua_24701.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 6 5.49 5 Mg 2 5.21 5 S 64 5.16 5 C 7350 2.51 5 N 1992 2.21 5 O 2188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11603 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" 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: "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: 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: "E" 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: "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: 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} Chain: "B" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1947 SG CYS A 283 54.502 65.935 97.337 1.00 99.40 S ATOM 1970 SG CYS A 286 55.392 68.382 94.693 1.00 92.44 S ATOM 4359 SG CYS B 283 52.748 69.358 97.346 1.00 99.64 S ATOM 4382 SG CYS B 286 51.857 66.912 94.703 1.00 92.38 S Time building chain proxies: 2.71, per 1000 atoms: 0.23 Number of scatterers: 11603 At special positions: 0 Unit cell: (108.075, 136.125, 112.2, 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 2188 8.00 N 1992 7.00 C 7350 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=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 561.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 403 " pdb="ZN ZN A 403 " - pdb=" SG CYS B 286 " pdb="ZN ZN A 403 " - pdb=" SG CYS A 286 " pdb="ZN ZN A 403 " - pdb=" SG CYS A 283 " pdb="ZN ZN A 403 " - pdb=" SG CYS B 283 " Number of angles added : 6 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2760 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 2 sheets defined 71.4% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 22 through 28 Processing helix chain 'A' and resid 43 through 57 removed outlier: 3.534A 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 133 removed outlier: 4.177A pdb=" N MET A 130 " --> pdb=" O MET A 126 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 3.837A 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 211 through 232 removed outlier: 4.382A pdb=" N LYS A 215 " --> pdb=" O GLN A 211 " (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: 3.546A pdb=" N GLN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 28 Processing helix chain 'B' and resid 43 through 57 removed outlier: 3.534A 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 133 removed outlier: 4.178A pdb=" N MET B 130 " --> pdb=" O MET B 126 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER B 131 " --> pdb=" O GLN B 127 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 152 Processing helix chain 'B' and resid 163 through 187 Proline residue: B 174 - end of helix Processing helix chain 'B' and resid 211 through 232 removed outlier: 4.383A 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: 3.546A pdb=" N GLN B 331 " --> pdb=" O THR B 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 37 removed outlier: 3.619A 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 97 Processing helix chain 'C' and resid 101 through 115 Processing helix chain 'C' and resid 119 through 133 removed outlier: 4.382A pdb=" N VAL C 123 " --> pdb=" O SER C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 157 removed outlier: 3.739A pdb=" N HIS C 146 " --> pdb=" O HIS C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 169 Processing helix chain 'C' and resid 172 through 186 Processing helix chain 'C' and resid 191 through 206 removed outlier: 3.821A 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 268 through 270 No H-bonds generated for 'chain 'C' and resid 268 through 270' Processing helix chain 'C' and resid 271 through 284 Processing helix chain 'D' and resid 1009 through 1014 removed outlier: 4.320A pdb=" N ALA D1013 " --> pdb=" O PRO D1009 " (cutoff:3.500A) removed outlier: 3.749A 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 1032 removed outlier: 3.535A pdb=" N GLN D1023 " --> pdb=" O VAL D1019 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS D1031 " --> pdb=" O GLN D1027 " (cutoff:3.500A) Processing helix chain 'D' and resid 1039 through 1044 Processing helix chain 'D' and resid 1062 through 1075 Processing helix chain 'D' and resid 1081 through 1088 Processing helix chain 'D' and resid 1092 through 1113 removed outlier: 4.199A pdb=" N TYR D1098 " --> pdb=" O VAL D1094 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 104 Processing helix chain 'E' and resid 108 through 129 Processing helix chain 'E' and resid 131 through 140 Processing helix chain 'F' and resid 20 through 37 removed outlier: 3.619A pdb=" N GLN F 24 " --> pdb=" O ARG F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 56 Processing helix chain 'F' and resid 58 through 76 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: 4.381A pdb=" N VAL F 123 " --> pdb=" O SER F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 157 removed outlier: 3.738A 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 186 Processing helix chain 'F' and resid 191 through 206 removed outlier: 3.821A pdb=" N VAL F 196 " --> pdb=" O VAL F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 223 Processing helix chain 'F' and resid 234 through 250 Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 262 through 267 Processing helix chain 'F' and resid 268 through 270 No H-bonds generated for 'chain 'F' and resid 268 through 270' Processing helix chain 'F' and resid 271 through 284 Processing helix chain 'G' and resid 1009 through 1014 removed outlier: 4.320A pdb=" N ALA G1013 " --> pdb=" O PRO G1009 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL G1014 " --> pdb=" O TRP G1010 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1009 through 1014' Processing helix chain 'G' and resid 1015 through 1017 No H-bonds generated for 'chain 'G' and resid 1015 through 1017' Processing helix chain 'G' and resid 1018 through 1032 removed outlier: 3.534A pdb=" N GLN G1023 " --> pdb=" O VAL G1019 " (cutoff:3.500A) removed outlier: 3.692A 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 1057 through 1070 Processing helix chain 'G' and resid 1076 through 1083 