Starting phenix.real_space_refine on Sun Dec 29 23:55:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ru9_24700/12_2024/7ru9_24700.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ru9_24700/12_2024/7ru9_24700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ru9_24700/12_2024/7ru9_24700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ru9_24700/12_2024/7ru9_24700.map" model { file = "/net/cci-nas-00/data/ceres_data/7ru9_24700/12_2024/7ru9_24700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ru9_24700/12_2024/7ru9_24700.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 6 5.49 5 Mg 2 5.21 5 S 64 5.16 5 C 7344 2.51 5 N 1990 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 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11595 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2417 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 18, 'TRANS': 287} Chain breaks: 1 Chain: "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: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 781 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 12, 'TRANS': 86} 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 1952 SG CYS A 283 53.792 63.510 98.162 1.00 84.39 S ATOM 1975 SG CYS A 286 54.557 65.964 95.564 1.00 78.05 S Restraints were copied for chains: B, F, G, H Time building chain proxies: 9.20, per 1000 atoms: 0.79 Number of scatterers: 11595 At special positions: 0 Unit cell: (106.425, 131.175, 113.85, 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 1990 7.00 C 7344 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.50 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 403 " pdb="ZN ZN A 403 " - pdb=" SG CYS A 286 " pdb="ZN ZN A 403 " - pdb=" SG CYS B 286 " pdb="ZN ZN A 403 " - pdb=" SG CYS B 283 " pdb="ZN ZN A 403 " - pdb=" SG CYS A 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 72.1% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 22 through 28 Processing helix chain 'A' and resid 43 through 57 Processing helix chain 'A' and resid 72 through 78 Processing helix chain 'A' and resid 116 through 133 removed outlier: 4.289A pdb=" N SER A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY A 122 " --> pdb=" O MET A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 152 Processing helix chain 'A' and resid 163 through 187 Proline residue: A 174 - end of helix Processing helix chain 'A' and resid 210 through 231 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: 3.511A 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 Processing helix chain 'B' and resid 72 through 78 Processing helix chain 'B' and resid 116 through 133 removed outlier: 4.289A pdb=" N SER B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY B 122 " --> pdb=" O MET B 118 " (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 210 through 231 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: 3.510A pdb=" N GLN B 331 " --> pdb=" O THR B 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 37 removed outlier: 3.518A 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 removed outlier: 3.585A pdb=" N MET C 115 " --> pdb=" O VAL C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 133 removed outlier: 4.175A pdb=" N VAL C 123 " --> pdb=" O SER C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 156 removed outlier: 4.037A pdb=" N HIS C 146 " --> pdb=" O HIS C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 168 Processing helix chain 'C' and resid 171 through 186 removed outlier: 3.678A pdb=" N CYS C 175 " --> pdb=" O ASP C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 190 No H-bonds generated for 'chain 'C' and resid 188 through 190' Processing helix chain 'C' and resid 191 through 206 removed outlier: 4.127A pdb=" N VAL C 196 " --> pdb=" O VAL C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 223 Processing helix chain 'C' and resid 234 through 250 Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 262 through 267 Processing helix chain 'C' and resid 270 through 284 removed outlier: 4.151A pdb=" N GLU C 274 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN C 281 " --> pdb=" O ASP C 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 1008 through 1013 Processing helix chain 'D' and resid 1015 through 1017 No H-bonds generated for 'chain 'D' and resid 1015 through 1017' Processing helix chain 'D' and resid 1018 through 1030 Processing helix chain 'D' and resid 1039 through 1046 removed outlier: 3.921A pdb=" N GLY D1045 " --> pdb=" O ALA D1041 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET D1046 " --> pdb=" O TYR D1042 " (cutoff:3.500A) Processing helix chain 'D' and resid 1062 through 1075 Processing helix chain 'D' and resid 1081 through 1090 removed outlier: 3.764A pdb=" N LEU D1089 " --> pdb=" O LEU D1085 " (cutoff:3.500A) Processing helix chain 'D' and resid 1092 through 1113 removed outlier: 4.176A pdb=" N SER D1097 " --> pdb=" O GLU D1093 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N TYR D1098 " --> pdb=" O VAL D1094 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG D1099 " --> pdb=" O GLN D1095 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN D1111 " --> pdb=" O GLN D1107 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU D1112 " --> pdb=" O LYS D1108 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 107 removed outlier: 3.910A pdb=" N ARG E 105 " --> pdb=" O LYS E 101 " (cutoff:3.500A) 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: 3.518A 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 removed outlier: 3.586A pdb=" N MET F 115 " --> pdb=" O VAL F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 133 removed outlier: 4.176A pdb=" N VAL F 123 " --> pdb=" O SER F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 156 removed outlier: 4.036A pdb=" N HIS F 146 " --> pdb=" O