Starting phenix.real_space_refine on Tue Jul 29 20:58:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ru9_24700/07_2025/7ru9_24700.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ru9_24700/07_2025/7ru9_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_24700/07_2025/7ru9_24700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ru9_24700/07_2025/7ru9_24700.map" model { file = "/net/cci-nas-00/data/ceres_data/7ru9_24700/07_2025/7ru9_24700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ru9_24700/07_2025/7ru9_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 8.25, per 1000 atoms: 0.71 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: 3.14 Conformation dependent library (CDL) restraints added in 1.5 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: 3.39 Time building geometry restraints manager: 3.64 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: 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: 3.800 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 31.680 Find NCS groups from input model: 0.410 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.710 ------------------------------------------------------------------------------- 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 : 0.012 0.896 11842 Z= 1.173 Angle : 0.598 10.915 16018 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 Details of bonding type rmsd hydrogen bonds : bond 0.13487 ( 728) hydrogen bonds : angle 5.95885 ( 2160) metal coordination : bond 0.00163 ( 4) metal coordination : angle 4.42812 ( 6) covalent geometry : bond 0.00347 (11836) covalent geometry : angle 0.59152 (16012) Misc. bond : bond 0.89528 ( 2) *********************** 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 : 1.326 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: 0.2671 time to fit residues: 91.4308 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 : 1.265 ------------------------------------------------------------------------------- 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** C 198 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.183770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.144737 restraints weight = 15817.542| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.80 r_work: 0.3456 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11842 Z= 0.178 Angle : 0.607 8.033 16018 Z= 0.309 Chirality : 0.042 0.151 1766 Planarity : 0.005 0.057 2072 Dihedral : 7.587 86.116 1630 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.81 % Allowed : 5.34 % Favored : 92.86 % 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 (0.16), residues: 972 sheet: -0.39 (0.61), residues: 74 loop : -0.10 (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 0.002 PHE F 255 TYR 0.017 0.002 TYR B 250 ARG 0.005 0.001 ARG G1030 Details of bonding type rmsd hydrogen bonds : bond 0.04615 ( 728) hydrogen bonds : angle 4.28865 ( 2160) metal coordination : bond 0.00459 ( 4) metal coordination : angle 5.35686 ( 6) covalent geometry : bond 0.00417 (11836) covalent geometry : angle 0.59800 (16012) Misc. bond : bond 0.00195 ( 2) *********************** 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 203 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 1.871 Fit side-chains REVERT: A 130 MET cc_start: 0.5971 (tpt) cc_final: 0.4816 (mtt) REVERT: A 150 LYS cc_start: 0.7365 (mmtp) cc_final: 0.7037 (mmtt) REVERT: A 214 SER cc_start: 0.7721 (t) cc_final: 0.7429 (m) REVERT: A 296 TYR cc_start: 0.8762 (m-80) cc_final: 0.8458 (m-80) REVERT: B 130 MET cc_start: 0.5998 (tpt) cc_final: 0.4847 (mtt) REVERT: B 296 TYR cc_start: 0.8764 (m-80) cc_final: 0.8426 (m-80) REVERT: C 58 LYS cc_start: 0.8729 (mtpp) cc_final: 0.8468 (mttp) REVERT: C 95 LYS cc_start: 0.8938 (mmmm) cc_final: 0.8723 (mmmm) REVERT: C 121 GLU cc_start: 0.7426 (mp0) cc_final: 0.6964 (mm-30) REVERT: C 131 LYS cc_start: 0.8417 (ttpp) cc_final: 