Starting phenix.real_space_refine on Tue Nov 18 06:24:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rua_24701/11_2025/7rua_24701.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rua_24701/11_2025/7rua_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_24701/11_2025/7rua_24701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rua_24701/11_2025/7rua_24701.map" model { file = "/net/cci-nas-00/data/ceres_data/7rua_24701/11_2025/7rua_24701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rua_24701/11_2025/7rua_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11603 Number of models: 1 Model: "" Number of chains: 5 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: "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: "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} 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 Restraints were copied for chains: B, F, G, H Time building chain proxies: 3.27, per 1000 atoms: 0.28 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: 1.30 Conformation dependent library (CDL) restraints added in 566.0 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: 0.34 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: 1.83 Time building geometry restraints manager: 1.64 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: 6480 17.58 - 35.15: 648 35.15 - 52.73: 136 52.73 - 70.31: 34 70.31 - 87.89: 12 Dihedral angle restraints: 7310 sinusoidal: 3072 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 7307 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: 3.910 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.840 Find NCS groups from input model: 0.180 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: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 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 : 14.914 87.887 4550 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 covalent geometry : bond 0.00331 (11844) covalent geometry : angle 0.56579 (16020) hydrogen bonds : bond 0.13505 ( 718) hydrogen bonds : angle 5.61979 ( 2148) metal coordination : bond 0.00091 ( 4) metal coordination : angle 2.84458 ( 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 : 0.523 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: 0.1156 time to fit residues: 43.2953 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 : 0.502 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D1027 GLN ** G1023 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 = 0.4170 r_free = 0.4170 target = 0.180146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.140152 restraints weight = 16767.798| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.17 r_work: 0.3370 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11848 Z= 0.164 Angle : 0.625 10.910 16026 Z= 0.319 Chirality : 0.041 0.146 1766 Planarity : 0.005 0.056 2072 Dihedral : 7.859 75.912 1630 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.49 % Allowed : 8.78 % Favored : 89.73 % 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: 2.06 (0.23), residues: 1424 helix: 1.92 (0.17), residues: 976 sheet: -0.20 (0.60), residues: 74 loop : 0.36 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 267 TYR 0.025 0.002 TYR C 272 PHE 0.024 0.002 PHE C 232 TRP 0.009 0.002 TRP E 96 HIS 0.007 0.002 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00374 (11844) covalent geometry : angle 0.62117 (16020) hydrogen bonds : bond 0.04601 ( 718) hydrogen bonds : angle 4.42792 ( 2148) metal coordination : bond 0.00238 ( 4) metal coordination : angle 3.60811 ( 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 213 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 194 time to evaluate : 0.458 Fit side-chains REVERT: A 89 LYS cc_start: 0.8663 (tptt) cc_final: 0.8407 (mtmt) REVERT: A 118 MET cc_start: 0.3126 (mmt) cc_final: 0.2643 (mpp) REVERT: A 121 MET cc_start: 0.1766 (mtt) cc_final: 0.1281 (ptt) REVERT: A 126 MET cc_start: 0.5803 (ttt) cc_final: 0.4888 (tmm) REVERT: A 128 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7051 (pt0) REVERT: A 281 ARG cc_start: 0.6645 (ptm160) cc_final: 0.6415 (ptp-170) REVERT: B 89 LYS cc_start: 0.8325 (ttmm) cc_final: 0.8103 (mttt) REVERT: B 118 MET cc_start: 0.3405 (mmt) cc_final: 0.2963 (mpp) REVERT: B 121 MET cc_start: 0.2144 (mtt) cc_final: 0.1736 (ptt) REVERT: B 126 MET cc_start: 0.5721 (ttt) cc_final: 0.4851 (tmm) REVERT: B 179 ARG