HIS F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 168 Processing helix chain 'F' and resid 171 through 186 removed outlier: 3.679A pdb=" N CYS F 175 " --> pdb=" O ASP F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 190 No H-bonds generated for 'chain 'F' and resid 188 through 190' Processing helix chain 'F' and resid 191 through 206 removed outlier: 4.127A 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 270 through 284 removed outlier: 4.151A pdb=" N GLU F 274 " --> pdb=" O PRO F 270 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN F 281 " --> pdb=" O ASP F 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 1008 through 1013 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 1030 Processing helix chain 'G' and resid 1039 through 1046 removed outlier: 3.920A pdb=" N GLY G1045 " --> pdb=" O ALA G1041 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET G1046 " --> pdb=" O TYR G1042 " (cutoff:3.500A) Processing helix chain 'G' and resid 1062 through 1075 Processing helix chain 'G' and resid 1081 through 1090 removed outlier: 3.764A pdb=" N LEU G1089 " --> pdb=" O LEU G1085 " (cutoff:3.500A) Processing helix chain 'G' and resid 1092 through 1113 removed outlier: 4.176A pdb=" N SER G1097 " --> pdb=" O GLU G1093 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N TYR G1098 " --> pdb=" O VAL G1094 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG G1099 " --> pdb=" O GLN G1095 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN G1111 " --> pdb=" O GLN G1107 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU G1112 " --> pdb=" O LYS G1108 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 107 removed outlier: 3.909A pdb=" N ARG H 105 " --> pdb=" O LYS H 101 " (cutoff:3.500A) 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: 6.488A pdb=" N VAL A 62 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N MET A 97 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE A 64 " --> pdb=" O MET A 97 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU A 63 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ASP A 160 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE A 65 " --> pdb=" O ASP A 160 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TRP A 33 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ILE A 239 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE A 35 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL A 241 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N GLY A 37 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N ILE A 243 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASN A 268 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE A 269 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU A 312 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 6.439A 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: 6.487A pdb=" N VAL B 62 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N MET B 97 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE B 64 " --> pdb=" O MET B 97 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU B 63 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ASP B 160 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE B 65 " --> pdb=" O ASP B 160 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP B 33 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE B 239 " --> pdb=" O TRP B 33 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE B 35 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL B 241 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N GLY B 37 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N ILE B 243 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASN B 268 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE B 269 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU B 312 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL B 271 " --> pdb=" O LEU B 312 " (cutoff:3.500A) 728 hydrogen bonds defined for protein. 2160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.62 Time building geometry restraints manager: 3.81 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: 3815 1.34 - 1.46: 1992 1.46 - 1.58: 5913 1.58 - 1.70: 10 1.70 - 1.82: 106 Bond restraints: 11836 Sorted by residual: bond pdb=" CA LYS D1049 " pdb=" CB LYS D1049 " ideal model delta sigma weight residual 1.527 1.541 -0.015 1.39e-02 5.18e+03 1.13e+00 bond pdb=" C ALA G1048 " pdb=" N LYS G1049 " ideal model delta sigma weight residual 1.330 1.346 -0.015 1.43e-02 4.89e+03 1.13e+00 bond pdb=" CA LYS G1049 " pdb=" CB LYS G1049 " ideal model delta sigma weight residual 1.527 1.541 -0.014 1.39e-02 5.18e+03 1.06e+00 bond pdb=" CB GLN H 118 " pdb=" CG GLN H 118 " ideal model delta sigma weight residual 1.520 1.489 0.031 3.00e-02 1.11e+03 1.06e+00 bond pdb=" CB GLN E 118 " pdb=" CG GLN E 118 " ideal model delta sigma weight residual 1.520 1.489 0.031 3.00e-02 1.11e+03 1.03e+00 ... (remaining 11831 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 15821 2.18 - 4.37: 155 4.37 - 6.55: 24 6.55 - 8.73: 6 8.73 - 10.91: 6 Bond angle restraints: 16012 Sorted by residual: angle pdb=" CA LYS D1049 " pdb=" CB LYS D1049 " pdb=" CG LYS D1049 " ideal model delta sigma weight residual 114.10 124.58 -10.48 2.00e+00 2.50e-01 2.75e+01 angle pdb=" CA LYS G1049 " pdb=" CB LYS G1049 " pdb=" CG LYS G1049 " ideal model delta sigma weight residual 114.10 124.57 -10.47 2.00e+00 2.50e-01 2.74e+01 angle pdb=" CB LYS D1049 " pdb=" CG LYS D1049 " pdb=" CD LYS D1049 " ideal model delta sigma weight residual 111.30 119.72 -8.42 2.30e+00 1.89e-01 1.34e+01 angle pdb=" CB LYS G1049 " pdb=" CG LYS G1049 " pdb=" CD LYS G1049 " ideal model delta sigma weight residual 111.30 119.70 -8.40 2.30e+00 1.89e-01 1.33e+01 angle pdb=" CB LEU B 184 " pdb=" CG LEU B 184 " pdb=" CD2 LEU B 184 " ideal model