Processing helix chain 'G' and resid 1087 through 1108 removed outlier: 4.199A pdb=" N TYR G1093 " --> pdb=" O VAL G1089 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 104 Processing helix chain 'H' and resid 108 through 129 Processing helix chain 'H' and resid 131 through 140 Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87 removed outlier: 6.533A pdb=" N VAL A 62 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N MET A 97 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE A 64 " --> pdb=" O MET A 97 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU A 63 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ASP A 160 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE A 65 " --> pdb=" O ASP A 160 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE A 34 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TRP A 33 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE A 239 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N PHE A 35 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL A 241 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLY A 37 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N ILE A 243 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ASN A 268 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS A 240 " --> pdb=" O ASN A 268 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE A 269 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU A 312 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 6.497A 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: 6.534A pdb=" N VAL B 62 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N MET B 97 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE B 64 " --> pdb=" O MET B 97 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU B 63 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ASP B 160 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE B 65 " --> pdb=" O ASP B 160 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE B 34 " --> pdb=" O PHE B 159 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP B 33 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE B 239 " --> pdb=" O TRP B 33 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N PHE B 35 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL B 241 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLY B 37 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N ILE B 243 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ASN B 268 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS B 240 " --> pdb=" O ASN B 268 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE B 269 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU B 312 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL B 271 " --> pdb=" O LEU B 312 " (cutoff:3.500A) 718 hydrogen bonds defined for protein. 2148 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.71 Time building geometry restraints manager: 1.33 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: 3821 1.34 - 1.46: 2330 1.46 - 1.58: 5577 1.58 - 1.70: 10 1.70 - 1.82: 106 Bond restraints: 11844 Sorted by residual: bond pdb=" CA VAL D1019 " pdb=" CB VAL D1019 " ideal model delta sigma weight residual 1.539 1.544 -0.005 5.40e-03 3.43e+04 7.45e-01 bond pdb=" C1' ATP B 401 " pdb=" C2' ATP B 401 " ideal model delta sigma weight residual 1.531 1.521 0.010 1.20e-02 6.94e+03 6.72e-01 bond pdb=" CD ARG D1030 " pdb=" NE ARG D1030 " ideal model delta sigma weight residual 1.458 1.447 0.011 1.40e-02 5.10e+03 6.67e-01 bond pdb=" CD ARG G1030 " pdb=" NE ARG G1030 " ideal model delta sigma weight residual 1.458 1.447 0.011 1.40e-02 5.10e+03 6.67e-01 bond pdb=" CA VAL G1019 " pdb=" CB VAL G1019 " ideal model delta sigma weight residual 1.539 1.543 -0.004 5.40e-03 3.43e+04 6.44e-01 ... (remaining 11839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 15519 1.34 - 2.68: 372 2.68 - 4.02: 99 4.02 - 5.36: 22 5.36 - 6.70: 8 Bond angle restraints: 16020 Sorted by residual: angle pdb=" NE ARG A 224 " pdb=" CZ ARG A 224 " pdb=" NH2 ARG A 224 " ideal model delta sigma weight residual 119.20 121.62 -2.42 9.00e-01 1.23e+00 7.22e+00 angle pdb=" NE ARG B 224 " pdb=" CZ ARG B 224 " pdb=" NH2 ARG B 224 " ideal model delta sigma weight residual 119.20 121.59 -2.39 9.00e-01 1.23e+00 7.07e+00 angle pdb=" C ARG G1094 " pdb=" N GLN G1095 " pdb=" CA GLN G1095 " ideal model delta sigma weight residual 120.72 116.53 4.19 1.67e+00 3.59e-01 6.30e+00 angle pdb=" C ARG D1099 " pdb=" N GLN D1100 " pdb=" CA GLN D1100 " ideal model delta sigma weight residual 120.72 116.54 4.18 1.67e+00 3.59e-01 6.27e+00 angle pdb=" C1' ATP B 401 " pdb=" C2' ATP B 401 " pdb=" O2' ATP B 401 " ideal model delta sigma weight residual 110.58 103.88 6.70 2.79e+00 1.28e-01 5.76e+00 ... (remaining 16015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 6458 17.58 - 35.15: 644 35.15 - 52.73: 108 52.73 - 70.31: 28 70.31 - 87.89: 10 Dihedral angle restraints: 7248 sinusoidal: 3010 harmonic: 4238 Sorted by residual: dihedral pdb=" CA SER F 137 " pdb=" C SER F 137 " pdb=" N GLY F 138 " pdb=" CA GLY F 138 " ideal model delta harmonic sigma weight residual 180.00 161.03 18.97 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA SER C 137 " pdb=" C SER C 137 " pdb=" N GLY C 138 " pdb=" CA GLY C 138 " ideal model delta harmonic sigma weight residual 180.00 161.05 18.95 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CD ARG A 224 " pdb=" NE ARG A 224 " pdb=" CZ ARG A 224 " pdb=" NH1 ARG A 224 " ideal model delta sinusoidal sigma weight residual 0.00 -26.87 26.87 1 1.00e+01 1.00e-02 1.04e+01 ... (remaining 7245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1568 0.059 - 0.118: 184 0.118 - 0.177: 8 0.177 - 0.236: 2 0.236 - 0.295: 4 Chirality restraints: 1766 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 -2.97 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C2' ATP B 401 " pdb=" C1' ATP B 401 " pdb=" C3' ATP B 401 " pdb=" O2' ATP B 401 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.10e+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 -2.91 