cc_start: 0.7104 (mtm110) cc_final: 0.6902 (ttt-90) REVERT: B 281 ARG cc_start: 0.6610 (ptm160) cc_final: 0.6393 (ptp-170) REVERT: C 36 LYS cc_start: 0.8588 (mtpp) cc_final: 0.8362 (ttmt) REVERT: C 103 GLU cc_start: 0.7079 (pm20) cc_final: 0.6878 (pm20) REVERT: C 238 ASN cc_start: 0.8040 (m-40) cc_final: 0.7530 (m110) REVERT: C 271 MET cc_start: 0.6599 (mtt) cc_final: 0.6237 (mmp) REVERT: D 1042 TYR cc_start: 0.8002 (t80) cc_final: 0.7481 (t80) REVERT: F 36 LYS cc_start: 0.8593 (mtpp) cc_final: 0.8390 (ttmt) REVERT: F 238 ASN cc_start: 0.8029 (m-40) cc_final: 0.7454 (m110) REVERT: F 271 MET cc_start: 0.6745 (mtt) cc_final: 0.6341 (mmp) REVERT: G 1042 TYR cc_start: 0.7923 (t80) cc_final: 0.7466 (t80) outliers start: 19 outliers final: 8 residues processed: 204 average time/residue: 0.1120 time to fit residues: 32.9081 Evaluate side-chains 170 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 2 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 141 optimal weight: 20.0000 chunk 70 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS A 299 GLN ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.180162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.140057 restraints weight = 16941.199| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.02 r_work: 0.3358 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11848 Z= 0.154 Angle : 0.565 6.656 16026 Z= 0.293 Chirality : 0.040 0.147 1766 Planarity : 0.005 0.056 2072 Dihedral : 7.575 80.620 1630 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.80 % Allowed : 10.74 % Favored : 87.46 % 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: 1.92 (0.22), residues: 1424 helix: 1.88 (0.17), residues: 976 sheet: -0.85 (0.55), residues: 76 loop : 0.25 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 263 TYR 0.029 0.002 TYR C 272 PHE 0.017 0.001 PHE F 255 TRP 0.012 0.002 TRP F 241 HIS 0.005 0.001 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00357 (11844) covalent geometry : angle 0.56112 (16020) hydrogen bonds : bond 0.04214 ( 718) hydrogen bonds : angle 4.24814 ( 2148) metal coordination : bond 0.00069 ( 4) metal coordination : angle 3.65989 ( 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 201 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8850 (tptt) cc_final: 0.8488 (mtmt) REVERT: A 118 MET cc_start: 0.3248 (mmt) cc_final: 0.2641 (mpp) REVERT: A 121 MET cc_start: 0.1924 (mtt) cc_final: 0.1423 (ptt) REVERT: A 126 MET cc_start: 0.5923 (ttt) cc_final: 0.5117 (tmm) REVERT: A 128 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7056 (pt0) REVERT: A 157 VAL cc_start: 0.8892 (OUTLIER) cc_final: 0.8489 (t) REVERT: A 281 ARG cc_start: 0.6959 (ptm160) cc_final: 0.6715 (ptp-170) REVERT: B 78 ASP cc_start: 0.8349 (t0) cc_final: 0.8103 (m-30) REVERT: B 89 LYS cc_start: 0.8552 (ttmm) cc_final: 0.8343 (mtmt) REVERT: B 118 MET cc_start: 0.3293 (mmt) cc_final: 0.2743 (mpp) REVERT: B 121 MET cc_start: 0.1855 (mtt) cc_final: 0.1464 (ptt) REVERT: B 126 MET cc_start: 0.5986 (ttt) cc_final: 0.5111 (tmm) REVERT: B 128 GLU cc_start: 0.7564 (mm-30) cc_final: 0.6955 (pt0) REVERT: B 179 ARG cc_start: 0.7267 (mtm110) cc_final: 0.6889 (ttt-90) REVERT: B 281 ARG cc_start: 0.6908 (ptm160) cc_final: 0.6674 (ptp-170) REVERT: C 36 LYS cc_start: 0.8780 (mtpp) cc_final: 0.8483 (ttmt) REVERT: C 238 ASN cc_start: 0.8073 (m-40) cc_final: 0.7486 (m110) REVERT: C 271 MET cc_start: 0.6631 (mtt) cc_final: 0.6412 (mmp) REVERT: C 277 ASP cc_start: 0.7768 (t70) cc_final: 0.7397 (t0) REVERT: D 1024 GLN cc_start: 0.6993 (OUTLIER) cc_final: 0.6257 (tp-100) REVERT: D 1042 TYR cc_start: 0.7951 (t80) cc_final: 0.7488 (t80) REVERT: F 36 LYS cc_start: 0.8767 (mtpp) cc_final: 0.8498 (ttmt) REVERT: F 238 ASN cc_start: 0.8100 (m-40) cc_final: 0.7490 (m110) REVERT: F 251 LYS cc_start: 0.7336 (mptt) cc_final: 0.7075 (mmtp) REVERT: F 271 MET cc_start: 0.6754 (mtt) cc_final: 0.6440 (mmp) REVERT: F 277 ASP cc_start: 0.7746 (t0) cc_final: 0.7444 (t0) REVERT: G 1026 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7845 (tp) REVERT: G 1042 TYR cc_start: 0.7979 (t80) cc_final: 0.7646 (t80) outliers start: 23 outliers final: 17 residues processed: 191 average time/residue: 0.1097 time to fit residues: 30.5582 Evaluate side-chains 178 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 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: 50.0000 chunk 109 