delta sigma weight residual 110.70 121.61 -10.91 3.00e+00 1.11e-01 1.32e+01 ... (remaining 16007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 6496 17.56 - 35.12: 622 35.12 - 52.68: 130 52.68 - 70.24: 44 70.24 - 87.80: 10 Dihedral angle restraints: 7302 sinusoidal: 3064 harmonic: 4238 Sorted by residual: dihedral pdb=" CA GLY C 141 " pdb=" C GLY C 141 " pdb=" N HIS C 142 " pdb=" CA HIS C 142 " ideal model delta harmonic sigma weight residual 180.00 157.97 22.03 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA GLY F 141 " pdb=" C GLY F 141 " pdb=" N HIS F 142 " pdb=" CA HIS F 142 " ideal model delta harmonic sigma weight residual 180.00 157.99 22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CD ARG E 121 " pdb=" NE ARG E 121 " pdb=" CZ ARG E 121 " pdb=" NH1 ARG E 121 " ideal model delta sinusoidal sigma weight residual 0.00 33.89 -33.89 1 1.00e+01 1.00e-02 1.63e+01 ... (remaining 7299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.345: 1764 0.345 - 0.689: 0 0.689 - 1.034: 0 1.034 - 1.379: 0 1.379 - 1.724: 2 Chirality restraints: 1766 Sorted by residual: chirality pdb=" CG LEU B 184 " pdb=" CB LEU B 184 " pdb=" CD1 LEU B 184 " pdb=" CD2 LEU B 184 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.43e+01 chirality pdb=" CG LEU A 184 " pdb=" CB LEU A 184 " pdb=" CD1 LEU A 184 " pdb=" CD2 LEU A 184 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.40e+01 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 2.15e+00 ... (remaining 1763 not shown) Planarity restraints: 2072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 121 " -0.595 9.50e-02 1.11e+02 2.67e-01 4.34e+01 pdb=" NE ARG E 121 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG E 121 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG E 121 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG E 121 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 121 " 0.594 9.50e-02 1.11e+02 2.66e-01 4.33e+01 pdb=" NE ARG H 121 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG H 121 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG H 121 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG H 121 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D1051 " -0.213 9.50e-02 1.11e+02 9.57e-02 5.81e+00 pdb=" NE ARG D1051 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG D1051 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG D1051 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D1051 " -0.005 2.00e-02 2.50e+03 ... (remaining 2069 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 66 2.50 - 3.10: 9387 3.10 - 3.70: 18835 3.70 - 4.30: 26390 4.30 - 4.90: 43026 Nonbonded interactions: 97704 Sorted by model distance: nonbonded pdb=" OE1 GLN H 118 " pdb=" NH2 ARG H 121 " model vdw 1.899 3.120 nonbonded pdb=" OE1 GLN E 118 " pdb=" NH2 ARG E 121 " model vdw 1.899 3.120 nonbonded pdb=" O2G ATP A 401 " pdb="MG MG A 402 " model vdw 1.948 2.170 nonbonded pdb=" O2G ATP B 401 " pdb="MG MG B 402 " model vdw 1.949 2.170 nonbonded pdb=" OG1 THR B 45 " pdb="MG MG B 402 " model vdw 1.963 2.170 ... (remaining 97699 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 339 or resid 401 through 402)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.300 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 33.320 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 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:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 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 0.038 11836 Z= 0.227 Angle : 0.592 10.915 16012 Z= 0.300 Chirality : 0.070 1.724 1766 Planarity : 0.010 0.267 2072 Dihedral : 14.936 87.803 4542 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.24), residues: 1424 helix: 2.03 (0.18), residues: 934 sheet: -0.62 (0.53), residues: 84 loop : -0.15 (0.33), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 132 HIS 0.005 0.001 HIS C 43 PHE 0.008 0.001 PHE A 328 TYR 0.010 0.001 TYR A 250 ARG 0.014 0.001 ARG D1050 *********************** 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 248 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 1.350 Fit side-chains revert: symmetry clash REVERT: A 19 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7028 (tp30) REVERT: A 89 LYS cc_start: 0.7639 (ttmm) cc_final: 0.7353 (tmtt) REVERT: A 125 MET cc_start: 0.6261 (mmp) cc_final: 0.5873 (ttt) REVERT: A 130 MET cc_start: 0.5085 (tpt) cc_final: 0.4099 (mtt) REVERT: A 235 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7788 (mm110) REVERT: A 258 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6818 (mm-30) REVERT: A 298 ASP cc_start: 0.7576 (t70) cc_final: 0.7342 (t0) REVERT: B 19 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7037 (tp30) REVERT: B 89 LYS cc_start: 0.7616 (ttmm) cc_final: 0.7350 (tmtt) REVERT: B 125 MET cc_start: 0.6271 (mmp) cc_final: 0.5909 (ttt) REVERT: B 130 MET cc_start: 0.5037 (tpt) cc_final: 0.4091 (mtt) REVERT: B 235 GLN cc_start: 0.8237 (mm-40) cc_final: 0.7771 (mm110) REVERT: B 258 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6859 (mm-30) REVERT: B 298 ASP cc_start: 0.7575 (t70) cc_final: 0.7328 (t0) REVERT: C 58 LYS cc_start: 0.8231 (mtpp) cc_final: 0.7779 (mttp) REVERT: C 95 LYS cc_start: 0.8614 (mmmm) cc_final: 0.8372 (mmmm) REVERT: C 121 GLU cc_start: 0.7608 (mp0) cc_final: 0.6997 (mm-30) REVERT: C 131 LYS cc_start: 0.8501 (ttpp) cc_final: 0.8104 (ttpp) REVERT: C 155 LYS cc_start: 0.8241 (mttp) cc_final: 0.7956 (mmtp) REVERT: C 173 GLU cc_start: 0.7322 (mp0) cc_final: 0.7113 (mt-10) REVERT: C 218 THR cc_start: 0.8530 (m) cc_final: 0.8329 (m) REVERT: C 222 LYS cc_start: 0.8507 (mttm) cc_final: 0.8014 (mmtm) REVERT: C 264 PRO cc_start: 0.8118 (Cg_exo) cc_final: 0.7868 (Cg_endo) REVERT: F 58 LYS cc_start: 0.8237 (mtpp) cc_final: 0.7785 (mttp) REVERT: F 95 LYS cc_start: 0.8605 (mmmm) cc_final: 0.8364 (mmmm) REVERT: F 121 GLU cc_start: 0.7596 (mp0) cc_final: 0.6977 (mm-30) REVERT: F 131 LYS cc_start: 0.8502 (ttpp) cc_final: 0.8104 (ttpp) REVERT: F 155 LYS cc_start: 0.8250 (mttp) cc_final: 0.7966 (mmtp) REVERT: F 173 GLU cc_start: 0.7334 (mp0) cc_final: 0.7115 (mt-10) REVERT: F 222 LYS cc_start: 0.8511 (mttm) cc_final: 0.8026 (mmtm) REVERT: F 264 PRO cc_start: 0.8107 (Cg_exo) cc_final: 0.7848 (Cg_endo) REVERT: G 1023 GLN cc_start: 0.8025 (mt0) cc_final: 0.7819 (mm-40) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.2946 time to fit residues: 101.1589 Evaluate side-chains 158 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN A 186 GLN ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 GLN B 186 GLN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11836 Z= 0.268 Angle : 0.595 8.101 16012 Z= 0.307 Chirality : 0.042 0.150 1766 Planarity : 0.005 0.057 2072 Dihedral : 7.676 87.243 1630 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.88 % Allowed : 5.10 % Favored : 93.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.23), residues: 1424 helix: 2.02 (0.16), residues: 972 sheet: -0.39 (0.60), residues: 74 loop : -0.09 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D1010 HIS 0.005 0.002 HIS F 168 PHE 0.014 0.001 PHE C 255 TYR 0.017 0.002 TYR B 250 ARG 0.005 0.001 ARG G1030 *********************** 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 204 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 1.323 Fit side-chains REVERT: A 19 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7022 (tp30) REVERT: A 87 LYS cc_start: 0.8228 (tttt) cc_final: 0.7866 (mtpp) REVERT: A 89 LYS cc_start: 0.7695 (ttmm) cc_final: 0.7382 (tmtt) REVERT: A 125 MET cc_start: 0.6261 (mmp) cc_final: 0.5907 (ttt) REVERT: A 130 MET cc_start: 0.5071 (tpt) cc_final: 0.4061 (mtt) REVERT: A 186 GLN cc_start: 0.6380 (OUTLIER) cc_final: 0.6167 (pp30) REVERT: A 214 SER cc_start: 0.7550 (t) cc_final: 0.7237 (m) REVERT: A 235 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7659 (mm110) REVERT: A 258 GLU cc_start: 0.7269 (mm-30) cc_final: 0.6855 (mm-30) REVERT: A 296 TYR cc_start: 0.8170 (m-80) cc_final: 0.7735 (m-80) REVERT: A 298 ASP cc_start: 0.7664 (t70) cc_final: 0.7450 (t0) REVERT: B 19 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7021 (tp30) REVERT: B 87 LYS cc_start: 0.8228 (tttt) cc_final: 0.7879 (mtpp) REVERT: B 89 LYS cc_start: 0.7663 (ttmm) cc_final: 0.7375 (tmtt) REVERT: B 125 MET cc_start: 0.6232 (mmp) cc_final: 0.5906 (ttt) REVERT: B 130 MET cc_start: 0.5030 (tpt) cc_final: 0.4049 (mtt) REVERT: B 214 SER cc_start: 0.7519 (t) cc_final: 0.7181 (m) REVERT: B 235 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7674 (mm110) REVERT: B 258 GLU cc_start: 0.7259 (mm-30) cc_final: 0.6864 (mm-30) REVERT: B 296 TYR cc_start: 0.8195 (m-80) cc_final: 0.7702 (m-80) REVERT: B 298 ASP cc_start: 0.7711 (t70) cc_final: 0.7496 (t0) REVERT: C 58 LYS cc_start: 0.8181 (mtpp) cc_final: 0.7671 (mttp) REVERT: C 95 LYS cc_start: 0.8662 (mmmm) cc_final: 0.8414 (mmmm) REVERT: C 103 GLU cc_start: 0.7829 (tp30) cc_final: 0.7478 (tp30) REVERT: C 121 GLU cc_start: 0.7533 (mp0) cc_final: 0.6931 (mm-30) REVERT: C 131 LYS cc_start: 0.8498 (ttpp) cc_final: 0.8105 (ttpp) REVERT: C 155 LYS cc_start: 0.8036 (mttp) cc_final: 0.7752 (mptt) REVERT: C 173 GLU cc_start: 0.7471 (mp0) cc_final: 0.7126 (mt-10) REVERT: C 218 THR cc_start: 0.8571 (m) cc_final: 0.8280 (m) REVERT: C 222 LYS cc_start: 0.8633 (mttm) cc_final: 0.8041 (mmtm) REVERT: C 253 THR cc_start: 0.7667 (t) cc_final: 0.7307 (m) REVERT: C 257 VAL cc_start: 0.7851 (t) cc_final: 0.7552 (m) REVERT: F 58 LYS cc_start: 0.8172 (mtpp) cc_final: 0.7668 (mttp) REVERT: F 95 LYS cc_start: 0.8661 (mmmm) cc_final: 0.8417 (mmmm) REVERT: F 103 GLU cc_start: 0.7824 (tp30) cc_final: 0.7473 (tp30) REVERT: F 121 GLU cc_start: 0.7510 (mp0) cc_final: 0.6917 (mm-30) REVERT: F 131 LYS cc_start: 0.8501 (ttpp) cc_final: 0.8107 (ttpp) REVERT: F 155 LYS cc_start: 0.8051 (mttp) cc_final: 0.7767 (mptt) REVERT: F 173 GLU cc_start: 0.7482 (mp0) cc_final: 0.7132 (mt-10) REVERT: F 222 LYS cc_start: 0.8627 (mttm) cc_final: 0.8033 (mmtm) REVERT: F 253 THR cc_start: 0.7670 (t) cc_final: 0.7294 (m) REVERT: F 257 VAL cc_start: 0.7841 (t) cc_final: 0.7594 (m) outliers start: 24 outliers final: 10 residues processed: 201 average time/residue: 0.2800 time to fit residues: 78.1133 Evaluate side-chains 162 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 186 GLN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain F residue 274 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 HIS A 331 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 HIS B 331 GLN D1060 GLN E 118 GLN G1023 GLN G1060 GLN H 118 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11836 Z= 0.234 Angle : 0.540 7.867 16012 Z= 0.279 Chirality : 0.041 0.146 1766 Planarity : 0.005 0.062 2072 Dihedral : 7.355 81.124 1630 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.41 % Allowed : 8.48 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.23), residues: 1424 helix: 2.07 (0.16), residues: 972 sheet: -0.42 (0.64), residues: 74 loop : -0.16 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D1010 HIS 0.004 0.001 HIS F 43 PHE 0.032 0.001 PHE F 255 TYR 0.016 0.002 TYR A 250 ARG 0.005 0.000 ARG G1030 *********************** 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 176 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 1.317 Fit side-chains REVERT: A 19 GLU cc_start: 0.7296 (mm-30) cc_final: 0.6969 (tp30) REVERT: A 87 LYS cc_start: 0.8225 (tttt) cc_final: 0.7844 (mtpp) REVERT: A 89 LYS cc_start: 0.7737 (ttmm) cc_final: 0.7394 (tmtt) REVERT: A 125 MET cc_start: 0.6164 (mmp) cc_final: 0.5863 (ttt) REVERT: A 130 MET cc_start: 0.5091 (tpt) cc_final: 0.4056 (mtt) REVERT: A 235 