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 1763 not shown) Planarity restraints: 2072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 224 " -0.444 9.50e-02 1.11e+02 1.99e-01 2.51e+01 pdb=" NE ARG A 224 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 224 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 224 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 224 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 224 " 0.443 9.50e-02 1.11e+02 1.99e-01 2.50e+01 pdb=" NE ARG B 224 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG B 224 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 224 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B 224 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G1051 " -0.186 9.50e-02 1.11e+02 8.36e-02 4.41e+00 pdb=" NE ARG G1051 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG G1051 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG G1051 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG G1051 " -0.005 2.00e-02 2.50e+03 ... (remaining 2069 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 103 2.52 - 3.11: 9791 3.11 - 3.71: 19541 3.71 - 4.30: 26422 4.30 - 4.90: 43337 Nonbonded interactions: 99194 Sorted by model distance: nonbonded pdb=" O2G ATP A 401 " pdb="MG MG A 402 " model vdw 1.920 2.170 nonbonded pdb=" O2G ATP B 401 " pdb="MG MG B 402 " model vdw 1.921 2.170 nonbonded pdb=" OE1 GLU A 245 " pdb=" O3' ATP B 401 " model vdw 1.944 3.040 nonbonded pdb=" OE1 GLU B 245 " pdb=" O3' ATP A 401 " model vdw 1.946 3.040 nonbonded pdb=" OG1 THR B 45 " pdb="MG MG B 402 " model vdw 1.962 2.170 ... (remaining 99189 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 402) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'H' } 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 individual isotropic 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: 4.530 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.620 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 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 : 0.003 0.030 11848 Z= 0.147 Angle : 0.568 6.704 16026 Z= 0.294 Chirality : 0.040 0.295 1766 Planarity : 0.008 0.199 2072 Dihedral : 14.349 87.887 4488 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.23), residues: 1424 helix: 1.68 (0.17), residues: 944 sheet: 0.12 (0.61), residues: 82 loop : 0.34 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 224 TYR 0.011 0.001 TYR A 250 PHE 0.009 0.001 PHE B 328 TRP 0.009 0.001 TRP E 96 HIS 0.007 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (11844) covalent geometry : angle 0.56579 / 0.29 (16020) hydrogen bonds : bond 0.13505 / 9.23 ( 718) hydrogen bonds : angle 5.61979 / 3.95 ( 2148) metal coordination : bond 0.00091 / 0.05 ( 4) metal coordination : angle 2.84458 / 1.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 118 MET cc_start: 0.2998 (mmt) cc_final: 0.2504 (mmm) REVERT: A 121 MET cc_start: 0.1612 (mtt) cc_final: 0.1236 (ptp) REVERT: A 126 MET cc_start: 0.4497 (ttt) cc_final: 0.4144 (tmm) REVERT: A 281 ARG cc_start: 0.6460 (ptm160) cc_final: 0.6199 (ptp-170) REVERT: A 287 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7442 (mt-10) REVERT: B 89 LYS cc_start: 0.8138 (ttmm) cc_final: 0.7540 (mtmt) REVERT: B 118 MET cc_start: 0.3322 (mmt) cc_final: 0.2810 (mmm) REVERT: B 121 MET cc_start: 0.1677 (mtt) cc_final: 0.1370 (ptp) REVERT: B 126 MET cc_start: 0.4622 (ttt) cc_final: 0.4198 (tmm) REVERT: B 281 ARG cc_start: 0.6445 (ptm160) cc_final: 0.6183 (ptp-170) REVERT: B 287 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7434 (mt-10) REVERT: C 27 GLU cc_start: 0.7266 (tt0) cc_final: 0.6906 (mt-10) REVERT: C 36 LYS cc_start: 0.8199 (mtpp) cc_final: 0.7983 (ttpt) REVERT: C 66 MET cc_start: 0.8502 (mmm) cc_final: 0.8278 (mmm) REVERT: C 128 ARG cc_start: 0.7385 (mmm-85) cc_final: 0.7124 (mtp180) REVERT: C 238 ASN cc_start: 0.7991 (m-40) cc_final: 0.7717 (m110) REVERT: C 258 LEU cc_start: 0.7103 (mm) cc_final: 0.6854 (mt) REVERT: C 260 GLU cc_start: 0.8121 (tp30) cc_final: 0.7812 (tm-30) REVERT: D 1042 TYR cc_start: 0.7344 (t80) cc_final: 0.7132 (t80) REVERT: F 27 GLU cc_start: 0.7259 (tt0) cc_final: 0.6905 (mt-10) REVERT: F 36 LYS cc_start: 0.8206 (mtpp) cc_final: 0.7993 (ttpt) REVERT: F 66 MET cc_start: 0.8500 (mmm) cc_final: 0.8259 (mmp) REVERT: F 128 ARG cc_start: 0.7408 (mmm-85) cc_final: 0.7116 (mtp180) REVERT: F 238 ASN cc_start: 0.8020 (m-40) cc_final: 0.7734 (m110) REVERT: F 255 PHE cc_start: 0.8342 (t80) cc_final: 0.8094 (t80) REVERT: F 260 GLU cc_start: 0.8140 (tp30) cc_final: 0.7744 (tm-30) REVERT: G 1042 TYR cc_start: 0.7279 (t80) cc_final: 0.6991 (t80) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.1128 time to fit residues: 42.4206 Evaluate side-chains 179 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 54 GLN ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 GLN ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1023 GLN D1024 GLN D1027 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.180276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.139238 restraints weight = 16768.788| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.95 r_work: 0.3385 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11848 Z= 0.162 Angle : 0.631 10.636 16026 Z= 0.322 Chirality : 0.042 0.147 1766 Planarity : 0.005 0.056 2072 Dihedral : 5.443 74.891 1568 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.72 % Allowed : 8.62 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.22), residues: 1424 helix: 1.90 (0.17), residues: 976 sheet: -0.24 (0.59), residues: 74 loop : 0.34 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 267 TYR 0.026 0.002 TYR C 272 PHE 0.024 0.002 PHE C 232 TRP 0.010 0.002 TRP F 241 HIS 0.007 0.002 HIS E 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (11844) covalent geometry : angle 0.62679 / 0.32 (16020) hydrogen bonds : bond 0.04469 / 3.00 ( 718) hydrogen bonds : angle 4.40010 / 3.11 ( 2148) metal coordination : bond 0.00253 / 0.13 ( 4) metal coordination : angle 3.70751 / 1.