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 11 optimal weight: 0.0770 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 HIS ** D1100 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 = 0.4164 r_free = 0.4164 target = 0.179380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.137818 restraints weight = 16843.368| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.19 r_work: 0.3329 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11848 Z= 0.145 Angle : 0.566 10.528 16026 Z= 0.289 Chirality : 0.040 0.145 1766 Planarity : 0.005 0.061 2072 Dihedral : 7.393 87.353 1630 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.12 % Allowed : 10.97 % Favored : 86.91 % 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: -1.14 (0.52), residues: 76 loop : 0.10 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 263 TYR 0.029 0.002 TYR C 272 PHE 0.015 0.001 PHE C 255 TRP 0.011 0.001 TRP F 241 HIS 0.004 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00338 (11844) covalent geometry : angle 0.56227 (16020) hydrogen bonds : bond 0.03959 ( 718) hydrogen bonds : angle 4.17996 ( 2148) metal coordination : bond 0.00080 ( 4) metal coordination : angle 3.60143 ( 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 201 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.470 Fit side-chains REVERT: A 78 ASP cc_start: 0.8353 (t0) cc_final: 0.8094 (m-30) REVERT: A 89 LYS cc_start: 0.8864 (tptt) cc_final: 0.8491 (mtmt) REVERT: A 118 MET cc_start: 0.3222 (mmt) cc_final: 0.2565 (mpp) REVERT: A 121 MET cc_start: 0.1972 (mtt) cc_final: 0.1469 (ptt) REVERT: A 126 MET cc_start: 0.6120 (ttt) cc_final: 0.5016 (tmm) REVERT: A 128 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7013 (pt0) REVERT: A 157 VAL cc_start: 0.8922 (OUTLIER) cc_final: 0.8533 (t) REVERT: A 306 ASP cc_start: 0.7163 (t70) cc_final: 0.6645 (m-30) REVERT: B 78 ASP cc_start: 0.8336 (t0) cc_final: 0.8095 (m-30) REVERT: B 89 LYS cc_start: 0.8604 (ttmm) cc_final: 0.8338 (mtmt) REVERT: B 118 MET cc_start: 0.3240 (mmt) cc_final: 0.2640 (mpp) REVERT: B 121 MET cc_start: 0.1992 (mtt) cc_final: 0.1519 (ptt) REVERT: B 126 MET cc_start: 0.6127 (ttt) cc_final: 0.4988 (tmm) REVERT: B 128 GLU cc_start: 0.7652 (mm-30) cc_final: 0.6997 (pt0) REVERT: B 157 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8501 (t) REVERT: B 179 ARG cc_start: 0.7348 (mtm110) cc_final: 0.6929 (ttt-90) REVERT: B 306 ASP cc_start: 0.7064 (t70) cc_final: 0.6534 (m-30) REVERT: C 36 LYS cc_start: 0.8827 (mtpp) cc_final: 0.8557 (ttmt) REVERT: C 238 ASN cc_start: 0.8078 (m-40) cc_final: 0.7426 (m110) REVERT: C 271 MET cc_start: 0.6757 (mtt) cc_final: 0.6495 (mmp) REVERT: C 277 ASP cc_start: 0.7822 (t70) cc_final: 0.7473 (t0) REVERT: D 1020 PRO cc_start: 0.7084 (Cg_exo) cc_final: 0.6523 (Cg_endo) REVERT: D 1024 GLN cc_start: 0.7027 (OUTLIER) cc_final: 0.6292 (tp-100) REVERT: D 1042 TYR cc_start: 0.8041 (t80) cc_final: 0.7461 (t80) REVERT: F 36 LYS cc_start: 0.8789 (mtpp) cc_final: 0.8524 (ttmt) REVERT: F 238 ASN cc_start: 0.8159 (m-40) cc_final: 0.7485 (m110) REVERT: F 251 LYS cc_start: 0.7338 (mptt) cc_final: 0.7054 (mmtp) REVERT: F 271 MET cc_start: 0.6884 (mtt) cc_final: 0.6620 (mmp) REVERT: F 277 ASP cc_start: 0.7790 (t0) cc_final: 0.7508 (t0) REVERT: G 1026 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7842 (tp) REVERT: G 1042 TYR cc_start: 0.8054 (t80) cc_final: 0.7620 (t80) outliers start: 27 outliers final: 15 residues processed: 192 average time/residue: 0.0989 time to fit residues: 28.3327 Evaluate side-chains 184 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 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 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 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: 0.5980 chunk 119 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 99 optimal weight: 30.0000 chunk 134 optimal weight: 20.0000 chunk 118 optimal weight: 1.9990 chunk 87 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 98 optimal weight: 50.