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7518 (mm-40) REVERT: A 296 TYR cc_start: 0.8078 (m-80) cc_final: 0.7654 (m-80) REVERT: A 323 ASP cc_start: 0.7600 (t0) cc_final: 0.7382 (m-30) REVERT: B 19 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6967 (tp30) REVERT: B 87 LYS cc_start: 0.8212 (tttt) cc_final: 0.7843 (mtpp) REVERT: B 89 LYS cc_start: 0.7699 (ttmm) cc_final: 0.7338 (tmtt) REVERT: B 125 MET cc_start: 0.6131 (mmp) cc_final: 0.5862 (ttt) REVERT: B 130 MET cc_start: 0.4996 (tpt) cc_final: 0.4037 (mtt) REVERT: B 235 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7550 (mm110) REVERT: B 296 TYR cc_start: 0.8097 (m-80) cc_final: 0.7690 (m-80) REVERT: B 323 ASP cc_start: 0.7593 (t0) cc_final: 0.7391 (m-30) REVERT: C 58 LYS cc_start: 0.8164 (mtpp) cc_final: 0.7700 (mttp) REVERT: C 103 GLU cc_start: 0.7850 (tp30) cc_final: 0.7612 (tp30) REVERT: C 121 GLU cc_start: 0.7562 (mp0) cc_final: 0.6970 (mm-30) REVERT: C 131 LYS cc_start: 0.8463 (ttpp) cc_final: 0.8066 (ttpp) REVERT: C 155 LYS cc_start: 0.8030 (mttp) cc_final: 0.7741 (mptt) REVERT: C 173 GLU cc_start: 0.7460 (mp0) cc_final: 0.7135 (mt-10) REVERT: C 222 LYS cc_start: 0.8680 (mttm) cc_final: 0.8234 (mmtm) REVERT: C 257 VAL cc_start: 0.7678 (t) cc_final: 0.7368 (m) REVERT: F 58 LYS cc_start: 0.8163 (mtpp) cc_final: 0.7699 (mttp) REVERT: F 103 GLU cc_start: 0.7845 (tp30) cc_final: 0.7607 (tp30) REVERT: F 121 GLU cc_start: 0.7555 (mp0) cc_final: 0.6963 (mm-30) REVERT: F 131 LYS cc_start: 0.8466 (ttpp) cc_final: 0.8069 (ttpp) REVERT: F 155 LYS cc_start: 0.8038 (mttp) cc_final: 0.7735 (mptt) REVERT: F 173 GLU cc_start: 0.7497 (mp0) cc_final: 0.7164 (mt-10) REVERT: F 222 LYS cc_start: 0.8677 (mttm) cc_final: 0.8039 (mmtm) REVERT: F 257 VAL cc_start: 0.7763 (t) cc_final: 0.7487 (m) outliers start: 18 outliers final: 8 residues processed: 170 average time/residue: 0.2473 time to fit residues: 60.7398 Evaluate side-chains 155 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 268 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 3.9990 chunk 95 optimal weight: 40.0000 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 135 optimal weight: 30.0000 chunk 121 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11836 Z= 0.248 Angle : 0.536 7.756 16012 Z= 0.278 Chirality : 0.041 0.149 1766 Planarity : 0.005 0.064 2072 Dihedral : 7.117 77.507 1630 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.65 % Allowed : 9.65 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.23), residues: 1424 helix: 2.01 (0.17), residues: 972 sheet: -0.34 (0.65), residues: 74 loop : -0.12 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 132 HIS 0.004 0.001 HIS F 165 PHE 0.023 0.001 PHE F 255 TYR 0.017 0.002 TYR B 250 ARG 0.003 0.000 ARG F 278 *********************** 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 181 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 1.226 Fit side-chains REVERT: A 19 GLU cc_start: 0.7324 (mm-30) cc_final: 0.7010 (tp30) REVERT: A 87 LYS cc_start: 0.8323 (tttt) cc_final: 0.7928 (mtpp) REVERT: A 89 LYS cc_start: 0.7734 (ttmm) cc_final: 0.7330 (tmtt) REVERT: A 125 MET cc_start: 0.6267 (mmp) cc_final: 0.5936 (ttt) REVERT: A 130 MET cc_start: 0.5116 (tpt) cc_final: 0.4104 (mtt) REVERT: A 144 GLU cc_start: 0.7889 (tp30) cc_final: 0.7594 (mm-30) REVERT: A 323 ASP cc_start: 0.7691 (t0) cc_final: 0.7433 (m-30) REVERT: B 19 GLU cc_start: 0.7324 (mm-30) cc_final: 0.7027 (tp30) REVERT: B 87 LYS cc_start: 0.8313 (tttt) cc_final: 0.7930 (mtpp) REVERT: B 89 LYS cc_start: 0.7713 (ttmm) cc_final: 0.7337 (tmtt) REVERT: B 125 MET cc_start: 0.6262 (mmp) cc_final: 0.5937 (ttt) REVERT: B 130 MET cc_start: 0.5184 (tpt) cc_final: 0.4178 (mtt) REVERT: B 144 GLU cc_start: 0.7883 (tp30) cc_final: 0.7583 (mm-30) REVERT: B 186 GLN cc_start: 0.6313 (OUTLIER) cc_final: 0.6092 (pp30) REVERT: B 296 TYR cc_start: 0.8174 (m-80) cc_final: 0.7653 (m-80) REVERT: B 323 ASP cc_start: 0.7692 (t0) cc_final: 0.7446 (m-30) REVERT: C 58 LYS cc_start: 0.8136 (mtpp) cc_final: 0.7668 (mttp) REVERT: C 103 GLU cc_start: 0.7887 (tp30) cc_final: 0.7631 (tp30) REVERT: C 121 GLU cc_start: 0.7621 (mp0) cc_final: 0.7043 (mm-30) REVERT: C 131 LYS cc_start: 0.8463 (ttpp) cc_final: 0.8036 (ttpp) REVERT: C 173 GLU cc_start: 0.7675 (mp0) cc_final: 0.7342 (mt-10) REVERT: C 257 VAL cc_start: 0.7725 (t) cc_final: 0.7418 (m) REVERT: F 58 LYS cc_start: 0.8139 (mtpp) cc_final: 0.7667 (mttp) REVERT: F 103 GLU cc_start: 0.7886 (tp30) cc_final: 0.7623 (tp30) REVERT: F 121 GLU cc_start: 0.7614 (mp0) cc_final: 0.7034 (mm-30) REVERT: F 131 LYS cc_start: 0.8471 (ttpp) cc_final: 0.8039 (ttpp) REVERT: F 173 GLU cc_start: 0.7683 (mp0) cc_final: 0.7345 (mt-10) REVERT: F 257 VAL cc_start: 0.7820 (t) cc_final: 0.7536 (m) outliers start: 21 outliers final: 12 residues processed: 176 average time/residue: 0.2288 time to fit residues: 58.8391 Evaluate side-chains 155 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 310 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 2.9990 chunk 1 optimal weight: 0.0870 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 93 optimal weight: 50.0000 chunk 0 optimal weight: 1.9990 chunk 69 optimal weight: 0.0020 chunk 121 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.2172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1023 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11836 Z= 0.312 Angle : 0.556 7.722 16012 Z= 0.290 Chirality : 0.042 0.166 1766 Planarity : 0.005 0.064 2072 Dihedral : 7.198 81.660 1630 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.81 % Allowed : 10.52 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.23), residues: 1424 helix: 1.89 (0.17), residues: 968 sheet: -0.39 (0.63), residues: 74 loop : -0.19 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 132 HIS 0.006 0.001 HIS C 165 PHE 0.018 