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 198 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8773 (tptt) cc_final: 0.8425 (mtmt) REVERT: A 118 MET cc_start: 0.3219 (mmt) cc_final: 0.2722 (mpp) REVERT: A 121 MET cc_start: 0.1743 (mtt) cc_final: 0.1270 (ptt) REVERT: A 126 MET cc_start: 0.5925 (ttt) cc_final: 0.4951 (tmm) REVERT: A 128 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7055 (pt0) REVERT: A 281 ARG cc_start: 0.6787 (ptm160) cc_final: 0.6530 (ptp-170) REVERT: B 89 LYS cc_start: 0.8481 (ttmm) cc_final: 0.8170 (mttt) REVERT: B 118 MET cc_start: 0.3473 (mmt) cc_final: 0.2995 (mpp) REVERT: B 121 MET cc_start: 0.2143 (mtt) cc_final: 0.1718 (ptt) REVERT: B 126 MET cc_start: 0.5834 (ttt) cc_final: 0.4844 (tmm) REVERT: B 179 ARG cc_start: 0.7251 (mtm110) cc_final: 0.6921 (ttt-90) REVERT: B 281 ARG cc_start: 0.6784 (ptm160) cc_final: 0.6542 (ptp-170) REVERT: C 36 LYS cc_start: 0.8773 (mtpp) cc_final: 0.8503 (ttmt) REVERT: C 103 GLU cc_start: 0.7322 (pm20) cc_final: 0.7098 (pm20) REVERT: C 238 ASN cc_start: 0.8103 (m-40) cc_final: 0.7566 (m110) REVERT: C 271 MET cc_start: 0.6646 (mtt) cc_final: 0.6273 (mmp) REVERT: D 1042 TYR cc_start: 0.8027 (t80) cc_final: 0.7350 (t80) REVERT: F 36 LYS cc_start: 0.8771 (mtpp) cc_final: 0.8527 (ttmt) REVERT: F 103 GLU cc_start: 0.7338 (pm20) cc_final: 0.7120 (pm20) REVERT: F 238 ASN cc_start: 0.8081 (m-40) cc_final: 0.7516 (m110) REVERT: F 255 PHE cc_start: 0.8411 (t80) cc_final: 0.8191 (t80) REVERT: F 271 MET cc_start: 0.6832 (mtt) cc_final: 0.6410 (mmp) REVERT: G 1042 TYR cc_start: 0.7973 (t80) cc_final: 0.7477 (t80) outliers start: 22 outliers final: 10 residues processed: 210 average time/residue: 0.1034 time to fit residues: 31.1929 Evaluate side-chains 175 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 165 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain D residue 1023 GLN Chi-restraints excluded: chain G residue 1028 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 2 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 141 optimal weight: 20.0000 chunk 70 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 58 optimal weight: 0.4980 chunk 50 optimal weight: 0.3980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 HIS A 299 GLN B 267 HIS ** G1095 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 = 0.4172 r_free = 0.4172 target = 0.180256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.140264 restraints weight = 16955.442| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.02 r_work: 0.3364 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11848 Z= 0.151 Angle : 0.565 6.546 16026 Z= 0.293 Chirality : 0.040 0.140 1766 Planarity : 0.005 0.057 2072 Dihedral : 5.430 73.293 1568 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.80 % Allowed : 10.89 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.22), residues: 1424 helix: 1.85 (0.16), residues: 976 sheet: -0.83 (0.55), residues: 76 loop : 0.23 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 263 TYR 0.020 0.002 TYR A 336 PHE 0.014 0.001 PHE C 239 TRP 0.014 0.002 TRP F 241 HIS 0.005 0.001 HIS E 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (11844) covalent geometry : angle 0.56107 / 0.29 (16020) hydrogen bonds : bond 0.04196 / 2.79 ( 718) hydrogen bonds : angle 4.22750 / 2.99 ( 2148) metal coordination : bond 0.00086 / 0.04 ( 4) metal coordination : angle 3.65546 / 1.95 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8859 (tptt) cc_final: 0.8479 (mtmt) REVERT: A 118 MET cc_start: 0.3291 (mmt) cc_final: 0.2659 (mpp) REVERT: A 121 MET cc_start: 0.1931 (mtt) cc_final: 0.1427 (ptt) REVERT: A 126 MET cc_start: 0.5947 (ttt) cc_final: 0.5119 (tmm) REVERT: A 128 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7041 (pt0) REVERT: A 157 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8505 (t) REVERT: A 281 ARG cc_start: 0.6914 (ptm160) cc_final: 0.6676 (ptp-170) REVERT: B 78 ASP cc_start: 0.8290 (t0) cc_final: 0.8045 (m-30) REVERT: B 89 LYS cc_start: 0.8601 (ttmm) cc_final: 0.8341 (mtmt) REVERT: B 118 MET cc_start: 0.3345 (mmt) cc_final: 0.2780 (mpp) REVERT: B 121 MET cc_start: 0.1859 (mtt) cc_final: 0.1465 (ptt) REVERT: B 126 MET cc_start: 0.6021 (ttt) cc_final: 0.5029 (tmm) REVERT: B 128 GLU cc_start: 0.7550 (mm-30) cc_final: 0.6946 (pt0) REVERT: B 179 ARG cc_start: 0.7292 (mtm110) cc_final: 0.6874 (ttt-90) REVERT: B 281 ARG cc_start: 0.6904 (ptm160) cc_final: 0.6679 (ptp-170) REVERT: B 306 ASP cc_start: 0.6979 (t70) cc_final: 0.6584 (m-30) REVERT: C 36 LYS cc_start: 0.8797 (mtpp) cc_final: 0.8507 (ttmt) REVERT: C 238 ASN cc_start: 0.8066 (m-40) cc_final: 0.7485 (m110) REVERT: C 277 ASP cc_start: 0.7747 (t70) cc_final: 0.7382 (t0) REVERT: D 1024 GLN cc_start: 0.7019 (OUTLIER) cc_final: 0.6236 (tp-100) REVERT: D 1042 TYR cc_start: 0.7963 (t80) cc_final: 0.7484 (t80) REVERT: F 36 LYS cc_start: 0.8793 (mtpp) cc_final: 0.8528 (ttmt) REVERT: F 238 ASN cc_start: 0.8123 (m-40) cc_final: 0.7526 (m110) REVERT: F 251 LYS cc_start: 0.7214 (mptt) cc_final: 0.6939 (mmtp) REVERT: F 271 MET cc_start: 0.6784 (mtt) cc_final: 0.6468 (mmp) REVERT: F 277 ASP cc_start: 0.7763 (t70) cc_final: 0.7439 (t0) REVERT: G 1026 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7830 (tp) REVERT: G 1042 TYR cc_start: 0.7970 (t80) cc_final: 0.7631 (t80) outliers start: 23 outliers final: 18 residues processed: 188 average time/residue: 0.0979 time to fit residues: 26.8684 Evaluate side-chains 180 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 1023 GLN Chi-restraints excluded: chain D residue 1024 GLN Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 1026 ILE Chi-restraints excluded: chain G residue 1044 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 116 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 30.0000 chunk 109 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 58 optimal weight: 0.0970 chunk 53 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 GLN G1027 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.179650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.138414 restraints weight = 