Starting phenix.real_space_refine on Thu Feb 15 07:43:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru9_24700/02_2024/7ru9_24700_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru9_24700/02_2024/7ru9_24700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru9_24700/02_2024/7ru9_24700.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru9_24700/02_2024/7ru9_24700.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru9_24700/02_2024/7ru9_24700_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru9_24700/02_2024/7ru9_24700_updated.pdb" } 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 Residue "C ASP 38": "OD1" <-> "OD2" Residue "C ASP 84": "OD1" <-> "OD2" Residue "D TYR 1098": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 121": "NH1" <-> "NH2" Residue "F ASP 38": "OD1" <-> "OD2" Residue "F ASP 84": "OD1" <-> "OD2" Residue "G TYR 1098": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 121": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11595 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2417 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 18, 'TRANS': 287} Chain breaks: 1 Chain: "B" Number of atoms: 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: "F" Number of atoms: 2175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2175 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 11, 'TRANS': 259} Chain: "G" Number of atoms: 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: "H" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 392 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 47} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 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 ATOM 4369 SG CYS B 283 51.806 66.851 98.150 1.00 84.50 S ATOM 4392 SG CYS B 286 51.039 64.395 95.554 1.00 77.94 S Time building chain proxies: 7.01, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 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: 4.71 Conformation dependent library (CDL) restraints added in 2.0 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... running ksdssp... Secondary structure from input PDB file: 68 helices and 2 sheets defined 63.8% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 22 through 27 Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 117 through 132 removed outlier: 3.702A pdb=" N GLY A 122 " --> pdb=" O MET A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 151 Processing helix chain 'A' and resid 164 through 186 Proline residue: A 174 - end of helix Processing helix chain 'A' and resid 210 through 230 Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 246 through 262 Processing helix chain 'A' and resid 284 through 303 Processing helix chain 'A' and resid 322 through 333 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 27 Processing helix chain 'B' and resid 44 through 56 Processing helix chain 'B' and resid 73 through 77 Processing helix chain 'B' and resid 117 through 132 removed outlier: 3.702A pdb=" N GLY B 122 " --> pdb=" O MET B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 151 Processing helix chain 'B' and resid 164 through 186 Proline residue: B 174 - end of helix Processing helix chain 'B' and resid 210 through 230 Proline residue: B 221 - end of helix Processing helix chain 'B' and resid 246 through 262 Processing helix chain 'B' and resid 284 through 303 Processing helix chain 'B' and resid 322 through 333 removed outlier: 3.510A pdb=" N GLN B 331 " --> pdb=" O THR B 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 36 Processing helix chain 'C' and resid 39 through 55 Processing helix chain 'C' and resid 59 through 75 Processing helix chain 'C' and resid 79 through 96 Processing helix chain 'C' and resid 102 through 114 Processing helix chain 'C' and resid 120 through 132 Processing helix chain 'C' and resid 143 through 155 Processing