0.001 PHE F 255 TYR 0.018 0.002 TYR B 250 ARG 0.004 0.000 ARG F 278 *********************** 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 178 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 1.384 Fit side-chains REVERT: A 19 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7019 (tp30) REVERT: A 87 LYS cc_start: 0.8341 (tttt) cc_final: 0.7957 (mtpp) REVERT: A 89 LYS cc_start: 0.7753 (ttmm) cc_final: 0.7438 (tmtt) REVERT: A 125 MET cc_start: 0.6287 (mmp) cc_final: 0.5944 (ttt) REVERT: A 130 MET cc_start: 0.5185 (tpt) cc_final: 0.4144 (mtp) REVERT: A 296 TYR cc_start: 0.8260 (m-80) cc_final: 0.7730 (m-80) REVERT: A 323 ASP cc_start: 0.7715 (t0) cc_final: 0.7416 (m-30) REVERT: B 19 GLU cc_start: 0.7326 (mm-30) cc_final: 0.7011 (tp30) REVERT: B 87 LYS cc_start: 0.8355 (tttt) cc_final: 0.7974 (mtpp) REVERT: B 89 LYS cc_start: 0.7743 (ttmm) cc_final: 0.7392 (tmtt) REVERT: B 125 MET cc_start: 0.6287 (mmp) cc_final: 0.5956 (ttt) REVERT: B 130 MET cc_start: 0.5138 (tpt) cc_final: 0.4139 (mtp) REVERT: B 296 TYR cc_start: 0.8262 (m-80) cc_final: 0.7750 (m-80) REVERT: B 323 ASP cc_start: 0.7730 (t0) cc_final: 0.7444 (m-30) REVERT: C 24 GLN cc_start: 0.7956 (tp40) cc_final: 0.7733 (tm-30) REVERT: C 58 LYS cc_start: 0.8174 (mtpp) cc_final: 0.7691 (mttp) REVERT: C 121 GLU cc_start: 0.7677 (mp0) cc_final: 0.7089 (mm-30) REVERT: C 131 LYS cc_start: 0.8541 (ttpp) cc_final: 0.8101 (ttpp) REVERT: C 166 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.8051 (m-80) REVERT: C 173 GLU cc_start: 0.7714 (mp0) cc_final: 0.7404 (mt-10) REVERT: F 58 LYS cc_start: 0.8173 (mtpp) cc_final: 0.7689 (mttp) REVERT: F 121 GLU cc_start: 0.7681 (mp0) cc_final: 0.7095 (mm-30) REVERT: F 131 LYS cc_start: 0.8542 (ttpp) cc_final: 0.8102 (ttpp) REVERT: F 166 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.8058 (m-80) REVERT: F 173 GLU cc_start: 0.7727 (mp0) cc_final: 0.7415 (mt-10) REVERT: G 1023 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7688 (mm110) outliers start: 23 outliers final: 13 residues processed: 170 average time/residue: 0.2554 time to fit residues: 62.0611 Evaluate side-chains 155 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain F residue 166 PHE Chi-restraints excluded: chain G residue 1023 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 135 optimal weight: 30.0000 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11836 Z= 0.233 Angle : 0.528 7.805 16012 Z= 0.276 Chirality : 0.040 0.144 1766 Planarity : 0.005 0.065 2072 Dihedral : 6.981 75.702 1630 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.81 % Allowed : 11.15 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.23), residues: 1424 helix: 1.96 (0.17), residues: 970 sheet: -0.50 (0.64), residues: 74 loop : -0.14 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 132 HIS 0.004 0.001 HIS C 43 PHE 0.015 0.001 PHE C 255 TYR 0.016 0.001 TYR B 250 ARG 0.004 0.000 ARG F 278 *********************** 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 165 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 1.361 Fit side-chains REVERT: A 19 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7024 (tp30) REVERT: A 87 LYS cc_start: 0.8338 (tttt) cc_final: 0.7952 (mtpp) REVERT: A 89 LYS cc_start: 0.7746 (ttmm) cc_final: 0.7432 (tmtt) REVERT: A 125 MET cc_start: 0.6279 (mmp) cc_final: 0.5941 (ttt) REVERT: A 130 MET cc_start: 0.5133 (tpt) cc_final: 0.4114 (mtt) REVERT: A 296 TYR cc_start: 0.8185 (m-80) cc_final: 0.7704 (m-80) REVERT: A 323 ASP cc_start: 0.7718 (t0) cc_final: 0.7448 (m-30) REVERT: B 19 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7015 (tp30) REVERT: B 87 LYS cc_start: 0.8342 (tttt) cc_final: 0.7955 (mtpp) REVERT: B 89 LYS cc_start: 0.7762 (ttmm) cc_final: 0.7445 (tmtt) REVERT: B 125 MET cc_start: 0.6283 (mmp) cc_final: 0.5957 (ttt) REVERT: B 130 MET cc_start: 0.5161 (tpt) cc_final: 0.4092 (mtp) REVERT: B 296 TYR cc_start: 0.8201 (m-80) cc_final: 0.7674 (m-80) REVERT: B 323 ASP cc_start: 0.7726 (t0) cc_final: 0.7464 (m-30) REVERT: C 58 LYS cc_start: 0.8151 (mtpp) cc_final: 0.7670 (mttp) REVERT: C 121 GLU cc_start: 0.7651 (mp0) cc_final: 0.7081 (mm-30) REVERT: C 131 LYS cc_start: 0.8486 (ttpp) cc_final: 0.8048 (ttpp) REVERT: C 166 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.7962 (m-80) REVERT: C 173 GLU cc_start: 0.7755 (mp0) cc_final: 0.7451 (mt-10) REVERT: F 58 LYS cc_start: 0.8149 (mtpp) cc_final: 0.7665 (mttp) REVERT: F 121 GLU cc_start: 0.7645 (mp0) cc_final: 0.7076 (mm-30) REVERT: F 131 LYS cc_start: 0.8485 (ttpp) cc_final: 0.8043 (ttpp) REVERT: F 166 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.7897 (m-80) REVERT: F 173 GLU cc_start: 0.7766 (mp0) cc_final: 0.7459 (mt-10) outliers start: 23 outliers final: 14 residues processed: 160 average time/residue: 0.2471 time to fit residues: 57.0153 Evaluate side-chains 150 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain F residue 166 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 98 optimal weight: 20.0000 chunk 76 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 84 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11836 Z= 0.334 Angle : 0.582 7.641 16012 Z= 0.302 Chirality : 0.043 0.182 1766 Planarity : 0.005 0.063 2072 Dihedral : 7.181 83.173 1630 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.65 % Allowed : 11.54 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.23), residues: 1424 helix: 1.82 (0.17), residues: 968 sheet: -0.61 (0.62), residues: 74 loop : -0.29 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 132 HIS 0.005 0.001 HIS C 165 PHE 0.013 0.002 PHE C 255 TYR 0.018 0.002 TYR A 250 ARG 0.003 0.000 ARG A 224 *********************** 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 161 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 1.315 Fit side-chains REVERT: A 19 