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1024 GLN G1027 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.179171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.136025 restraints weight = 16789.452| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.83 r_work: 0.3377 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2572 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= 0.143 Angle : 0.548 6.477 16026 Z= 0.284 Chirality : 0.040 0.148 1766 Planarity : 0.005 0.060 2072 Dihedral : 7.118 86.088 1630 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.66 % Allowed : 10.34 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.22), residues: 1424 helix: 1.86 (0.17), residues: 976 sheet: -1.37 (0.49), residues: 78 loop : 0.06 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 263 TYR 0.028 0.002 TYR C 272 PHE 0.020 0.001 PHE F 255 TRP 0.013 0.002 TRP F 241 HIS 0.004 0.001 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00334 (11844) covalent geometry : angle 0.54349 (16020) hydrogen bonds : bond 0.03900 ( 718) hydrogen bonds : angle 4.13434 ( 2148) metal coordination : bond 0.00081 ( 4) metal coordination : angle 3.75023 ( 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 204 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8204 (t0) cc_final: 0.7959 (m-30) REVERT: A 89 LYS cc_start: 0.8814 (tptt) cc_final: 0.8475 (mtmt) REVERT: A 118 MET cc_start: 0.3170 (mmt) cc_final: 0.2459 (mpp) REVERT: A 121 MET cc_start: 0.2001 (mtt) cc_final: 0.1466 (ptt) REVERT: A 126 MET cc_start: 0.5892 (ttt) cc_final: 0.5100 (tmm) REVERT: A 128 GLU cc_start: 0.7517 (mm-30) cc_final: 0.6936 (pt0) REVERT: A 157 VAL cc_start: 0.8863 (OUTLIER) cc_final: 0.8461 (t) REVERT: A 306 ASP cc_start: 0.6852 (t70) cc_final: 0.6482 (m-30) REVERT: B 78 ASP cc_start: 0.8184 (t0) cc_final: 0.7951 (m-30) REVERT: B 89 LYS cc_start: 0.8561 (ttmm) cc_final: 0.8308 (mtmt) REVERT: B 118 MET cc_start: 0.3146 (mmt) cc_final: 0.2484 (mpp) REVERT: B 121 MET cc_start: 0.2044 (mtt) cc_final: 0.1622 (ptt) REVERT: B 126 MET cc_start: 0.5948 (ttt) cc_final: 0.5120 (tmm) REVERT: B 128 GLU cc_start: 0.7565 (mm-30) cc_final: 0.6922 (pt0) REVERT: B 157 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8446 (t) REVERT: B 179 ARG cc_start: 0.7264 (mtm110) cc_final: 0.6921 (ttt-90) REVERT: B 306 ASP cc_start: 0.6873 (t70) cc_final: 0.6369 (m-30) REVERT: C 36 LYS cc_start: 0.8796 (mtpp) cc_final: 0.8524 (ttmt) REVERT: C 238 ASN cc_start: 0.8081 (m-40) cc_final: 0.7436 (m110) REVERT: C 260 GLU cc_start: 0.7755 (tp30) cc_final: 0.7450 (tm-30) REVERT: C 271 MET cc_start: 0.6816 (mtt) cc_final: 0.6437 (mmp) REVERT: C 277 ASP cc_start: 0.7750 (t70) cc_final: 0.7365 (t0) REVERT: D 1024 GLN cc_start: 0.6938 (OUTLIER) cc_final: 0.6303 (tp-100) REVERT: D 1042 TYR cc_start: 0.7980 (t80) cc_final: 0.7470 (t80) REVERT: F 36 LYS cc_start: 0.8749 (mtpp) cc_final: 0.8501 (ttmt) REVERT: F 238 ASN cc_start: 0.8162 (m-40) cc_final: 0.7495 (m110) REVERT: F 251 LYS cc_start: 0.7342 (mptt) cc_final: 0.7023 (mmtp) REVERT: F 271 MET cc_start: 0.6700 (mtt) cc_final: 0.6498 (mmp) REVERT: F 277 ASP cc_start: 0.7675 (t70) cc_final: 0.7384 (t0) REVERT: G 1026 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7794 (tp) REVERT: G 1042 TYR cc_start: 0.7998 (t80) cc_final: 0.7582 (t80) outliers start: 34 outliers final: 20 residues processed: 191 average time/residue: 0.1039 time to fit residues: 29.3065 Evaluate side-chains 185 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 126 VAL Chi-restraints excluded: chain C residue 194 MET 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 Chi-restraints excluded: chain G residue 1023 GLN Chi-restraints excluded: chain G residue 1026 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 85 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 93 optimal weight: 30.0000 chunk 19 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.175609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.131751 restraints weight = 16803.605| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.73 r_work: 0.3265 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11848 Z= 0.226 Angle : 0.644 14.611 16026 Z= 0.327 Chirality : 0.043 0.168 1766 Planarity : 0.005 0.064 2072 Dihedral : 7.162 87.759 1630 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.66 % Allowed : 10.58 % Favored : 86.76 % 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: 1.46 (0.22), residues: 1424 helix: 1.64 (0.17), residues: 974 sheet: -1.62 (0.47), residues: 78 loop : -0.09 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 263 TYR 0.020 0.002 TYR F 272 PHE 0.022 0.002 PHE F 255 TRP 0.012 0.002 TRP F 241 HIS 0.006 0.002 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00550 (11844) covalent