0.8115 (ttpp) REVERT: C 173 GLU cc_start: 0.7290 (mp0) cc_final: 0.7042 (mt-10) REVERT: C 222 LYS cc_start: 0.8438 (mttm) cc_final: 0.7973 (mmtm) REVERT: C 253 THR cc_start: 0.7605 (t) cc_final: 0.7232 (m) REVERT: C 257 VAL cc_start: 0.7904 (t) cc_final: 0.7603 (m) REVERT: F 58 LYS cc_start: 0.8722 (mtpp) cc_final: 0.8470 (mttp) REVERT: F 95 LYS cc_start: 0.8940 (mmmm) cc_final: 0.8726 (mmmm) REVERT: F 121 GLU cc_start: 0.7397 (mp0) cc_final: 0.6942 (mm-30) REVERT: F 131 LYS cc_start: 0.8410 (ttpp) cc_final: 0.8098 (ttpp) REVERT: F 173 GLU cc_start: 0.7321 (mp0) cc_final: 0.7065 (mt-10) REVERT: F 222 LYS cc_start: 0.8441 (mttm) cc_final: 0.7977 (mmtm) REVERT: F 251 LYS cc_start: 0.6273 (mmmt) cc_final: 0.6073 (mmtt) REVERT: F 253 THR cc_start: 0.7599 (t) cc_final: 0.7212 (m) REVERT: F 257 VAL cc_start: 0.7876 (t) cc_final: 0.7645 (m) outliers start: 23 outliers final: 8 residues processed: 201 average time/residue: 0.3057 time to fit residues: 85.2949 Evaluate side-chains 158 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 150 time to evaluate : 2.296 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 10.0000 chunk 17 optimal weight: 0.0770 chunk 99 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 136 optimal weight: 40.0000 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 HIS A 331 GLN B 235 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 GLN D1060 GLN E 118 GLN G1023 GLN G1060 GLN H 118 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.180062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.139188 restraints weight = 16082.708| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.96 r_work: 0.3363 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11842 Z= 0.154 Angle : 0.558 7.843 16018 Z= 0.283 Chirality : 0.041 0.163 1766 Planarity : 0.005 0.059 2072 Dihedral : 7.289 80.144 1630 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.10 % Allowed : 8.63 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.23), residues: 1424 helix: 2.08 (0.17), residues: 972 sheet: -0.42 (0.64), residues: 74 loop : -0.15 (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 0.029 0.001 PHE F 255 TYR 0.017 0.002 TYR B 250 ARG 0.005 0.000 ARG G1030 Details of bonding type rmsd hydrogen bonds : bond 0.04267 ( 728) hydrogen bonds : angle 4.12514 ( 2160) metal coordination : bond 0.00403 ( 4) metal coordination : angle 5.89477 ( 6) covalent geometry : bond 0.00360 (11836) covalent geometry : angle 0.54632 (16012) Misc. bond : bond 0.00001 ( 2) *********************** 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 167 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 1.357 Fit side-chains REVERT: A 130 MET cc_start: 0.5933 (tpt) cc_final: 0.4660 (mtt) REVERT: A 150 LYS cc_start: 0.7361 (mmtp) cc_final: 0.6916 (mmtt) REVERT: A 296 TYR cc_start: 0.8745 (m-80) cc_final: 0.8352 (m-80) REVERT: B 130 MET cc_start: 0.5807 (tpt) cc_final: 0.4601 (mtt) REVERT: B 296 TYR cc_start: 0.8755 (m-80) cc_final: 0.8391 (m-80) REVERT: C 58 LYS cc_start: 0.8707 (mtpp) cc_final: 0.8385 (mttp) REVERT: C 121 GLU cc_start: 0.7752 (mp0) cc_final: 0.7190 (mm-30) REVERT: C 131 LYS cc_start: 0.8460 (ttpp) cc_final: 0.8071 (ttpp) REVERT: C 155 LYS cc_start: 0.8396 (mptt) cc_final: 0.8179 (mptt) REVERT: C 173 GLU cc_start: 0.7402 (mp0) cc_final: 0.7104 (mt-10) REVERT: C 222 LYS cc_start: 0.8618 (mttm) cc_final: 0.8050 (mmtm) REVERT: C 257 VAL cc_start: 0.7757 (t) cc_final: 0.7459 (m) REVERT: F 58 LYS cc_start: 0.8705 (mtpp) cc_final: 0.8385 (mttp) REVERT: F 121 GLU cc_start: 0.7758 (mp0) cc_final: 0.7187 (mm-30) REVERT: F 131 LYS cc_start: 0.8459 (ttpp) cc_final: 0.8075 (ttpp) REVERT: F 173 GLU cc_start: 0.7378 (mp0) cc_final: 0.7091 (mt-10) REVERT: F 257 VAL cc_start: 0.7838 (t) cc_final: 0.7578 (m) outliers start: 14 outliers final: 8 residues processed: 162 average time/residue: 0.2239 time to fit