GLU cc_start: 0.7327 (mm-30) cc_final: 0.7001 (tp30) REVERT: A 87 LYS cc_start: 0.8334 (tttt) cc_final: 0.7948 (mtpp) REVERT: A 89 LYS cc_start: 0.7788 (ttmm) cc_final: 0.7464 (tmtt) REVERT: A 125 MET cc_start: 0.6312 (mmp) cc_final: 0.5969 (ttt) REVERT: A 130 MET cc_start: 0.5191 (tpt) cc_final: 0.4218 (mtp) REVERT: A 296 TYR cc_start: 0.8313 (m-80) cc_final: 0.7713 (m-80) REVERT: A 323 ASP cc_start: 0.7764 (t0) cc_final: 0.7486 (m-30) REVERT: B 19 GLU cc_start: 0.7320 (mm-30) cc_final: 0.6995 (tp30) REVERT: B 87 LYS cc_start: 0.8335 (tttt) cc_final: 0.7949 (mtpp) REVERT: B 89 LYS cc_start: 0.7802 (ttmm) cc_final: 0.7470 (tmtt) REVERT: B 125 MET cc_start: 0.6345 (mmp) cc_final: 0.5962 (ttt) REVERT: B 130 MET cc_start: 0.5177 (tpt) cc_final: 0.4198 (mtp) REVERT: B 296 TYR cc_start: 0.8233 (m-80) cc_final: 0.7670 (m-80) REVERT: C 24 GLN cc_start: 0.7999 (tp40) cc_final: 0.7762 (tm-30) REVERT: C 58 LYS cc_start: 0.8173 (mtpp) cc_final: 0.7714 (mttp) REVERT: C 121 GLU cc_start: 0.7687 (mp0) cc_final: 0.7116 (mm-30) REVERT: C 131 LYS cc_start: 0.8525 (ttpp) cc_final: 0.8083 (ttpp) REVERT: C 166 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.7802 (m-80) REVERT: C 173 GLU cc_start: 0.7783 (mp0) cc_final: 0.7491 (mt-10) REVERT: F 24 GLN cc_start: 0.7996 (tp40) cc_final: 0.7759 (tm-30) REVERT: F 58 LYS cc_start: 0.8170 (mtpp) cc_final: 0.7711 (mttp) REVERT: F 121 GLU cc_start: 0.7677 (mp0) cc_final: 0.7107 (mm-30) REVERT: F 131 LYS cc_start: 0.8526 (ttpp) cc_final: 0.8087 (ttpp) REVERT: F 166 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.7814 (m-80) REVERT: F 173 GLU cc_start: 0.7791 (mp0) cc_final: 0.7481 (mt-10) outliers start: 21 outliers final: 17 residues processed: 156 average time/residue: 0.2489 time to fit residues: 55.7394 Evaluate side-chains 156 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain F residue 166 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 85 optimal weight: 0.0050 chunk 91 optimal weight: 0.0010 chunk 66 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 129 optimal weight: 0.8980 overall best weight: 0.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1023 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11836 Z= 0.187 Angle : 0.519 7.863 16012 Z= 0.269 Chirality : 0.040 0.167 1766 Planarity : 0.005 0.066 2072 Dihedral : 6.707 68.316 1630 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.57 % Allowed : 11.62 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.23), residues: 1424 helix: 1.98 (0.17), residues: 972 sheet: -0.71 (0.61), residues: 74 loop : -0.16 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 132 HIS 0.005 0.001 HIS C 43 PHE 0.013 0.001 PHE F 255 TYR 0.016 0.001 TYR G1042 ARG 0.002 0.000 ARG C 278 *********************** 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 178 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 1.289 Fit side-chains REVERT: A 19 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6990 (tp30) REVERT: A 87 LYS cc_start: 0.8354 (tttt) cc_final: 0.7957 (mtpp) REVERT: A 89 LYS cc_start: 0.7764 (ttmm) cc_final: 0.7474 (tmtt) REVERT: A 125 MET cc_start: 0.6266 (mmp) cc_final: 0.5931 (ttt) REVERT: A 130 MET cc_start: 0.4950 (tpt) cc_final: 0.3973 (mtt) REVERT: A 296 TYR cc_start: 0.8117 (m-80) cc_final: 0.7713 (m-80) REVERT: A 323 ASP cc_start: 0.7678 (t0) cc_final: 0.7454 (m-30) REVERT: B 19 GLU cc_start: 0.7340 (mm-30) cc_final: 0.6986 (tp30) REVERT: B 87 LYS cc_start: 0.8360 (tttt) cc_final: 0.7959 (mtpp) REVERT: B 89 LYS cc_start: 0.7764 (ttmm) cc_final: 0.7475 (tmtt) REVERT: B 125 MET cc_start: 0.6380 (mmp) cc_final: 0.6036 (ttt) REVERT: B 130 MET cc_start: 0.4927 (tpt) cc_final: 0.3944 (mtp) REVERT: B 296 TYR cc_start: 0.8139 (m-80) cc_final: 0.7715 (m-80) REVERT: B 323 ASP cc_start: 0.7685 (t0) cc_final: 0.7464 (m-30) REVERT: C 58 LYS cc_start: 0.8127 (mtpp) cc_final: 0.7649 (mttp) REVERT: C 121 GLU cc_start: 0.7630 (mp0) cc_final: 0.7088 (mm-30) REVERT: C 131 LYS cc_start: 0.8428 (ttpp) cc_final: 0.7991 (ttpp) REVERT: C 166 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.7656 (m-80) REVERT: C 173 GLU cc_start: 0.7774 (mp0) cc_final: 0.7453 (mt-10) REVERT: C 271 MET cc_start: 0.6879 (mmt) cc_final: 0.6494 (mmt) REVERT: F 58 LYS cc_start: 0.8124 (mtpp) cc_final: 0.7647 (mttp) REVERT: F 121 GLU cc_start: 0.7622 (mp0) cc_final: 0.7081 (mm-30) REVERT: F 131 LYS cc_start: 0.8435 (ttpp) cc_final: 0.7995 (ttpp) REVERT: F 166 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.7665 (m-80) REVERT: F 173 GLU cc_start: 0.7706 (mp0) cc_final: 0.7432 (mt-10) REVERT: F 271 MET cc_start: 0.6890 (mmt) cc_final: 0.6446 (mmt) REVERT: G 1023 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7876 (mm110) outliers start: 20 outliers final: 12 residues processed: 173 average time/residue: 0.2472 time to fit residues: 62.4022 Evaluate side-chains 148 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain F residue 166 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 3.9990 chunk 125 optimal weight: 0.0670 chunk 129 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 98 optimal weight: 20.0000 chunk 38 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 132 optimal weight: 20.0000 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11836 Z= 0.292 Angle : 0.559 7.723 16012 Z= 0.290 Chirality : 0.042 0.164 1766 Planarity : 0.005 0.062 2072 Dihedral : 6.900 77.749 1630 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.57 % Allowed : 12.01 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.23), residues: 1424 helix: 1.90 (0.17), residues: 972 sheet: -0.90 (0.59), residues: 74 loop : -0.25 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 132 HIS 0.004 0.001 HIS C 165 PHE 0.044 0.002 PHE C 255 TYR 0.018 0.002 TYR B 250 ARG 0.002 0.000 ARG C 278 *********************** 