geometry : angle 0.63803 (16020) hydrogen bonds : bond 0.04340 ( 718) hydrogen bonds : angle 4.31325 ( 2148) metal coordination : bond 0.00279 ( 4) metal coordination : angle 4.39963 ( 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 201 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 0.503 Fit side-chains REVERT: A 78 ASP cc_start: 0.8321 (t0) cc_final: 0.8016 (m-30) REVERT: A 89 LYS cc_start: 0.8857 (tptt) cc_final: 0.8472 (mtmt) REVERT: A 118 MET cc_start: 0.3025 (mmt) cc_final: 0.2207 (mpp) REVERT: A 121 MET cc_start: 0.2097 (mtt) cc_final: 0.1479 (ptt) REVERT: A 126 MET cc_start: 0.6275 (ttt) cc_final: 0.5268 (tmm) REVERT: A 179 ARG cc_start: 0.7482 (mtm110) cc_final: 0.7243 (mtm110) REVERT: A 306 ASP cc_start: 0.7401 (t70) cc_final: 0.7032 (m-30) REVERT: B 78 ASP cc_start: 0.8316 (t0) cc_final: 0.8026 (m-30) REVERT: B 89 LYS cc_start: 0.8691 (ttmm) cc_final: 0.8306 (mttt) REVERT: B 118 MET cc_start: 0.3272 (mmt) cc_final: 0.2508 (mpp) REVERT: B 121 MET cc_start: 0.2179 (mtt) cc_final: 0.1674 (ptt) REVERT: B 126 MET cc_start: 0.6294 (ttt) cc_final: 0.5340 (tmm) REVERT: B 128 GLU cc_start: 0.7551 (mm-30) cc_final: 0.6934 (pt0) REVERT: B 179 ARG cc_start: 0.7487 (mtm110) cc_final: 0.6957 (ttt-90) REVERT: C 181 GLU cc_start: 0.7666 (tp30) cc_final: 0.7443 (tt0) REVERT: C 238 ASN cc_start: 0.8084 (m-40) cc_final: 0.7466 (m110) REVERT: C 260 GLU cc_start: 0.7904 (tp30) cc_final: 0.7580 (tm-30) REVERT: C 271 MET cc_start: 0.6901 (mtt) cc_final: 0.6528 (mmp) REVERT: C 277 ASP cc_start: 0.7787 (t70) cc_final: 0.7427 (t0) REVERT: D 1024 GLN cc_start: 0.7049 (OUTLIER) cc_final: 0.6369 (tp-100) REVERT: D 1042 TYR cc_start: 0.7998 (t80) cc_final: 0.7545 (t80) REVERT: F 112 PHE cc_start: 0.9087 (t80) cc_final: 0.8879 (t80) REVERT: F 181 GLU cc_start: 0.7649 (tp30) cc_final: 0.7429 (tt0) REVERT: F 238 ASN cc_start: 0.8203 (m-40) cc_final: 0.7505 (m110) REVERT: F 251 LYS cc_start: 0.7431 (mptt) cc_final: 0.7107 (mmtp) REVERT: F 271 MET cc_start: 0.7006 (mtt) cc_final: 0.6714 (mmp) REVERT: F 277 ASP cc_start: 0.7840 (t70) cc_final: 0.7563 (t0) REVERT: G 1042 TYR cc_start: 0.8026 (t80) cc_final: 0.7573 (t80) outliers start: 34 outliers final: 28 residues processed: 192 average time/residue: 0.1014 time to fit residues: 29.1438 Evaluate side-chains 189 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 218 GLU 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 81 SER 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 257 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: 0.6980 chunk 129 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 128 optimal weight: 0.8980 chunk 136 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1024 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.177976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.135617 restraints weight = 16687.443| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.64 r_work: 0.3326 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11848 Z= 0.153 Angle : 0.576 8.124 16026 Z= 0.299 Chirality : 0.041 0.165 1766 Planarity : 0.005 0.063 2072 Dihedral : 6.932 81.683 1630 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.66 % Allowed : 11.29 % Favored : 86.05 % 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: 1.58 (0.22), residues: 1424 helix: 1.75 (0.17), residues: 976 sheet: -1.81 (0.44), residues: 88 loop : 0.00 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 263 TYR 0.016 0.002 TYR A 250 PHE 0.042 0.001 PHE C 112 TRP 0.017 0.002 TRP F 241 HIS 0.005 0.001 HIS F 43 Details of bonding type rmsd covalent geometry : bond 0.00358 (11844) covalent geometry : angle 0.57063 (16020) hydrogen bonds : bond 0.03972 ( 718) hydrogen bonds : angle 4.23999 ( 2148) metal coordination : bond 0.00191 ( 4) metal coordination : angle 4.05193 ( 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 206 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8120 (t0) cc_final: 0.7843 (m-30) REVERT: A 89 LYS cc_start: 0.8808 (tptt) cc_final: 0.8436 (mtmt) REVERT: A 118 MET cc_start: 0.3066 (mmt) cc_final: 0.2152 (mpp) REVERT: A 121 MET cc_start: 0.2165 (mtt) cc_final: 0.1557 (ptt) REVERT: A 126 MET cc_start: 0.6220 (ttt) cc_final: 0.5358 (tmm) REVERT: A 157 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8469 (t) REVERT: A 306 ASP cc_start: 0.7378 (t70) cc_final: 0.7006 (m-30) REVERT: B 78 ASP cc_start: 