residues: 53.6312 Evaluate side-chains 153 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 1.363 ------------------------------------------------------------------------------- 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 134 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 131 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 GLN B 308 HIS G1023 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.178371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.136747 restraints weight = 15782.481| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.98 r_work: 0.3324 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11842 Z= 0.187 Angle : 0.570 8.492 16018 Z= 0.290 Chirality : 0.042 0.163 1766 Planarity : 0.005 0.064 2072 Dihedral : 7.240 81.802 1630 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.04 % Allowed : 9.65 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.86 (0.23), residues: 1424 helix: 1.94 (0.17), residues: 970 sheet: -0.37 (0.65), residues: 74 loop : -0.19 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 132 HIS 0.005 0.002 HIS F 165 PHE 0.022 0.001 PHE F 255 TYR 0.018 0.002 TYR B 250 ARG 0.004 0.000 ARG F 278 Details of bonding type rmsd hydrogen bonds : bond 0.04336 ( 728) hydrogen bonds : angle 4.11689 ( 2160) metal coordination : bond 0.00577 ( 4) metal coordination : angle 6.68041 ( 6) covalent geometry : bond 0.00452 (11836) covalent geometry : angle 0.55518 (16012) Misc. bond : bond 0.00172 ( 2) *********************** 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 190 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 1.413 Fit side-chains REVERT: A 130 MET cc_start: 0.6089 (tpt) cc_final: 0.4854 (mtt) REVERT: A 296 TYR cc_start: 0.8820 (m-80) cc_final: 0.8382 (m-80) REVERT: B 130 MET cc_start: 0.6183 (tpt) cc_final: 0.4928 (mtt) REVERT: B 296 TYR cc_start: 0.8824 (m-80) cc_final: 0.8388 (m-80) REVERT: B 323 ASP cc_start: 0.8193 (t0) cc_final: 0.7986 (m-30) REVERT: C 58 LYS cc_start: 0.8751 (mtpp) cc_final: 0.8434 (mttp) REVERT: C 121 GLU cc_start: 0.7686 (mp0) cc_final: 0.7270 (mm-30) REVERT: C 131 LYS cc_start: 0.8521 (ttpp) cc_final: 0.8107 (ttpp) REVERT: C 173 GLU cc_start: 0.7579 (mp0) cc_final: 0.7289 (mt-10) REVERT: C 257 VAL cc_start: 0.7811 (t) cc_final: 0.7521 (m) REVERT: F 58 LYS cc_start: 0.8746 (mtpp) cc_final: 0.8421 (mttp) REVERT: F 121 GLU cc_start: 0.7669 (mp0) cc_final: 0.7265 (mm-30) REVERT: F 131 LYS cc_start: 0.8535 (ttpp) cc_final: 0.8127 (ttpp) REVERT: F 155 LYS cc_start: 0.8378 (mptt) cc_final: 0.8129 (mptt) REVERT: F 173 GLU cc_start: 0.7529 (mp0) cc_final: 0.7238 (mt-10) REVERT: F 222 LYS cc_start: 0.8657 (mttm) cc_final: 0.8254 (mmtm) REVERT: F 257 VAL cc_start: 0.7900 (t) cc_final: 0.7633 (m) outliers start: 26 outliers final: 12 residues processed: 183 average time/residue: 0.2768 time to fit residues: 72.5944 Evaluate side-chains 151 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 1.786 ------------------------------------------------------------------------------- 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 157 VAL 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 108 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 131 optimal weight: 0.4980 chunk 137 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** C 198 GLN ** G1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1095 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.178834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.136898 restraints weight = 15802.555| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.36 r_work: 0.3325 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11842 Z= 0.166 Angle : 0.544 7.775 16018 Z= 0.279 Chirality : 0.041 0.151 1766 Planarity : 0.005 0.065 2072 Dihedral : 7.045 77.124 1630 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.73 % Allowed : 11.22 % 