helix chain 'C' and resid 159 through 167 Processing helix chain 'C' and resid 172 through 185 Processing helix chain 'C' and resid 189 through 206 removed outlier: 3.886A pdb=" N VAL C 192 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ASP C 193 " --> pdb=" O SER C 190 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE C 195 " --> pdb=" O VAL C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 222 Processing helix chain 'C' and resid 235 through 249 Processing helix chain 'C' and resid 252 through 261 Processing helix chain 'C' and resid 263 through 268 removed outlier: 3.878A pdb=" N ARG C 268 " --> pdb=" O PRO C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 283 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 1009 through 1012 Processing helix chain 'D' and resid 1016 through 1029 Proline residue: D1020 - end of helix Processing helix chain 'D' and resid 1040 through 1045 removed outlier: 3.921A pdb=" N GLY D1045 " --> pdb=" O ALA D1041 " (cutoff:3.500A) Processing helix chain 'D' and resid 1063 through 1074 Processing helix chain 'D' and resid 1082 through 1089 removed outlier: 3.764A pdb=" N LEU D1089 " --> pdb=" O LEU D1085 " (cutoff:3.500A) Processing helix chain 'D' and resid 1093 through 1112 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 95 through 106 removed outlier: 3.910A pdb=" N ARG E 105 " --> pdb=" O LYS E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 128 Processing helix chain 'E' and resid 132 through 139 Processing helix chain 'F' and resid 21 through 36 Processing helix chain 'F' and resid 39 through 55 Processing helix chain 'F' and resid 59 through 75 Processing helix chain 'F' and resid 79 through 96 Processing helix chain 'F' and resid 102 through 114 Processing helix chain 'F' and resid 120 through 132 Processing helix chain 'F' and resid 143 through 155 Processing helix chain 'F' and resid 159 through 167 Processing helix chain 'F' and resid 172 through 185 Processing helix chain 'F' and resid 189 through 206 removed outlier: 3.885A pdb=" N VAL F 192 " --> pdb=" O ARG F 189 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ASP F 193 " --> pdb=" O SER F 190 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE F 195 " --> pdb=" O VAL F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 222 Processing helix chain 'F' and resid 235 through 249 Processing helix chain 'F' and resid 252 through 261 Processing helix chain 'F' and resid 263 through 268 removed outlier: 3.878A pdb=" N ARG F 268 " --> pdb=" O PRO F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 283 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 1009 through 1012 Processing helix chain 'G' and resid 1016 through 1029 Proline residue: G1020 - end of helix Processing helix chain 'G' and resid 1040 through 1045 removed outlier: 3.920A pdb=" N GLY G1045 " --> pdb=" O ALA G1041 " (cutoff:3.500A) Processing helix chain 'G' and resid 1063 through 1074 Processing helix chain 'G' and resid 1082 through 1089 removed outlier: 3.764A pdb=" N LEU G1089 " --> pdb=" O LEU G1085 " (cutoff:3.500A) Processing helix chain 'G' and resid 1093 through 1112 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 95 through 106 removed outlier: 3.909A pdb=" N ARG H 105 " --> pdb=" O LYS H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 128 Processing helix chain 'H' and resid 132 through 139 Processing sheet with id= A, first strand: chain 'A' and resid 308 through 311 removed outlier: 9.996A pdb=" N ASN A 268 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE A 238 " --> pdb=" O ASN A 268 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ILE A 270 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS A 240 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASN A 272 " --> pdb=" O CYS A 240 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N CYS A 242 " --> pdb=" O ASN A 272 " (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: 6.409A pdb=" N VAL A 157 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL A 36 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE A 159 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 308 through 311 removed outlier: 9.996A pdb=" N ASN B 268 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE B 238 " --> pdb=" O ASN B 268 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ILE B 270 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS B 240 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASN B 272 " --> pdb=" O CYS B 240 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N CYS B 242 " --> pdb=" O ASN B 272 " (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: 6.409A pdb=" N VAL B 157 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL B 36 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N PHE B 159 " --> pdb=" O VAL B 36 " (cutoff:3.500A) 634 hydrogen bonds defined for protein. 1668 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: 3.36 Time building geometry restraints manager: 5.05 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: 99.74 - 107.74: 548 107.74 - 115.74: 7149 115.74 - 123.74: 8031 123.74 - 131.75: 264 131.75 - 139.75: 20 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: 70 2.50 - 3.10: 9439 3.10 - 3.70: 18853 3.70 - 4.30: 26650 4.30 - 4.90: 43068 Nonbonded interactions: 98080 Sorted by model distance: nonbonded pdb=" OE1 GLN H 118 " pdb=" NH2 ARG H 121 " model vdw 1.899 2.520 nonbonded pdb=" OE1 GLN E 118 " pdb=" NH2 ARG E 121 " model vdw 1.899 2.520 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 98075 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 339 or resid 401 through 402)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.060 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: 10.410 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 35.920 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.090 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11836 Z= 0.231 Angle : 0.592 10.915 16012 Z= 0.300 Chirality : 0.070 1.724 1766 Planarity : 0.010 0.267 2072 Dihedral : 14.936 87.803 4542 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.24), residues: 1424 helix: 2.03 (0.18), residues: 934 sheet: -0.62 (0.53), residues: 84 loop : -0.15 (0.33), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 132 HIS 0.005 0.001 HIS C 43 PHE 0.008 0.001 PHE A 328 TYR 0.010 0.001 TYR A 250 ARG 0.014 0.001 ARG D1050 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 1.432 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: 0.2633 time to fit residues: 90.2767 Evaluate side-chains 158 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.332 ------------------------------------------------------------------------------- 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: 0.8980 chunk 106 optimal weight: 0.8980 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: 0.7980 chunk 42 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 GLN G1029 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11836 Z= 0.252 Angle : 0.549 7.562 16012 Z= 0.279 Chirality : 0.041 0.132 1766 Planarity : 0.005 0.047 2072 Dihedral : 7.671 82.944 1630 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.04 % Allowed : 5.18 % Favored : 92.78 % 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: 1.77 (0.23), residues: 1424 helix: 1.86 (0.17), residues: 946 sheet: -0.17 (0.58), residues: 74 loop : -0.11 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D1010 HIS 0.005 0.001 HIS F 165 PHE 0.016 0.001 PHE C 255 TYR 0.018 0.002 TYR B 250 ARG 0.005 0.001 ARG D1050 *********************** 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 207 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 181 time to evaluate : 1.206 Fit side-chains