0.8132 (t0) cc_final: 0.7862 (m-30) REVERT: B 89 LYS cc_start: 0.8590 (ttmm) cc_final: 0.8286 (mtmt) REVERT: B 118 MET cc_start: 0.3265 (mmt) cc_final: 0.2474 (mpp) REVERT: B 121 MET cc_start: 0.2161 (mtt) cc_final: 0.1602 (ptt) REVERT: B 126 MET cc_start: 0.6260 (ttt) cc_final: 0.5347 (tmm) REVERT: B 128 GLU cc_start: 0.7511 (mm-30) cc_final: 0.6843 (pt0) REVERT: C 238 ASN cc_start: 0.8013 (m-40) cc_final: 0.7342 (m110) REVERT: C 258 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7020 (mm) REVERT: C 260 GLU cc_start: 0.7740 (tp30) cc_final: 0.7259 (tm-30) REVERT: C 271 MET cc_start: 0.6745 (mtt) cc_final: 0.6458 (mmp) REVERT: C 277 ASP cc_start: 0.7750 (t70) cc_final: 0.7459 (t0) REVERT: D 1024 GLN cc_start: 0.7039 (OUTLIER) cc_final: 0.6430 (tp-100) REVERT: F 36 LYS cc_start: 0.8782 (mtpp) cc_final: 0.8524 (ttmt) REVERT: F 112 PHE cc_start: 0.9014 (t80) cc_final: 0.8807 (t80) REVERT: F 181 GLU cc_start: 0.7533 (tp30) cc_final: 0.7332 (tt0) REVERT: F 238 ASN cc_start: 0.8180 (m-40) cc_final: 0.7454 (m110) REVERT: F 251 LYS cc_start: 0.7417 (mptt) cc_final: 0.7177 (mmtp) REVERT: F 260 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7264 (mm-30) REVERT: F 271 MET cc_start: 0.6894 (mtt) cc_final: 0.6614 (mmp) REVERT: F 277 ASP cc_start: 0.7857 (t70) cc_final: 0.7580 (t0) REVERT: G 1042 TYR cc_start: 0.8034 (t80) cc_final: 0.7547 (t80) outliers start: 34 outliers final: 26 residues processed: 195 average time/residue: 0.0989 time to fit residues: 29.2780 Evaluate side-chains 188 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 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 258 LEU Chi-restraints excluded: chain D residue 1024 GLN Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 81 SER 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 1023 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 35 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 99 optimal weight: 20.0000 chunk 123 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1024 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.176995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.134062 restraints weight = 16771.943| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.50 r_work: 0.3299 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11848 Z= 0.191 Angle : 0.622 16.129 16026 Z= 0.314 Chirality : 0.042 0.168 1766 Planarity : 0.005 0.064 2072 Dihedral : 6.934 82.529 1630 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.82 % Allowed : 12.07 % Favored : 85.11 % 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: 1.48 (0.22), residues: 1424 helix: 1.69 (0.17), residues: 976 sheet: -1.91 (0.44), residues: 88 loop : -0.07 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 263 TYR 0.017 0.002 TYR A 250 PHE 0.032 0.002 PHE C 112 TRP 0.019 0.002 TRP F 241 HIS 0.007 0.002 HIS B 308 Details of bonding type rmsd covalent geometry : bond 0.00460 (11844) covalent geometry : angle 0.61710 (16020) hydrogen bonds : bond 0.04123 ( 718) hydrogen bonds : angle 4.28544 ( 2148) metal coordination : bond 0.00218 ( 4) metal coordination : angle 4.26571 ( 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 195 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 0.499 Fit side-chains REVERT: A 78 ASP cc_start: 0.8172 (t0) cc_final: 0.7871 (m-30) REVERT: A 89 LYS cc_start: 0.8832 (tptt) cc_final: 0.8438 (mtmt) REVERT: A 118 MET cc_start: 0.3145 (mmt) cc_final: 0.2213 (mpp) REVERT: A 121 MET cc_start: 0.2292 (mtt) cc_final: 0.1678 (ptt) REVERT: A 126 MET cc_start: 0.6280 (ttt) cc_final: 0.5507 (tmm) REVERT: A 306 ASP cc_start: 0.7382 (t70) cc_final: 0.7076 (m-30) REVERT: B 78 ASP cc_start: 0.8155 (t0) cc_final: 0.7865 (m-30) REVERT: B 89 LYS cc_start: 0.8623 (ttmm) cc_final: 0.8279 (mtmt) REVERT: B 118 MET cc_start: 0.3302 (mmt) cc_final: 0.2519 (mpp) REVERT: B 121 MET cc_start: 0.2222 (mtt) cc_final: 0.1646 (ptt) REVERT: B 126 MET cc_start: 0.6348 (ttt) cc_final: 0.5523 (tmm) REVERT: B 179 ARG cc_start: 0.7449 (mtm110) cc_final: 0.6908 (ttt-90) REVERT: C 238 ASN cc_start: 0.8063 (m-40) cc_final: 0.7397 (m110) REVERT: C 258 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7008 (mm) REVERT: C 260 GLU cc_start: 0.7803 (tp30) cc_final: 0.7342 (tm-30) REVERT: C 271 MET cc_start: 0.6819 (mtt) cc_final: 0.6547 (mmp) REVERT: C 277 ASP cc_start: 0.7751 (t70) cc_final: 0.7462 (t0) REVERT: D 1024 GLN cc_start: 