16812.579| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.33 r_work: 0.3334 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11848 Z= 0.139 Angle : 0.555 11.073 16026 Z= 0.283 Chirality : 0.040 0.137 1766 Planarity : 0.005 0.061 2072 Dihedral : 5.384 73.367 1568 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.74 % Allowed : 10.03 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.22), residues: 1424 helix: 1.84 (0.16), residues: 976 sheet: -1.13 (0.52), residues: 76 loop : 0.10 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 52 TYR 0.020 0.002 TYR B 336 PHE 0.019 0.001 PHE C 255 TRP 0.013 0.001 TRP F 241 HIS 0.005 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (11844) covalent geometry : angle 0.55049 / 0.28 (16020) hydrogen bonds : bond 0.03931 / 2.61 ( 718) hydrogen bonds : angle 4.14167 / 2.92 ( 2148) metal coordination : bond 0.00077 / 0.04 ( 4) metal coordination : angle 3.60510 / 1.92 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8000 (t0) cc_final: 0.7740 (m-30) REVERT: A 89 LYS cc_start: 0.8709 (tptt) cc_final: 0.8452 (mtmt) REVERT: A 118 MET cc_start: 0.3081 (mmt) cc_final: 0.2391 (mpp) REVERT: A 121 MET cc_start: 0.1967 (mtt) cc_final: 0.1505 (ptt) REVERT: A 126 MET cc_start: 0.5971 (ttt) cc_final: 0.5005 (tmm) REVERT: A 128 GLU cc_start: 0.7536 (mm-30) cc_final: 0.6986 (pt0) REVERT: A 157 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8426 (t) REVERT: A 306 ASP cc_start: 0.6777 (t70) cc_final: 0.6407 (m-30) REVERT: B 78 ASP cc_start: 0.7960 (t0) cc_final: 0.7737 (m-30) REVERT: B 118 MET cc_start: 0.3146 (mmt) cc_final: 0.2550 (mpp) REVERT: B 121 MET cc_start: 0.1978 (mtt) cc_final: 0.1525 (ptt) REVERT: B 126 MET cc_start: 0.5917 (ttt) cc_final: 0.5081 (tmm) REVERT: B 128 GLU cc_start: 0.7558 (mm-30) cc_final: 0.6948 (pt0) REVERT: B 157 VAL cc_start: 0.8797 (OUTLIER) cc_final: 0.8413 (t) REVERT: B 179 ARG cc_start: 0.7154 (mtm110) cc_final: 0.6909 (ttt-90) REVERT: B 306 ASP cc_start: 0.6675 (t70) cc_final: 0.6342 (m-30) REVERT: C 36 LYS cc_start: 0.8628 (mtpp) cc_final: 0.8380 (ttmt) REVERT: C 238 ASN cc_start: 0.8013 (m-40) cc_final: 0.7365 (m110) REVERT: C 277 ASP cc_start: 0.7729 (t70) cc_final: 0.7377 (t0) REVERT: D 1024 GLN cc_start: 0.7024 (OUTLIER) cc_final: 0.6437 (tp-100) REVERT: D 1042 TYR cc_start: 0.8025 (t80) cc_final: 0.7486 (t80) REVERT: F 36 LYS cc_start: 0.8576 (mtpp) cc_final: 0.8372 (ttmt) REVERT: F 238 ASN cc_start: 0.8073 (m-40) cc_final: 0.7383 (m110) REVERT: F 271 MET cc_start: 0.6674 (mtt) cc_final: 0.6457 (mmp) REVERT: F 277 ASP cc_start: 0.7718 (t70) cc_final: 0.7406 (t0) REVERT: G 1026 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7826 (tp) REVERT: G 1042 TYR cc_start: 0.8016 (t80) cc_final: 0.7603 (t80) outliers start: 35 outliers final: 18 residues processed: 191 average time/residue: 0.1003 time to fit residues: 27.7491 Evaluate side-chains 181 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain D residue 1024 GLN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 194 MET Chi-restraints excluded: chain G residue 1023 GLN Chi-restraints excluded: chain G residue 1026 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 21 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 99 optimal weight: 20.0000 chunk 134 optimal weight: 30.0000 chunk 118 optimal weight: 0.8980 chunk 87 optimal weight: 0.0980 chunk 8 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 98 optimal weight: 40.0000 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G1024 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.179986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.137488 restraints weight = 16747.188| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.47 r_work: 0.3350 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11848 Z= 0.131 Angle : 0.539 6.425 16026 Z= 0.276 Chirality : 0.039 0.144 1766 Planarity : 0.005 0.060 2072 Dihedral : 5.336 73.105 1568 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.27 % Allowed : 10.34 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.22), residues: 1424 helix: 1.89 (0.17), residues: 976 sheet: -1.15 (0.50), residues: 76 loop : 0.05 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 122 TYR 0.025 0.002 TYR F 272 PHE 0.016 0.001 PHE C 255 TRP 0.013 0.001 TRP F 241 HIS 0.004 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (11844) covalent geometry : angle 0.53424 / 0.28 (16020) hydrogen bonds : bond 0.03754 / 2.48 ( 718) hydrogen bonds : angle 4.08116 / 2.88 ( 2148) metal coordination : bond 0.00058 / 0.03 ( 4) metal coordination : angle 3.70204 / 1.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.277 Fit side-chains REVERT: A 78 ASP cc_start: 0.8290 (t0) cc_final: 0.8054 (m-30) REVERT: A 89 LYS cc_start: 0.8819 (tptt) cc_final: 0.8468 (mtmt) REVERT: A 118 MET cc_start: 0.2978 (mmt) cc_final: 0.2127 (mpp) REVERT: A 121 MET cc_start: 0.2006 (mtt) cc_final: 0.1497 (ptt) REVERT: A 126 MET cc_start: 0.5913 (ttt) cc_final: 0.5067 (tmm) REVERT: A 128 GLU cc_start: 0.7599 (mm-30) cc_final: 0.6906 (pt0) REVERT: A 157 VAL cc_start: 0.8881 (OUTLIER) cc_final: 0.8486 (t) REVERT: A 306 ASP cc_start: 0.7018 (t70) cc_final: 0.6589 (m-30) REVERT: B 78 ASP cc_start: 0.8285 (t0) cc_final: 0.8049 (m-30) REVERT: B 118 MET cc_start: 0.3099 (mmt) cc_final: 0.2366 (mpp) REVERT: B 121 MET cc_start: 0.2072 (mtt) cc_final: 0.1627 (ptt) REVERT: B 126 MET cc_start: 0.5881 (ttt) cc_final: 0.5022 (tmm) REVERT: B 128 GLU cc_start: 0.7625 (mm-30) cc_final: 0.6916 (pt0) REVERT: B 157 VAL cc_start: 0.8869 (OUTLIER) cc_final: 0.8486 (t) REVERT: B 306 ASP cc_start: 0.6907 (t70) cc_final: 0.6486 (m-30) REVERT: C 36 LYS cc_start: 0.8841 (mtpp) cc_final: 0.8573 (ttmt) REVERT: C 238 ASN cc_start: 0.8119 (m-40) cc_final: 0.7476 (m110) REVERT: C 244 LEU cc_start: 0.8765 (mp) cc_final: 0.8341 (mp) REVERT: C 260 GLU cc_start: 0.7855 (tp30) cc_final: 0.7528 (tm-30) REVERT: C 277 ASP cc_start: 0.7710 (t70) cc_final: 0.7363 (t0) REVERT: D 1024 GLN cc_start: 0.7061 (OUTLIER) cc_final: 0.6324 (tp-100) REVERT: D 1042 TYR cc_start: 0.7973 (t80) cc_final: 0.7452 (t80) REVERT: F 36 LYS cc_start: 0.8815 (mtpp) cc_final: 0.8584 (ttmt) REVERT: F 230 PRO cc_start: 0.7651 (Cg_exo) cc_final: 0.7009 (Cg_endo) REVERT: F 238 ASN cc_start: 0.8144 (m-40) cc_final: 0.7466 (m110) REVERT: F 271 MET cc_start: 0.6808 (mtt) cc_final: 0.6593 (mmp) REVERT: F 277 ASP cc_start: 0.7691 (t70) cc_final: 0.7392 (t0) REVERT: G 1042 TYR cc_start: 0.7954 (t80) cc_final: 0.7442 (t80) outliers start: 29 outliers final: 18 residues processed: 196 average time/residue: 0.0793 time to fit residues: 23.4360 Evaluate side-chains 179 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 1024 GLN Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 194 MET Chi-restraints excluded: chain F residue 233 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 85 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 93 optimal weight: 50.0000 chunk 19 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 136 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.176442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.131030 restraints weight = 16803.703| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.38 r_work: 0.3300 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 11848 Z= 0.229 Angle : 0.632 16.275 16026 Z= 0.321 Chirality : 0.042 0.167 1766 Planarity : 0.005 0.063 2072 Dihedral : 5.422 69.182 1568 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.51 % Allowed : 11.29 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.22), residues: 1424 helix: 1.68 (0.16), residues: 976 sheet: -1.48 (0.48), residues: 78 loop : -0.03 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 263 TYR 0.020 0.002 TYR F 272 PHE 0.034 0.002 PHE F 112 TRP 0.018 0.002 TRP F 241 HIS 0.007 0.002 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.23 (11844) covalent geometry : angle 0.62752 / 0.32 (16020) hydrogen bonds : bond 0.04288 / 2.86 ( 718) hydrogen bonds : angle 4.25790 / 3.01 ( 2148) metal coordination : bond 0.00242 / 0.12 ( 4) metal coordination : angle 4.10070 / 2.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.340 Fit side-chains REVERT: A 78 ASP cc_start: 0.7997 (t0) cc_final: 0.7686 (m-30) REVERT: A 118 MET cc_start: 0.2921 (mmt) cc_final: 0.2189 (mpp) REVERT: A 121 MET cc_start: 0.1915 (mtt) cc_final: 0.1398 (ptt) REVERT: A 126 MET cc_start: 0.6197 (ttt) cc_final: 0.5379 (tmm) REVERT: A 179 ARG cc_start: 0.7282 (mtm110) cc_final: 0.7065 (mtm110) REVERT: A 306 ASP cc_start: 0.7022 (t70) cc_final: 0.6682 (m-30) REVERT: B 78 ASP cc_start: 0.7961 (t0) cc_final: 0.7661 (m-30) REVERT: B 118 MET cc_start: 0.3300 (mmt) cc_final: 0.2631 (mpp) REVERT: B 121 MET cc_start: 0.2028 (mtt) cc_final: 0.1632 (ptt) REVERT: B 126 MET cc_start: 0.6200 (ttt) cc_final: 0.5465 (tmm) REVERT: B 128 GLU cc_start: 0.7468 (mm-30) cc_final: 0.6917 (pt0) REVERT: B 179 ARG cc_start: 0.7325 (mtm110) cc_final: 0.6971 (ttt-90) REVERT: B 306 ASP cc_start: 0.6850 (t70) cc_final: 0.6567 (m-30) REVERT: C 238 ASN cc_start: 0.7956 (m-40) cc_final: 0.7397 (m110) REVERT: C 260 GLU cc_start: 0.7565 (tp30) cc_final: 0.7266 (tm-30) REVERT: C 277 ASP cc_start: 0.7417 (t70) cc_final: 0.7104 (t0) REVERT: D 1024 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6278 (tp-100) REVERT: D 1042 TYR cc_start: 0.8053 (t80) cc_final: 0.7678 (t80) REVERT: F 36 LYS cc_start: 0.8668 (mtpp) cc_final: 0.8425 (ttmt) REVERT: F 238 ASN cc_start: 0.8067 (m-40) cc_final: 0.7416 (m110) REVERT: F 251 LYS cc_start: 0.7451 (mptt) cc_final: 0.7148 (mmtp) REVERT: F 271 MET cc_start: 0.6760 (mtt) cc_final: 0.6538 (mmp) REVERT: F 277 ASP cc_start: 0.7375 (t70) cc_final: 0.7093 (t0) REVERT: G 1042 TYR cc_start: 0.8044 (t80) cc_final: 0.7669 (t80) outliers start: 32 outliers final: 26 residues processed: 187 average time/residue: 0.0906 time to fit residues: 24.8581 Evaluate side-chains 183 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 1024 GLN Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 194 MET Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain H residue 130 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 41 optimal weight: 0.5980 chunk 129 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 128 optimal weight: 0.0370 chunk 136 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.178976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.136169 restraints weight = 16684.844| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.95 r_work: 0.3355 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11848 Z= 0.140 Angle : 0.559 7.901 16026 Z= 0.287 Chirality : 0.040 0.153 1766 Planarity : 0.005 0.062 2072 Dihedral : 5.349 70.924 1568 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.66 % Allowed : 11.21 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.22), residues: 1424 helix: 1.81 (0.17), residues: 976 sheet: -1.68 (0.45), residues: 88 loop : 0.01 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 263 TYR 0.018 0.002 TYR F 272 PHE 0.028 0.001 PHE C 112 TRP 0.015 0.001 TRP F 241 HIS 0.005 0.001 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (11844) covalent geometry : angle 0.55436 / 0.29 (16020) hydrogen bonds : bond 0.03852 / 2.56 ( 718) hydrogen bonds : angle 4.16003 / 2.93 ( 2148) metal coordination : bond 0.00133 / 0.07 ( 4) metal coordination : angle 3.77050 / 1.99 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 0.369 Fit side-chains REVERT: A 78 ASP cc_start: 0.8192 (t0) cc_final: 0.7939 (m-30) REVERT: A 118 MET cc_start: 0.2894 (mmt) cc_final: 0.1959 (mpp) REVERT: A 121 MET cc_start: 0.2095 (mtt) cc_final: 0.1544 (ptt) REVERT: A 126 MET cc_start: 0.6092 (ttt) cc_final: 0.5196 (tmm) REVERT: A 157 VAL cc_start: 0.8901 (OUTLIER) cc_final: 0.8491 (t) REVERT: A 306 ASP cc_start: 0.7105 (t70) cc_final: 0.6799 (m-30) REVERT: B 78 ASP cc_start: 0.8204 (t0) cc_final: 0.7953 (m-30) REVERT: B 118 MET cc_start: 0.3109 (mmt) cc_final: 0.2284 (mpp) REVERT: B 121 MET cc_start: 0.2072 (mtt) cc_final: 0.1510 (ptt) REVERT: B 126 MET cc_start: 0.6118 (ttt) cc_final: 0.5202 (tmm) REVERT: B 128 GLU cc_start: 0.7677 (mm-30) cc_final: 0.6906 (pt0) REVERT: B 157 