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: 1.87 (0.23), residues: 1424 helix: 1.96 (0.17), residues: 968 sheet: -0.49 (0.64), residues: 74 loop : -0.19 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 132 HIS 0.004 0.001 HIS F 43 PHE 0.017 0.001 PHE F 255 TYR 0.017 0.002 TYR A 250 ARG 0.005 0.000 ARG F 278 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 728) hydrogen bonds : angle 4.07324 ( 2160) metal coordination : bond 0.00503 ( 4) metal coordination : angle 6.04279 ( 6) covalent geometry : bond 0.00396 (11836) covalent geometry : angle 0.53106 (16012) Misc. bond : bond 0.00119 ( 2) *********************** 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 173 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 1.549 Fit side-chains REVERT: A 130 MET cc_start: 0.6031 (tpt) cc_final: 0.4682 (mtp) REVERT: A 296 TYR cc_start: 0.8823 (m-80) cc_final: 0.8390 (m-80) REVERT: B 130 MET cc_start: 0.5978 (tpt) cc_final: 0.4738 (mtt) REVERT: B 296 TYR cc_start: 0.8829 (m-80) cc_final: 0.8403 (m-80) REVERT: B 323 ASP cc_start: 0.8233 (t0) cc_final: 0.8013 (m-30) REVERT: C 58 LYS cc_start: 0.8778 (mtpp) cc_final: 0.8427 (mttp) REVERT: C 121 GLU cc_start: 0.7699 (mp0) cc_final: 0.7296 (mm-30) REVERT: C 131 LYS cc_start: 0.8536 (ttpp) cc_final: 0.8115 (ttpp) REVERT: C 166 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8486 (m-80) REVERT: C 173 GLU cc_start: 0.7597 (mp0) cc_final: 0.7320 (mt-10) REVERT: F 58 LYS cc_start: 0.8771 (mtpp) cc_final: 0.8417 (mttp) REVERT: F 121 GLU cc_start: 0.7695 (mp0) cc_final: 0.7299 (mm-30) REVERT: F 166 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8479 (m-80) REVERT: F 173 GLU cc_start: 0.7622 (mp0) cc_final: 0.7351 (mt-10) REVERT: F 257 VAL cc_start: 0.7951 (t) cc_final: 0.7600 (m) REVERT: G 1023 GLN cc_start: 0.8191 (mm-40) cc_final: 0.7942 (mm-40) outliers start: 22 outliers final: 15 residues processed: 168 average time/residue: 0.2999 time to fit residues: 73.8057 Evaluate side-chains 155 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 1.411 ------------------------------------------------------------------------------- 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 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 123 LYS 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 30 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 109 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 137 optimal weight: 40.0000 chunk 80 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 186 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 ASN ** G1023 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 = 0.4096 r_free = 0.4096 target = 0.177612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.135425 restraints weight = 15938.759| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.79 r_work: 0.3339 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11842 Z= 0.196 Angle : 0.573 8.521 16018 Z= 0.292 Chirality : 0.042 0.166 1766 Planarity : 0.005 0.063 2072 Dihedral : 7.101 81.091 1630 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.81 % Allowed : 11.54 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.74 (0.23), residues: 1424 helix: 1.88 (0.17), residues: 970 sheet: -0.60 (0.63), residues: 74 loop : -0.28 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 132 HIS 0.005 0.001 HIS F 165 PHE 0.014 0.001 PHE F 255 TYR 0.018 0.002 TYR A 250 ARG 0.005 0.000 ARG C 278 Details of bonding type rmsd hydrogen bonds : bond 0.04313 ( 728) hydrogen bonds : angle 4.10117 ( 2160) metal coordination : bond 0.00639 ( 4) metal coordination : angle 6.85802 ( 6) covalent geometry : bond 0.00472 (11836) covalent geometry : angle 0.55793 (16012) Misc. bond : bond 0.00123 ( 2) *********************** 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 163 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 1.279 Fit side-chains REVERT: A 130 MET