0.7080 (OUTLIER) cc_final: 0.6452 (tp-100) REVERT: F 181 GLU cc_start: 0.7551 (tp30) cc_final: 0.7341 (tt0) REVERT: F 238 ASN cc_start: 0.8215 (m-40) cc_final: 0.7483 (m110) REVERT: F 251 LYS cc_start: 0.7367 (mptt) cc_final: 0.7136 (mmtp) REVERT: F 260 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7299 (mm-30) REVERT: F 271 MET cc_start: 0.6976 (mtt) cc_final: 0.6675 (mmp) REVERT: F 277 ASP cc_start: 0.7817 (t70) cc_final: 0.7577 (t0) REVERT: G 1042 TYR cc_start: 0.8046 (t80) cc_final: 0.7576 (t80) outliers start: 36 outliers final: 31 residues processed: 184 average time/residue: 0.0981 time to fit residues: 27.1402 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 : 0.467 ------------------------------------------------------------------------------- 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 218 GLU 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 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 81 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 12 optimal weight: 0.9980 chunk 140 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.177830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.136840 restraints weight = 16575.276| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.94 r_work: 0.3332 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11848 Z= 0.166 Angle : 0.628 18.411 16026 Z= 0.316 Chirality : 0.041 0.162 1766 Planarity : 0.005 0.064 2072 Dihedral : 6.839 79.922 1630 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.74 % Allowed : 12.38 % Favored : 84.87 % 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: 1.49 (0.22), residues: 1424 helix: 1.71 (0.17), residues: 976 sheet: -1.98 (0.44), residues: 88 loop : -0.09 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 263 TYR 0.018 0.002 TYR F 272 PHE 0.034 0.002 PHE F 112 TRP 0.027 0.002 TRP C 241 HIS 0.005 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00395 (11844) covalent geometry : angle 0.62322 (16020) hydrogen bonds : bond 0.04013 ( 718) hydrogen bonds : angle 4.26058 ( 2148) metal coordination : bond 0.00186 ( 4) metal coordination : angle 4.20349 ( 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 195 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 0.611 Fit side-chains REVERT: A 78 ASP cc_start: 0.8122 (t0) cc_final: 0.7854 (m-30) REVERT: A 89 LYS cc_start: 0.8786 (tptt) cc_final: 0.8436 (mtmt) REVERT: A 118 MET cc_start: 0.2900 (mmt) cc_final: 0.2002 (mpp) REVERT: A 121 MET cc_start: 0.2213 (mtt) cc_final: 0.1676 (ptt) REVERT: A 126 MET cc_start: 0.6236 (ttt) cc_final: 0.5461 (tmm) REVERT: B 78 ASP cc_start: 0.8111 (t0) cc_final: 0.7857 (m-30) REVERT: B 89 LYS cc_start: 0.8578 (ttmm) cc_final: 0.8277 (mtmt) REVERT: B 118 MET cc_start: 0.3022 (mmt) cc_final: 0.2236 (mpp) REVERT: B 121 MET cc_start: 0.2285 (mtt) cc_final: 0.1679 (ptt) REVERT: B 126 MET cc_start: 0.6305 (ttt) cc_final: 0.5530 (tmm) REVERT: C 238 ASN cc_start: 0.8093 (m-40) cc_final: 0.7393 (m110) REVERT: C 258 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7015 (mm) REVERT: C 271 MET cc_start: 0.6863 (mtt) cc_final: 0.6595 (mmp) REVERT: C 277 ASP cc_start: 0.7772 (t70) cc_final: 0.7491 (t0) REVERT: D 1024 GLN cc_start: 0.7074 (OUTLIER) cc_final: 0.6456 (tp-100) REVERT: F 238 ASN cc_start: 0.8221 (m-40) cc_final: 0.7468 (m110) REVERT: F 260 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7344 (mm-30) REVERT: F 271 MET cc_start: 0.6809 (mtt) cc_final: 0.6591 (mmp) REVERT: F 277 ASP cc_start: 0.7758 (t70) cc_final: 0.7529 (t0) REVERT: G 1042 TYR cc_start: 0.8090 (t80) cc_final: 0.7600 (t80) outliers start: 35 outliers final: 31 residues processed: 183 average time/residue: 0.0970 time to fit residues: 27.1347 Evaluate side-chains 186 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 218 GLU 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 306 ASP 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 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 81 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 0 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 133 optimal weight: 40.0000 chunk 57 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 13 optimal weight: 0.0170 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.177806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.130388 restraints weight = 16774.437| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.25 