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 165 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 1.324 Fit side-chains REVERT: A 19 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7006 (tp30) REVERT: A 87 LYS cc_start: 0.8331 (tttt) cc_final: 0.7934 (mtpp) REVERT: A 89 LYS cc_start: 0.7787 (ttmm) cc_final: 0.7500 (tmtt) REVERT: A 125 MET cc_start: 0.6406 (mmp) cc_final: 0.6004 (ttt) REVERT: A 130 MET cc_start: 0.5084 (tpt) cc_final: 0.4118 (mtp) REVERT: A 296 TYR cc_start: 0.8204 (m-80) cc_final: 0.7692 (m-80) REVERT: A 323 ASP cc_start: 0.7738 (t0) cc_final: 0.7488 (m-30) REVERT: B 19 GLU cc_start: 0.7332 (mm-30) cc_final: 0.7001 (tp30) REVERT: B 87 LYS cc_start: 0.8327 (tttt) cc_final: 0.7927 (mtpp) REVERT: B 89 LYS cc_start: 0.7781 (ttmm) cc_final: 0.7495 (tmtt) REVERT: B 125 MET cc_start: 0.6382 (mmp) cc_final: 0.6024 (ttt) REVERT: B 130 MET cc_start: 0.5051 (tpt) cc_final: 0.4096 (mtp) REVERT: B 296 TYR cc_start: 0.8247 (m-80) cc_final: 0.7728 (m-80) REVERT: C 24 GLN cc_start: 0.8000 (tp40) cc_final: 0.7769 (tm-30) REVERT: C 58 LYS cc_start: 0.8144 (mtpp) cc_final: 0.7681 (mttp) REVERT: C 121 GLU cc_start: 0.7700 (mp0) cc_final: 0.7126 (mm-30) REVERT: C 131 LYS cc_start: 0.8511 (ttpp) cc_final: 0.8071 (ttpp) REVERT: C 166 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.7706 (m-80) REVERT: C 173 GLU cc_start: 0.7801 (mp0) cc_final: 0.7485 (mt-10) REVERT: C 271 MET cc_start: 0.6954 (mmt) cc_final: 0.6564 (mmt) REVERT: F 24 GLN cc_start: 0.8004 (tp40) cc_final: 0.7771 (tm-30) REVERT: F 58 LYS cc_start: 0.8148 (mtpp) cc_final: 0.7685 (mttp) REVERT: F 121 GLU cc_start: 0.7693 (mp0) cc_final: 0.7123 (mm-30) REVERT: F 131 LYS cc_start: 0.8512 (ttpp) cc_final: 0.8069 (ttpp) REVERT: F 166 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.7727 (m-80) REVERT: F 173 GLU cc_start: 0.7726 (mp0) cc_final: 0.7457 (mt-10) outliers start: 20 outliers final: 16 residues processed: 158 average time/residue: 0.2529 time to fit residues: 57.2312 Evaluate side-chains 160 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain F residue 166 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 85 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 118 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11836 Z= 0.219 Angle : 0.531 7.938 16012 Z= 0.275 Chirality : 0.040 0.169 1766 Planarity : 0.005 0.065 2072 Dihedral : 6.705 70.812 1630 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.10 % Allowed : 12.72 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.23), residues: 1424 helix: 1.97 (0.17), residues: 972 sheet: -1.04 (0.59), residues: 74 loop : -0.21 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 132 HIS 0.004 0.001 HIS F 43 PHE 0.040 0.001 PHE C 255 TYR 0.019 0.001 TYR D1042 ARG 0.002 0.000 ARG F 278 ********************** 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 163 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 1.397 Fit side-chains REVERT: A 19 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6996 (tp30) REVERT: A 87 LYS cc_start: 0.8349 (tttt) cc_final: 0.7930 (mtpp) REVERT: A 89 LYS cc_start: 0.7783 (ttmm) cc_final: 0.7495 (tmtt) REVERT: A 125 MET cc_start: 0.6394 (mmp) cc_final: 0.6007 (ttt) REVERT: A 130 MET cc_start: 0.4952 (tpt) cc_final: 0.4004 (mtt) REVERT: A 296 TYR cc_start: 0.8123 (m-80) cc_final: 0.7623 (m-80) REVERT: A 323 ASP cc_start: 0.7692 (t0) cc_final: 0.7465 (m-30) REVERT: B 19 GLU cc_start: 0.7329 (mm-30) cc_final: 0.6991 (tp30) REVERT: B 87 LYS cc_start: 0.8352 (tttt) cc_final: 0.7933 (mtpp) REVERT: B 89 LYS cc_start: 0.7780 (ttmm) cc_final: 0.7494 (tmtt) REVERT: B 125 MET cc_start: 0.6377 (mmp) cc_final: 0.6001 (ttt) REVERT: B 130 MET cc_start: 0.4966 (tpt) cc_final: 0.3991 (mtp) REVERT: B 296 TYR cc_start: 0.8186 (m-80) cc_final: 0.7667 (m-80) REVERT: C 58 LYS cc_start: 0.8132 (mtpp) cc_final: 0.7674 (mttp) REVERT: C 121 GLU cc_start: 0.7650 (mp0) cc_final: 0.7102 (mm-30) REVERT: C 131 LYS cc_start: 0.8447 (ttpp) cc_final: 0.8005 (ttpp) REVERT: C 166 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.7685 (m-80) REVERT: C 173 GLU cc_start: 0.7796 (mp0) cc_final: 0.7545 (mt-10) REVERT: C 271 MET cc_start: 0.6908 (mmt) cc_final: 0.6541 (mmt) REVERT: F 58 LYS cc_start: 0.8125 (mtpp) cc_final: 0.7668 (mttp) REVERT: F 121 GLU cc_start: 0.7644 (mp0) cc_final: 0.7096 (mm-30) REVERT: F 131 LYS cc_start: 0.8459 (ttpp) cc_final: 0.8019 (ttpp) REVERT: F 166 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.7683 (m-80) REVERT: F 173 GLU cc_start: 0.7767 (mp0) cc_final: 0.7483 (mt-10) outliers start: 14 outliers final: 12 residues processed: 159 average time/residue: 0.2320 time to fit residues: 54.1818 Evaluate side-chains 154 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain F residue 166 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 0.0980 chunk 97 optimal weight: 30.0000 chunk 6 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.178930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.138442 restraints weight = 15650.852| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.28 r_work: 0.3300 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11836 Z= 0.225 Angle : 0.537 7.913 16012 Z= 0.278 Chirality : 0.040 0.167 1766 Planarity : 0.005 0.063 2072 Dihedral : 6.678 71.851 1630 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.26 % Allowed : 12.56 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.23), residues: 1424 helix: 2.01 (0.17), residues: 972 sheet: -1.05 (0.58), residues: 74 loop : -0.25 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 241 HIS 0.004 0.001 HIS C 43 PHE 0.038 0.001 PHE F 255 TYR 0.016 0.001 TYR B 250 ARG 0.004 0.000 ARG F 278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2362.13 seconds wall clock time: 45 minutes 4.04 seconds (2704.04 seconds total)