cc_start: 0.5821 (tpt) cc_final: 0.4679 (mtp) REVERT: A 181 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7506 (tp) REVERT: A 296 TYR cc_start: 0.8805 (m-80) cc_final: 0.8318 (m-80) REVERT: B 130 MET cc_start: 0.5872 (tpt) cc_final: 0.4723 (mtp) REVERT: B 296 TYR cc_start: 0.8812 (m-80) cc_final: 0.8335 (m-80) REVERT: C 58 LYS cc_start: 0.8688 (mtpp) cc_final: 0.8375 (mttp) REVERT: C 121 GLU cc_start: 0.7364 (mp0) cc_final: 0.7094 (mm-30) REVERT: C 131 LYS cc_start: 0.8408 (ttpp) cc_final: 0.8026 (ttpp) REVERT: C 166 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.8093 (m-80) REVERT: C 173 GLU cc_start: 0.7455 (mp0) cc_final: 0.7220 (mt-10) REVERT: F 58 LYS cc_start: 0.8694 (mtpp) cc_final: 0.8378 (mttp) REVERT: F 121 GLU cc_start: 0.7378 (mp0) cc_final: 0.7096 (mm-30) REVERT: F 166 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.8088 (m-80) REVERT: F 173 GLU cc_start: 0.7453 (mp0) cc_final: 0.7219 (mt-10) outliers start: 23 outliers final: 16 residues processed: 155 average time/residue: 0.2431 time to fit residues: 55.3863 Evaluate side-chains 157 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 1.341 ------------------------------------------------------------------------------- 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 152 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 181 LEU 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 123 LYS Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 152 MET 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 59 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 138 optimal weight: 50.0000 chunk 78 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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** D1023 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.177852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.135779 restraints weight = 16009.122| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.79 r_work: 0.3349 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11842 Z= 0.176 Angle : 0.561 7.849 16018 Z= 0.285 Chirality : 0.042 0.184 1766 Planarity : 0.005 0.065 2072 Dihedral : 7.016 78.280 1630 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.88 % Allowed : 11.70 % 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: 970 sheet: -0.67 (0.61), residues: 74 loop : -0.30 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 132 HIS 0.004 0.001 HIS C 43 PHE 0.013 0.001 PHE C 255 TYR 0.017 0.001 TYR B 250 ARG 0.003 0.000 ARG F 278 Details of bonding type rmsd hydrogen bonds : bond 0.04157 ( 728) hydrogen bonds : angle 4.08230 ( 2160) metal coordination : bond 0.00584 ( 4) metal coordination : angle 6.44131 ( 6) covalent geometry : bond 0.00419 (11836) covalent geometry : angle 0.54657 (16012) Misc. bond : bond 0.00108 ( 2) *********************** 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 162 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 1.400 Fit side-chains REVERT: A 130 MET cc_start: 0.6075 (tpt) cc_final: 0.4855 (mtp) REVERT: A 167 THR cc_start: 0.8921 (m) cc_final: 0.8613 (m) REVERT: A 181 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7597 (tp) REVERT: A 296 TYR cc_start: 0.8832 (m-80) cc_final: 0.8419 (m-80) REVERT: B 130 MET cc_start: 0.6070 (tpt) cc_final: 0.4837 (mtp) REVERT: B 296 TYR cc_start: 0.8846 (m-80) cc_final: 0.8365 (m-80) REVERT: C 58 LYS cc_start: 0.8747 (mtpp) cc_final: 0.8418 (mttp) REVERT: C 121 GLU cc_start: 0.7565 (mp0) cc_final: 0.7237 (mm-30) REVERT: C 131 LYS cc_start: 0.8414 (ttpp) cc_final: 0.8020 (ttpp) REVERT: C 166 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8133 (m-80) REVERT: C 173 GLU cc_start: 0.7639 (mp0) cc_final: 0.7377 (mt-10) REVERT: C 271 MET cc_start: 0.7266 (mmt) cc_final: 0.6918 (mmt) REVERT: F 58 LYS cc_start: 0.8753 (mtpp) cc_final: 0.8423 (mttp) REVERT: F 121 GLU cc_start: 0.7601 (mp0) cc_final: 0.7255 (mm-30) REVERT: F 166 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8126 (m-80) REVERT: F 173 GLU cc_start: 0.7618 (mp0) cc_final: 0.7369 (mt-10) outliers start: 24 outliers final: 17 residues processed: 156 average time/residue: 0.2560 time to fit residues: 59.1080 Evaluate side-chains 152 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 1.308 ------------------------------------------------------------------------------- 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 152 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 181 LEU 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 133 PHE Chi-restraints excluded: chain B residue 152 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 97 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 25 optimal weight: 0.0970 chunk 72 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- 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 G1023 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.179874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.137840 restraints weight = 15937.283| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.79 r_work: 0.3383 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11842 Z= 0.129 Angle : 0.526 7.859 16018 Z= 0.268 Chirality : 0.040 0.170 1766 Planarity : 0.005 0.064 2072 Dihedral : 6.696 69.420 1630 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.96 % Allowed : 12.09 % Favored : 85.95 % 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: 1.96 (0.23), residues: 1424 helix: 2.04 (0.17), residues: 972 sheet: -0.75 (0.61), residues: 74 loop : -0.13 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 132 HIS 0.004 0.001 HIS C 43 PHE 0.041 0.001 PHE F 255 TYR 0.016 0.001 TYR G1042 ARG 0.003 0.000 ARG F 278 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 728) hydrogen bonds : angle 3.99800 ( 2160) metal coordination : bond 0.00367 ( 4) metal coordination : angle 5.04701 ( 6) covalent geometry : bond 0.00292 (11836) covalent geometry : angle 0.51698 (16012) Misc. bond : bond 0.00074 ( 2) *********************** 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 190 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 1.254 Fit side-chains REVERT: A 130 MET cc_start: 0.5826 (tpt) cc_final: 0.4565 (mtp) REVERT: A 181 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7562 (tp) REVERT: A 296 TYR cc_start: 0.8781 (m-80) cc_final: 0.8404 (m-80) REVERT: B 130 MET cc_start: 0.5843 (tpt) cc_final: 0.4562 (mtp) REVERT: B 296 TYR cc_start: 0.8772 (m-80) cc_final: 0.8391 (m-80) REVERT: C 58 LYS cc_start: 0.8721 (mtpp) cc_final: 0.8373 (mttp) REVERT: C 121 GLU cc_start: 0.7590 (mp0) cc_final: 0.7254 (mm-30) REVERT: C 131 LYS cc_start: 0.8423 (ttpp) cc_final: 0.7998 (ttpp) REVERT: C 166 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.7983 (m-80) REVERT: C 173 GLU cc_start: 0.7490 (mp0) cc_final: 0.7217 (mt-10) REVERT: C 232 PHE cc_start: 0.7908 (m-80) cc_final: 0.7707 (m-80) REVERT: C 271 MET cc_start: 0.7160 (mmt) cc_final: 0.6924 (mmt) REVERT: C 274 GLU cc_start: 0.7727 (mp0) cc_final: 0.7429 (mp0) REVERT: F 58 LYS cc_start: 0.8711 (mtpp) cc_final: 0.8368 (mttp) REVERT: F 121 GLU cc_start: 0.7583 (mp0) cc_final: 0.7251 (mm-30) REVERT: F 131 LYS cc_start: 0.8401 (ttpp) cc_final: 0.7975 (ttpp) REVERT: F 155 LYS cc_start: 0.8423 (mptt) cc_final: 0.8118 (mptt) REVERT: F 166 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.7971 (m-80) REVERT: F 173 GLU cc_start: 0.7525 (mp0) cc_final: 0.7277 (mt-10) REVERT: F 222 LYS cc_start: 0.8667 (mttm) cc_final: 0.8210 (mmtm) REVERT: F 257 VAL cc_start: 0.7890 (t) cc_final: 0.7536 (m) REVERT: F 271 MET cc_start: 0.7236 (mmt) cc_final: 0.6898 (mmt) outliers start: 25 outliers final: 14 residues processed: 181 average time/residue: 0.2325 time to fit residues: 61.5003 Evaluate side-chains 164 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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 