revert: symmetry clash REVERT: A 19 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7079 (tp30) REVERT: A 87 LYS cc_start: 0.8219 (tttt) cc_final: 0.7852 (mtpp) REVERT: A 89 LYS cc_start: 0.7704 (ttmm) cc_final: 0.7388 (tmtt) REVERT: A 125 MET cc_start: 0.6268 (mmp) cc_final: 0.5909 (ttt) REVERT: A 130 MET cc_start: 0.5263 (tpt) cc_final: 0.4218 (mtt) REVERT: A 150 LYS cc_start: 0.6811 (mmtp) cc_final: 0.6465 (mmtt) REVERT: A 169 ARG cc_start: 0.7098 (mmt-90) cc_final: 0.6655 (mmt-90) REVERT: A 183 ARG cc_start: 0.6358 (mmp80) cc_final: 0.5893 (mmt180) REVERT: A 214 SER cc_start: 0.7481 (t) cc_final: 0.7162 (m) REVERT: A 235 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7665 (mm110) REVERT: A 258 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6773 (mm-30) REVERT: A 296 TYR cc_start: 0.8069 (m-80) cc_final: 0.7529 (m-80) REVERT: A 298 ASP cc_start: 0.7727 (t70) cc_final: 0.7519 (t0) REVERT: B 19 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7114 (tp30) REVERT: B 87 LYS cc_start: 0.8223 (tttt) cc_final: 0.7857 (mtpp) REVERT: B 89 LYS cc_start: 0.7670 (ttmm) cc_final: 0.7375 (tmtt) REVERT: B 125 MET cc_start: 0.6215 (mmp) cc_final: 0.5875 (ttt) REVERT: B 130 MET cc_start: 0.5288 (tpt) cc_final: 0.4242 (mtt) REVERT: B 169 ARG cc_start: 0.7121 (mmt-90) cc_final: 0.6679 (mmt-90) REVERT: B 183 ARG cc_start: 0.6303 (mmp80) cc_final: 0.5835 (mmt180) REVERT: B 214 SER cc_start: 0.7482 (t) cc_final: 0.7178 (m) REVERT: B 235 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7662 (mm110) REVERT: B 258 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6821 (mm-30) REVERT: B 296 TYR cc_start: 0.8126 (m-80) cc_final: 0.7573 (m-80) REVERT: B 298 ASP cc_start: 0.7772 (t70) cc_final: 0.7562 (t0) REVERT: C 58 LYS cc_start: 0.8219 (mtpp) cc_final: 0.7692 (mttp) REVERT: C 95 LYS cc_start: 0.8675 (mmmm) cc_final: 0.8401 (mmmm) REVERT: C 121 GLU cc_start: 0.7568 (mp0) cc_final: 0.6928 (mm-30) REVERT: C 131 LYS cc_start: 0.8476 (ttpp) cc_final: 0.8089 (ttpp) REVERT: C 155 LYS cc_start: 0.8171 (mttp) cc_final: 0.7872 (mmtp) REVERT: C 173 GLU cc_start: 0.7385 (mp0) cc_final: 0.7146 (mt-10) REVERT: C 218 THR cc_start: 0.8575 (m) cc_final: 0.8282 (m) REVERT: C 222 LYS cc_start: 0.8647 (mttm) cc_final: 0.8041 (mmtm) REVERT: C 282 LEU cc_start: 0.7874 (mp) cc_final: 0.6979 (mp) REVERT: F 58 LYS cc_start: 0.8220 (mtpp) cc_final: 0.7695 (mttp) REVERT: F 95 LYS cc_start: 0.8672 (mmmm) cc_final: 0.8404 (mmmm) REVERT: F 121 GLU cc_start: 0.7554 (mp0) cc_final: 0.6925 (mm-30) REVERT: F 131 LYS cc_start: 0.8480 (ttpp) cc_final: 0.8091 (ttpp) REVERT: F 155 LYS cc_start: 0.8169 (mttp) cc_final: 0.7868 (mmtp) REVERT: F 173 GLU cc_start: 0.7392 (mp0) cc_final: 0.7149 (mt-10) REVERT: F 222 LYS cc_start: 0.8636 (mttm) cc_final: 0.8025 (mmtm) outliers start: 26 outliers final: 15 residues processed: 203 average time/residue: 0.2795 time to fit residues: 77.4117 Evaluate side-chains 163 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 278 ASP 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 278 ASP Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 274 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN A 308 HIS A 331 GLN B 308 HIS D1060 GLN G1023 GLN G1060 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 11836 Z= 0.382 Angle : 0.601 7.577 16012 Z= 0.310 Chirality : 0.043 0.184 1766 Planarity : 0.006 0.050 2072 Dihedral : 7.444 81.858 1630 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.04 % Allowed : 9.50 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.48 (0.23), residues: 1424 helix: 1.62 (0.17), residues: 940 sheet: -0.12 (0.58), residues: 74 loop : -0.20 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 132 HIS 0.008 0.002 HIS C 165 PHE 0.036 0.002 PHE F 255 TYR 0.020 0.002 TYR A 250 ARG 0.006 0.001 ARG D1030 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 