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8475 (t) REVERT: B 306 ASP cc_start: 0.7031 (t70) cc_final: 0.6669 (m-30) REVERT: C 36 LYS cc_start: 0.8833 (mtpp) cc_final: 0.8562 (ttmt) REVERT: C 238 ASN cc_start: 0.8062 (m-40) cc_final: 0.7361 (m110) REVERT: C 260 GLU cc_start: 0.7788 (tp30) cc_final: 0.7311 (tm-30) REVERT: C 277 ASP cc_start: 0.7902 (t70) cc_final: 0.7546 (t0) REVERT: D 1024 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6323 (tp-100) REVERT: D 1042 TYR cc_start: 0.7992 (t80) cc_final: 0.7475 (t80) REVERT: F 36 LYS cc_start: 0.8834 (mtpp) cc_final: 0.8597 (ttmt) REVERT: F 230 PRO cc_start: 0.7567 (Cg_exo) cc_final: 0.7008 (Cg_endo) REVERT: F 238 ASN cc_start: 0.8205 (m-40) cc_final: 0.7407 (m110) REVERT: F 251 LYS cc_start: 0.7353 (mptt) cc_final: 0.7101 (mmtp) REVERT: F 271 MET cc_start: 0.6810 (mtt) cc_final: 0.6480 (mmp) REVERT: F 277 ASP cc_start: 0.7956 (t70) cc_final: 0.7664 (t0) REVERT: G 1042 TYR cc_start: 0.8023 (t80) cc_final: 0.7584 (t80) outliers start: 34 outliers final: 24 residues processed: 188 average time/residue: 0.0774 time to fit residues: 22.1420 Evaluate side-chains 186 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 1024 GLN Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 194 MET Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain H residue 130 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 35 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 99 optimal weight: 30.0000 chunk 123 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.176892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.131273 restraints weight = 16770.668| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.38 r_work: 0.3307 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11848 Z= 0.203 Angle : 0.624 15.489 16026 Z= 0.316 Chirality : 0.041 0.170 1766 Planarity : 0.005 0.064 2072 Dihedral : 5.379 68.434 1568 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.82 % Allowed : 11.60 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.22), residues: 1424 helix: 1.75 (0.17), residues: 974 sheet: -1.88 (0.44), residues: 88 loop : -0.06 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 263 TYR 0.017 0.002 TYR B 250 PHE 0.025 0.002 PHE C 255 TRP 0.016 0.002 TRP F 241 HIS 0.007 0.002 HIS B 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.20 (11844) covalent geometry : angle 0.61857 / 0.32 (16020) hydrogen bonds : bond 0.04135 / 2.75 ( 718) hydrogen bonds : angle 4.26318 / 3.01 ( 2148) metal coordination : bond 0.00181 / 0.09 ( 4) metal coordination : angle 4.17844 / 2.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 0.434 Fit side-chains REVERT: A 78 ASP cc_start: 0.8202 (t0) cc_final: 0.7909 (m-30) REVERT: A 118 MET cc_start: 0.2926 (mmt) cc_final: 0.1972 (mpp) REVERT: A 121 MET cc_start: 0.2226 (mtt) cc_final: 0.1647 (ptt) REVERT: A 126 MET cc_start: 0.6224 (ttt) cc_final: 0.5388 (tmm) REVERT: A 306 ASP cc_start: 0.7338 (t70) cc_final: 0.7019 (m-30) REVERT: B 78 ASP cc_start: 0.8193 (t0) cc_final: 0.7907 (m-30) REVERT: B 118 MET cc_start: 0.3105 (mmt) cc_final: 0.2179 (mpp) REVERT: B 121 MET cc_start: 0.2214 (mtt) cc_final: 0.1655 (ptt) REVERT: B 126 MET cc_start: 0.6290 (ttt) cc_final: 0.5424 (tmm) REVERT: B 179 ARG cc_start: 0.7436 (mtm110) cc_final: 0.6898 (ttt-90) REVERT: B 306 ASP cc_start: 0.7262 (t70) cc_final: 0.6867 (m-30) REVERT: C 238 ASN cc_start: 0.8048 (m-40) cc_final: 0.7444 (m110) REVERT: C 258 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7018 (mm) REVERT: C 260 GLU cc_start: 0.7894 (tp30) cc_final: 0.7449 (tm-30) REVERT: C 277 ASP cc_start: 0.7741 (t70) cc_final: 0.7448 (t0) REVERT: D 1024 GLN cc_start: 0.7161 (OUTLIER) cc_final: 0.6315 (tp-100) REVERT: D 1042 TYR cc_start: 0.8048 (t80) cc_final: 0.7454 (t80) REVERT: F 238 ASN cc_start: 0.8197 (m-40) cc_final: 0.7455 (m110) REVERT: F 251 LYS cc_start: 0.7407 (mptt) cc_final: 0.7159 (mmtp) REVERT: F 271 MET cc_start: 0.6995 (mtt) cc_final: 0.6695 (mmp) REVERT: F 277 ASP cc_start: 0.7842 (t70) cc_final: 0.7582 (t0) REVERT: G 1042 TYR cc_start: 0.8076 (t80) cc_final: 0.7614 (t80) outliers start: 36 outliers final: 30 residues processed: 190 average time/residue: 0.0814 time to fit residues: 23.4341 Evaluate side-chains 186 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain D residue 1024 GLN Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 194 MET Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain H residue 130 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 12 optimal weight: 0.6980 chunk 140 optimal weight: 40.0000 chunk 23 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 116 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 261 GLN ** G1023 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 = 0.4147 r_free = 0.4147 target = 0.178009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.133287 restraints weight = 16528.705| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.19 r_work: 0.3314 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11848 Z= 0.158 Angle : 0.598 18.238 16026 Z= 0.301 Chirality : 0.040 0.157 1766 Planarity : 0.005 0.064 2072 Dihedral : 5.339 69.091 1568 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.90 % Allowed : 11.83 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.22), residues: 1424 helix: 1.77 (0.17), residues: 976 sheet: -1.98 (0.44), residues: 88 loop : -0.06 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 263 TYR 0.018 0.002 TYR F 272 PHE 0.023 0.001 PHE F 112 TRP 0.026 0.002 TRP F 241 HIS 0.005 0.001 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (11844) covalent geometry : angle 0.59301 / 0.30 (16020) hydrogen bonds : bond 0.03935 / 2.59 ( 718) hydrogen bonds : angle 4.23675 / 2.99 ( 2148) metal coordination : bond 0.00198 / 0.10 ( 4) metal coordination : angle 4.07135 / 2.