133 PHE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 181 LEU 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 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 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 42 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 139 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 92 optimal weight: 20.0000 chunk 86 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 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 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 = 0.4107 r_free = 0.4107 target = 0.178427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.136685 restraints weight = 15979.769| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.11 r_work: 0.3317 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11842 Z= 0.163 Angle : 0.552 8.810 16018 Z= 0.280 Chirality : 0.041 0.166 1766 Planarity : 0.005 0.063 2072 Dihedral : 6.779 74.520 1630 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.57 % Allowed : 12.40 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.02 (0.17), residues: 972 sheet: -0.89 (0.59), residues: 74 loop : -0.23 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 241 HIS 0.004 0.001 HIS F 43 PHE 0.038 0.002 PHE F 255 TYR 0.017 0.001 TYR B 250 ARG 0.002 0.000 ARG C 278 Details of bonding type rmsd hydrogen bonds : bond 0.03973 ( 728) hydrogen bonds : angle 4.02080 ( 2160) metal coordination : bond 0.00467 ( 4) metal coordination : angle 5.82663 ( 6) covalent geometry : bond 0.00387 (11836) covalent geometry : angle 0.54026 (16012) Misc. bond : bond 0.00102 ( 2) *********************** 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 166 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 1.262 Fit side-chains REVERT: A 130 MET cc_start: 0.5908 (tpt) cc_final: 0.4650 (mtp) REVERT: A 181 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7594 (tp) REVERT: A 296 TYR cc_start: 0.8820 (m-80) cc_final: 0.8374 (m-80) REVERT: B 130 MET cc_start: 0.5970 (tpt) cc_final: 0.4681 (mtp) REVERT: B 296 TYR cc_start: 0.8795 (m-80) cc_final: 0.8340 (m-80) REVERT: C 58 LYS cc_start: 0.8758 (mtpp) cc_final: 0.8416 (mttp) REVERT: C 121 GLU cc_start: 0.7789 (mp0) cc_final: 0.7381 (mm-30) REVERT: C 131 LYS cc_start: 0.8505 (ttpp) cc_final: 0.8078 (ttpp) REVERT: C 166 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8053 (m-80) REVERT: C 173 GLU cc_start: 0.7650 (mp0) cc_final: 0.7356 (mt-10) REVERT: C 271 MET cc_start: 0.7228 (mmt) cc_final: 0.6988 (mmt) REVERT: C 274 GLU cc_start: 0.7832 (mp0) cc_final: 0.7534 (mp0) REVERT: F 58 LYS cc_start: 0.8759 (mtpp) cc_final: 0.8419 (mttp) REVERT: F 121 GLU cc_start: 0.7751 (mp0) cc_final: 0.7357 (mm-30) REVERT: F 166 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8045 (m-80) REVERT: F 173 GLU cc_start: 0.7660 (mp0) cc_final: 0.7397 (mt-10) REVERT: F 257 VAL cc_start: 0.7885 (t) cc_final: 0.7515 (m) REVERT: F 271 MET cc_start: 0.7293 (mmt) cc_final: 0.6909 (mmt) outliers start: 20 outliers final: 15 residues processed: 159 average time/residue: 0.2277 time to fit residues: 53.4470 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 : 1.392 ------------------------------------------------------------------------------- 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 133 PHE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 181 LEU 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 133 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 137 optimal weight: 40.0000 chunk 69 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.178058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.135580 restraints weight = 15815.561| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.06 r_work: 0.3334 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11842 Z= 0.167 Angle : 0.555 8.162 16018 Z= 0.282 