150 time to evaluate : 1.285 Fit side-chains REVERT: A 19 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7011 (tp30) REVERT: A 87 LYS cc_start: 0.8337 (tttt) cc_final: 0.7997 (mtpp) REVERT: A 89 LYS cc_start: 0.7726 (ttmm) cc_final: 0.7425 (tmtt) REVERT: A 125 MET cc_start: 0.6213 (mmp) cc_final: 0.5674 (ttt) REVERT: A 130 MET cc_start: 0.5616 (tpt) cc_final: 0.4467 (mtp) REVERT: A 167 THR cc_start: 0.8131 (m) cc_final: 0.7815 (m) REVERT: B 19 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7005 (tp30) REVERT: B 87 LYS cc_start: 0.8331 (tttt) cc_final: 0.8011 (mtpp) REVERT: B 89 LYS cc_start: 0.7724 (ttmm) cc_final: 0.7428 (tmtt) REVERT: B 125 MET cc_start: 0.6180 (mmp) cc_final: 0.5659 (ttt) REVERT: B 130 MET cc_start: 0.5490 (tpt) cc_final: 0.4418 (mtp) REVERT: B 167 THR cc_start: 0.8138 (m) cc_final: 0.7830 (m) REVERT: C 24 GLN cc_start: 0.7978 (tp40) cc_final: 0.7750 (tm-30) REVERT: C 58 LYS cc_start: 0.8213 (mtpp) cc_final: 0.7715 (mttp) REVERT: C 121 GLU cc_start: 0.7744 (mp0) cc_final: 0.7103 (mm-30) REVERT: C 131 LYS cc_start: 0.8557 (ttpp) cc_final: 0.8119 (ttpp) REVERT: C 173 GLU cc_start: 0.7445 (mp0) cc_final: 0.7179 (mt-10) REVERT: F 24 GLN cc_start: 0.7972 (tp40) cc_final: 0.7739 (tm-30) REVERT: F 58 LYS cc_start: 0.8208 (mtpp) cc_final: 0.7715 (mttp) REVERT: F 121 GLU cc_start: 0.7730 (mp0) cc_final: 0.7106 (mm-30) REVERT: F 131 LYS cc_start: 0.8560 (ttpp) cc_final: 0.8117 (ttpp) REVERT: F 173 GLU cc_start: 0.7459 (mp0) cc_final: 0.7188 (mt-10) REVERT: G 1023 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7692 (mm-40) outliers start: 26 outliers final: 14 residues processed: 171 average time/residue: 0.2275 time to fit residues: 57.2242 Evaluate side-chains 151 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 1.327 ------------------------------------------------------------------------------- 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 278 ASP 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 278 ASP Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 1023 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 3.9990 chunk 95 optimal weight: 40.0000 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 60 optimal weight: 0.0770 chunk 85 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 135 optimal weight: 30.0000 chunk 121 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 235 GLN B 54 GLN B 235 GLN D1060 GLN G1023 GLN G1029 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11836 Z= 0.221 Angle : 0.516 9.518 16012 Z= 0.264 Chirality : 0.039 0.127 1766 Planarity : 0.005 0.056 2072 Dihedral : 6.986 80.646 1630 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.41 % Allowed : 11.22 % Favored : 87.36 % 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: 1.56 (0.23), residues: 1424 helix: 1.72 (0.17), residues: 952 sheet: -0.29 (0.59), residues: 74 loop : -0.27 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D1010 HIS 0.004 0.001 HIS F 43 PHE 0.021 0.001 PHE F 255 TYR 0.016 0.001 TYR A 250 ARG 0.003 0.000 ARG G1030 *********************** 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 175 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 157 time to evaluate : 1.382 Fit side-chains revert: symmetry clash REVERT: A 19 GLU cc_start: 0.7339 (mm-30) cc_final: 0.7041 (tp30) REVERT: A 87 LYS cc_start: 0.8285 (tttt) cc_final: 0.7949 (mtpp) REVERT: A 89 LYS cc_start: 0.7701 (ttmm) cc_final: 0.7341 (tmtt) REVERT: A 125 MET cc_start: 0.5990 (mmp) cc_final: 0.5730 (ttt) REVERT: A 130 MET cc_start: 0.5574 (tpt) cc_final: 0.4433 (mtp) REVERT: A 167 THR cc_start: 0.8095 (m) cc_final: 0.7783 (m) REVERT: A 296 TYR cc_start: 0.8109 (m-80) cc_final: 0.7575 (m-80) REVERT: B 19 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7050 (tp30) REVERT: B 87 LYS cc_start: 0.8292 (tttt) cc_final: 0.7951 (mtpp) REVERT: B 89 LYS