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 0.393 Fit side-chains REVERT: A 78 ASP cc_start: 0.8190 (t0) cc_final: 0.7916 (m-30) REVERT: A 118 MET cc_start: 0.3054 (mmt) cc_final: 0.2133 (mpp) REVERT: A 121 MET cc_start: 0.2225 (mtt) cc_final: 0.1704 (ptt) REVERT: A 126 MET cc_start: 0.6355 (ttt) cc_final: 0.5597 (tmm) REVERT: A 306 ASP cc_start: 0.7265 (t70) cc_final: 0.7054 (m-30) REVERT: B 78 ASP cc_start: 0.8215 (t0) cc_final: 0.7946 (m-30) REVERT: B 118 MET cc_start: 0.3202 (mmt) cc_final: 0.2309 (mpp) REVERT: B 121 MET cc_start: 0.2274 (mtt) cc_final: 0.1720 (ptt) REVERT: B 126 MET cc_start: 0.6343 (ttt) cc_final: 0.5570 (tmm) REVERT: B 306 ASP cc_start: 0.7040 (t70) cc_final: 0.6718 (m-30) REVERT: C 36 LYS cc_start: 0.8796 (mtpp) cc_final: 0.8527 (ttmt) REVERT: C 238 ASN cc_start: 0.8039 (m-40) cc_final: 0.7393 (m110) REVERT: C 277 ASP cc_start: 0.7674 (t70) cc_final: 0.7393 (t0) REVERT: D 1024 GLN cc_start: 0.7120 (OUTLIER) cc_final: 0.6348 (tp-100) REVERT: F 36 LYS cc_start: 0.8821 (mtpp) cc_final: 0.8535 (ttmt) REVERT: F 230 PRO cc_start: 0.7579 (Cg_exo) cc_final: 0.7135 (Cg_endo) REVERT: F 238 ASN cc_start: 0.8163 (m-40) cc_final: 0.7441 (m110) REVERT: F 271 MET cc_start: 0.6811 (mtt) cc_final: 0.6513 (mmp) REVERT: F 277 ASP cc_start: 0.7747 (t70) cc_final: 0.7492 (t0) REVERT: G 1042 TYR cc_start: 0.8103 (t80) cc_final: 0.7626 (t80) outliers start: 37 outliers final: 33 residues processed: 180 average time/residue: 0.0812 time to fit residues: 21.8976 Evaluate side-chains 185 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain D residue 1024 GLN Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 194 MET Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain G residue 1028 SER Chi-restraints excluded: chain H residue 130 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 0 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 133 optimal weight: 40.0000 chunk 57 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 13 optimal weight: 0.0970 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 261 GLN ** G1023 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 = 0.4154 r_free = 0.4154 target = 0.178646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.133129 restraints weight = 16744.879| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.54 r_work: 0.3318 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11848 Z= 0.148 Angle : 0.617 21.488 16026 Z= 0.309 Chirality : 0.040 0.174 1766 Planarity : 0.005 0.063 2072 Dihedral : 5.338 69.485 1568 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.82 % Allowed : 12.15 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.22), residues: 1424 helix: 1.78 (0.17), residues: 976 sheet: -2.01 (0.44), residues: 88 loop : -0.05 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 263 TYR 0.016 0.002 TYR A 250 PHE 0.023 0.001 PHE C 112 TRP 0.028 0.002 TRP C 241 HIS 0.005 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (11844) covalent geometry : angle 0.61195 / 0.31 (16020) hydrogen bonds : bond 0.03897 / 2.58 ( 718) hydrogen bonds : angle 4.21090 / 2.97 ( 2148) metal coordination : bond 0.00176 / 0.09 ( 4) metal coordination : angle 3.99613 / 2.12 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 0.363 Fit side-chains REVERT: A 78 ASP cc_start: 0.7834 (t0) cc_final: 0.7563 (m-30) REVERT: A 118 MET cc_start: 0.3259 (mmt) cc_final: 0.2343 (mpp) REVERT: A 121 MET cc_start: 0.2165 (mtt) cc_final: 0.1768 (ptt) REVERT: A 126 MET cc_start: 0.6230 (ttt) cc_final: 0.5630 (tmm) REVERT: B 78 ASP cc_start: 0.7852 (t0) cc_final: 0.7595 (m-30) REVERT: B 118 MET cc_start: 0.3254 (mmt) cc_final: 0.2370 (mpp) REVERT: B 121 MET cc_start: 0.2139 (mtt) cc_final: 0.1719 (ptt) REVERT: B 126 MET cc_start: 0.6226 (ttt) cc_final: 0.5585 (tmm) REVERT: B 306 ASP cc_start: 0.6745 (t70) cc_final: 0.6526 (m-30) REVERT: C 36 LYS cc_start: 0.8645 (mtpp) cc_final: 0.8420 (ttmt) REVERT: C 230 PRO cc_start: 0.7464 (Cg_exo) cc_final: 0.7063 (Cg_endo) REVERT: C 238 ASN cc_start: 0.7901 (m-40) cc_final: 0.7377 (m110) REVERT: C 258 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7185 (mt) REVERT: C 277 ASP cc_start: 0.7424 (t70) cc_final: 0.7188 (t0) REVERT: D 1024 GLN cc_start: 0.6989 (OUTLIER) cc_final: 0.6375 (tp-100) REVERT: F 36 LYS cc_start: 0.8691 (mtpp) cc_final: 0.8453 (ttmt) REVERT: F 230 PRO cc_start: 0.7523 (Cg_exo) cc_final: 0.7165 (Cg_endo) REVERT: F 238 ASN cc_start: 0.8002 (m-40) cc_final: 0.7391 (m110) REVERT: G 1042 TYR cc_start: 0.8087 (t80) cc_final: 0.7590 (t80) outliers start: 36 outliers final: 34 residues processed: 183 average time/residue: 0.0760 time to fit residues: 21.4075 Evaluate side-chains 190 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain D residue 1024 GLN Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 194 MET Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain G residue 1028 SER Chi-restraints excluded: chain H residue 130 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 35 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 261 GLN ** G1023 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 = 0.4153 r_free = 0.4153 target = 0.178613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.132356 restraints weight = 16552.515| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.62 r_work: 0.3318 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11848 Z= 0.157 Angle : 0.616 21.241 16026 Z= 0.309 Chirality : 0.040 0.152 1766 Planarity : 0.005 0.064 2072 Dihedral : 5.332 69.400 1568 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.90 % Allowed : 12.07 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.22), residues: 1424 helix: 1.81 (0.17), residues: 976 sheet: -2.02 (0.44), residues: 88 loop : -0.09 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 263 TYR 0.016 0.002 TYR A 250 PHE 0.020 0.001 PHE C 112 TRP 0.023 0.002 TRP F 241 HIS 0.004 0.001 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (11844) covalent geometry : angle 0.61168 / 0.31 (16020) hydrogen bonds : bond 0.03912 / 2.60 ( 718) hydrogen bonds : angle 4.20989 / 2.97 ( 2148) metal coordination : bond 0.00174 / 0.09 ( 4) metal coordination : angle 3.96969 / 2.11 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2831.99 seconds wall clock time: 49 minutes 18.31 seconds (2958.31 seconds total)