Chirality : 0.041 0.164 1766 Planarity : 0.005 0.064 2072 Dihedral : 6.816 75.636 1630 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.49 % Allowed : 12.48 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.85 (0.23), residues: 1424 helix: 2.00 (0.17), residues: 972 sheet: -1.03 (0.57), residues: 74 loop : -0.27 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 241 HIS 0.004 0.001 HIS C 165 PHE 0.036 0.002 PHE F 255 TYR 0.017 0.001 TYR A 250 ARG 0.004 0.000 ARG F 278 Details of bonding type rmsd hydrogen bonds : bond 0.03982 ( 728) hydrogen bonds : angle 4.03438 ( 2160) metal coordination : bond 0.00519 ( 4) metal coordination : angle 5.90392 ( 6) covalent geometry : bond 0.00398 (11836) covalent geometry : angle 0.54333 (16012) Misc. bond : bond 0.00105 ( 2) ********************** 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 166 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 1.393 Fit side-chains REVERT: A 130 MET cc_start: 0.6000 (tpt) cc_final: 0.4771 (mtp) REVERT: A 181 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7577 (tp) REVERT: A 296 TYR cc_start: 0.8821 (m-80) cc_final: 0.8401 (m-80) REVERT: B 130 MET cc_start: 0.5949 (tpt) cc_final: 0.4739 (mtp) REVERT: B 296 TYR cc_start: 0.8805 (m-80) cc_final: 0.8376 (m-80) REVERT: C 58 LYS cc_start: 0.8743 (mtpp) cc_final: 0.8404 (mttp) REVERT: C 121 GLU cc_start: 0.7669 (mp0) cc_final: 0.7303 (mm-30) REVERT: C 131 LYS cc_start: 0.8473 (ttpp) cc_final: 0.8062 (ttpp) REVERT: C 166 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.7933 (m-80) REVERT: C 173 GLU cc_start: 0.7641 (mp0) cc_final: 0.7367 (mt-10) REVERT: C 274 GLU cc_start: 0.7775 (mp0) cc_final: 0.7497 (mp0) REVERT: F 58 LYS cc_start: 0.8737 (mtpp) cc_final: 0.8410 (mttp) REVERT: F 121 GLU cc_start: 0.7669 (mp0) cc_final: 0.7304 (mm-30) REVERT: F 166 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.7939 (m-80) REVERT: F 173 GLU cc_start: 0.7651 (mp0) cc_final: 0.7368 (mt-10) outliers start: 19 outliers final: 14 residues processed: 160 average time/residue: 0.2305 time to fit residues: 53.9209 Evaluate side-chains 163 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 1.298 ------------------------------------------------------------------------------- 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 133 PHE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 268 ASN 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 133 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 8 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 114 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 110 optimal weight: 0.0000 overall best weight: 0.4584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.179495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.136010 restraints weight = 15768.889| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.45 r_work: 0.3347 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11842 Z= 0.129 Angle : 0.534 10.211 16018 Z= 0.271 Chirality : 0.040 0.168 1766 Planarity : 0.005 0.064 2072 Dihedral : 6.641 69.630 1630 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.41 % Allowed : 13.11 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.96 (0.23), residues: 1424 helix: 2.11 (0.17), residues: 970 sheet: -1.19 (0.57), residues: 74 loop : -0.23 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 241 HIS 0.004 0.001 HIS F 43 PHE 0.034 0.001 PHE F 255 TYR 0.014 0.001 TYR B 250 ARG 0.003 0.000 ARG F 278 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 728) hydrogen bonds : angle 4.00215 ( 2160) metal coordination : bond 0.00386 ( 4) metal coordination : angle 5.10452 ( 6) covalent geometry : bond 0.00293 (11836) covalent geometry : angle 0.52471 (16012) Misc. bond : bond 0.00071 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7100.01 seconds wall clock time: 125 minutes 57.08 seconds (7557.08 seconds total)