cc_start: 0.7681 (ttmm) cc_final: 0.7316 (tmtt) REVERT: B 125 MET cc_start: 0.5946 (mmp) cc_final: 0.5698 (ttt) REVERT: B 130 MET cc_start: 0.5588 (tpt) cc_final: 0.4486 (mtt) REVERT: B 167 THR cc_start: 0.8099 (m) cc_final: 0.7796 (m) REVERT: B 296 TYR cc_start: 0.8111 (m-80) cc_final: 0.7593 (m-80) REVERT: C 24 GLN cc_start: 0.7980 (tp40) cc_final: 0.7761 (tm-30) REVERT: C 58 LYS cc_start: 0.8207 (mtpp) cc_final: 0.7712 (mttp) REVERT: C 121 GLU cc_start: 0.7726 (mp0) cc_final: 0.7076 (mm-30) REVERT: C 131 LYS cc_start: 0.8498 (ttpp) cc_final: 0.8057 (ttpp) REVERT: F 24 GLN cc_start: 0.7974 (tp40) cc_final: 0.7751 (tm-30) REVERT: F 58 LYS cc_start: 0.8220 (mtpp) cc_final: 0.7728 (mttp) REVERT: F 121 GLU cc_start: 0.7702 (mp0) cc_final: 0.7069 (mm-30) REVERT: F 131 LYS cc_start: 0.8497 (ttpp) cc_final: 0.8050 (ttpp) REVERT: G 1023 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7572 (mm110) outliers start: 18 outliers final: 8 residues processed: 172 average time/residue: 0.2398 time to fit residues: 59.1518 Evaluate side-chains 150 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 141 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain G residue 1023 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 100 optimal weight: 0.2980 chunk 55 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN D1060 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11836 Z= 0.216 Angle : 0.502 7.710 16012 Z= 0.258 Chirality : 0.039 0.158 1766 Planarity : 0.005 0.055 2072 Dihedral : 6.748 77.131 1630 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.57 % Allowed : 11.46 % Favored : 86.97 % 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: 1.57 (0.23), residues: 1424 helix: 1.74 (0.17), residues: 952 sheet: -0.25 (0.60), residues: 74 loop : -0.31 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G1010 HIS 0.003 0.001 HIS F 43 PHE 0.018 0.001 PHE C 255 TYR 0.016 0.001 TYR A 250 ARG 0.002 0.000 ARG G1030 *********************** 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 166 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 1.385 Fit side-chains REVERT: A 19 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7071 (tp30) REVERT: A 87 LYS cc_start: 0.8248 (tttt) cc_final: 0.7935 (mtpp) REVERT: A 89 LYS cc_start: 0.7699 (ttmm) cc_final: 0.7345 (tmtt) REVERT: A 125 MET cc_start: 0.5982 (mmp) cc_final: 0.5723 (ttt) REVERT: A 130 MET cc_start: 0.5591 (tpt) cc_final: 0.4456 (mtp) REVERT: A 167 THR cc_start: 0.8117 (m) cc_final: 0.7807 (m) REVERT: A 296 TYR cc_start: 0.8094 (m-80) cc_final: 0.7575 (m-80) REVERT: B 19 GLU cc_start: 0.7340 (mm-30) cc_final: 0.7099 (tp30) REVERT: B 87 LYS cc_start: 0.8246 (tttt) cc_final: 0.7944 (mtpp) REVERT: B 89 LYS cc_start: 0.7680 (ttmm) cc_final: 0.7314 (tmtt) REVERT: B 125 MET cc_start: 0.5979 (mmp) cc_final: 0.5733 (ttt) REVERT: B 130 MET cc_start: 0.5648 (tpt) cc_final: 0.4485 (mtp) REVERT: B 167 THR cc_start: 0.8121 (m) cc_final: 0.7821 (m) REVERT: B 296 TYR cc_start: 0.8126 (m-80) cc_final: 0.7524 (m-80) REVERT: C 58 LYS cc_start: 0.8240 (mtpp) cc_final: 0.7761 (mttp) REVERT: C 121 GLU cc_start: 0.7732 (mp0) cc_final: 0.7096 (mm-30) REVERT: C 131 LYS cc_start: 0.8489 (ttpp) cc_final: 0.8044 (ttpp) REVERT: F 24 GLN cc_start: 0.7956 (tp40) cc_final: 0.7724 (tm-30) REVERT: F 58 LYS cc_start: 0.8246 (mtpp) cc_final: 0.7764 (mttp) REVERT: F 121 GLU cc_start: 0.7686 (mp0) cc_final: 0.7055 (mm-30) REVERT: F 131 LYS cc_start: 0.8490 (ttpp) cc_final: 0.8044 (ttpp) REVERT: G 1023 GLN cc_start: 0.8148 (mm-40) cc_final: 0.7871 (mm-40) outliers start: 20 outliers final: 11 residues processed: 163 average time/residue: 0.2356 time to fit residues: 55.5099 Evaluate side-chains 150 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 139 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 310 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.0010 