r_work: 0.3354 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11848 Z= 0.168 Angle : 0.643 22.175 16026 Z= 0.318 Chirality : 0.041 0.160 1766 Planarity : 0.005 0.064 2072 Dihedral : 6.779 78.967 1630 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.98 % Allowed : 12.38 % Favored : 84.64 % 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: 1.51 (0.22), residues: 1424 helix: 1.74 (0.17), residues: 976 sheet: -2.03 (0.43), residues: 88 loop : -0.10 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 263 TYR 0.022 0.002 TYR C 272 PHE 0.029 0.002 PHE C 112 TRP 0.025 0.002 TRP F 241 HIS 0.005 0.001 HIS B 308 Details of bonding type rmsd covalent geometry : bond 0.00403 (11844) covalent geometry : angle 0.63840 (16020) hydrogen bonds : bond 0.04005 ( 718) hydrogen bonds : angle 4.25892 ( 2148) metal coordination : bond 0.00197 ( 4) metal coordination : angle 4.17270 ( 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 190 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 0.497 Fit side-chains REVERT: A 78 ASP cc_start: 0.8128 (t0) cc_final: 0.7857 (m-30) REVERT: A 89 LYS cc_start: 0.8828 (tptt) cc_final: 0.8445 (mtmt) REVERT: A 118 MET cc_start: 0.2951 (mmt) cc_final: 0.2034 (mpp) REVERT: A 121 MET cc_start: 0.2251 (mtt) cc_final: 0.1740 (ptt) REVERT: A 126 MET cc_start: 0.6229 (ttt) cc_final: 0.5465 (tmm) REVERT: B 78 ASP cc_start: 0.8134 (t0) cc_final: 0.7876 (m-30) REVERT: B 89 LYS cc_start: 0.8615 (ttmm) cc_final: 0.8272 (mtmt) REVERT: B 118 MET cc_start: 0.2929 (mmt) cc_final: 0.2018 (mpp) REVERT: B 121 MET cc_start: 0.2247 (mtt) cc_final: 0.1740 (ptt) REVERT: B 126 MET cc_start: 0.6274 (ttt) cc_final: 0.5508 (tmm) REVERT: C 27 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7892 (mt-10) REVERT: C 238 ASN cc_start: 0.8128 (m-40) cc_final: 0.7427 (m110) REVERT: C 258 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.6937 (mm) REVERT: C 271 MET cc_start: 0.6662 (mtt) cc_final: 0.6333 (mmp) REVERT: C 277 ASP cc_start: 0.7766 (t70) cc_final: 0.7557 (t0) REVERT: D 1024 GLN cc_start: 0.7107 (OUTLIER) cc_final: 0.6472 (tp-100) REVERT: F 66 MET cc_start: 0.8619 (mmm) cc_final: 0.8407 (mmm) REVERT: F 230 PRO cc_start: 0.7552 (Cg_exo) cc_final: 0.7165 (Cg_endo) REVERT: F 238 ASN cc_start: 0.8265 (m-40) cc_final: 0.7507 (m110) REVERT: F 260 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7460 (mm-30) REVERT: F 271 MET cc_start: 0.6701 (mtt) cc_final: 0.6407 (mmp) REVERT: F 277 ASP cc_start: 0.7831 (t70) cc_final: 0.7600 (t0) outliers start: 38 outliers final: 32 residues processed: 178 average time/residue: 0.0935 time to fit residues: 25.6855 Evaluate side-chains 185 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 218 GLU 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 261 GLN 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 81 SER 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 1019 VAL 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: 0.7980 chunk 120 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 128 optimal weight: 0.4980 chunk 86 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 261 GLN 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 = 0.178147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.135121 restraints weight = 16627.807| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.94 r_work: 0.3290 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11848 Z= 0.159 Angle : 0.645 22.171 16026 Z= 0.319 Chirality : 0.041 0.161 1766 Planarity : 0.005 0.064 2072 Dihedral : 6.738 77.854 1630 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.66 % Allowed : 12.70 % Favored : 84.64 % 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: 1.54 (0.22), residues: 1424 helix: 1.77 (0.17), residues: 976 sheet: -2.06 (0.43), residues: 88 loop : -0.10 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 263 TYR 0.021 0.002 TYR C 272 PHE 0.031 0.002 PHE F 112 TRP 0.026 0.002 TRP C 241 HIS 0.005 0.001 HIS B 308 Details of bonding type rmsd covalent geometry : bond 0.00379 (11844) covalent geometry : angle 0.64023 (16020) hydrogen bonds : bond 0.03996 ( 718) hydrogen bonds : angle 4.23364 ( 2148) metal coordination : bond 0.00193 ( 4) metal coordination : angle 4.12184 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3511.02 seconds wall clock time: 60 minutes 54.74 seconds (3654.74 seconds total)