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 135 optimal weight: 50.0000 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN B 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11836 Z= 0.340 Angle : 0.560 7.582 16012 Z= 0.289 Chirality : 0.041 0.167 1766 Planarity : 0.005 0.055 2072 Dihedral : 7.025 85.433 1630 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.04 % Allowed : 11.15 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.23), residues: 1424 helix: 1.64 (0.17), residues: 946 sheet: -0.41 (0.58), residues: 74 loop : -0.30 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G1010 HIS 0.006 0.001 HIS C 165 PHE 0.017 0.002 PHE C 255 TYR 0.018 0.002 TYR B 250 ARG 0.006 0.000 ARG C 268 *********************** 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 177 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 1.526 Fit side-chains REVERT: A 19 GLU cc_start: 0.7364 (mm-30) cc_final: 0.7042 (tp30) REVERT: A 89 LYS cc_start: 0.7743 (ttmm) cc_final: 0.7462 (tmtt) REVERT: A 125 MET cc_start: 0.6073 (mmp) cc_final: 0.5809 (ttt) REVERT: A 130 MET cc_start: 0.5437 (tpt) cc_final: 0.4613 (ttt) REVERT: A 167 THR cc_start: 0.8119 (m) cc_final: 0.7802 (m) REVERT: A 296 TYR cc_start: 0.8231 (m-80) cc_final: 0.7617 (m-80) REVERT: B 19 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7043 (tp30) REVERT: B 87 LYS cc_start: 0.8332 (tttt) cc_final: 0.8028 (mtpp) REVERT: B 89 LYS cc_start: 0.7721 (ttmm) cc_final: 0.7433 (tmtt) REVERT: B 125 MET cc_start: 0.6041 (mmp) cc_final: 0.5803 (ttt) REVERT: B 130 MET cc_start: 0.5496 (tpt) cc_final: 0.4646 (ttt) REVERT: B 167 THR cc_start: 0.8124 (m) cc_final: 0.7814 (m) REVERT: B 184 LEU cc_start: 0.7257 (mt) cc_final: 0.6984 (tp) REVERT: B 296 TYR cc_start: 0.8219 (m-80) cc_final: 0.7618 (m-80) REVERT: C 24 GLN cc_start: 0.8008 (tp40) cc_final: 0.7770 (tm-30) REVERT: C 58 LYS cc_start: 0.8238 (mtpp) cc_final: 0.7763 (mttp) REVERT: C 121 GLU cc_start: 0.7768 (mp0) cc_final: 0.7122 (mm-30) REVERT: F 24 GLN cc_start: 0.8002 (tp40) cc_final: 0.7762 (tm-30) REVERT: F 58 LYS cc_start: 0.8245 (mtpp) cc_final: 0.7764 (mttp) REVERT: F 121 GLU cc_start: 0.7746 (mp0) cc_final: 0.7113 (mm-30) REVERT: G 1023 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7914 (mm-40) outliers start: 26 outliers final: 16 residues processed: 173 average time/residue: 0.2312 time to fit residues: 57.4448 Evaluate side-chains 164 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 1.398 ------------------------------------------------------------------------------- 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 226 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 310 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 98 optimal weight: 50.0000 chunk 76 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 GLN F 168 HIS G1023 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11836 Z= 0.279 Angle : 0.532 7.609 16012 Z= 0.274 Chirality : 0.040 0.154 1766 Planarity : 0.005 0.055 2072 Dihedral : 6.757 77.850 1630 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.12 % Allowed : 11.22 % 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: 1.47 (0.23), residues: 1424 helix: 1.68 (0.17), residues: 946 sheet: -0.48 (0.58), residues: 74 loop : -0.32 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D1010 HIS 0.004 0.001 HIS C 165 PHE 0.015 0.001 PHE C 255 TYR 0.017 0.002 TYR A 250 ARG 0.004 0.000 ARG F 278 *********************** 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 173 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 146 time to evaluate : 1.350 Fit side-chains REVERT: A 19 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7049 (tp30) REVERT: A 89 LYS cc_start: 0.7753 (ttmm) cc_final: 0.7459 (tmtt) REVERT: A 125 MET cc_start: 0.6039 (mmp) cc_final: 0.5794 (ttt) REVERT: A 130 MET cc_start: 0.5433 (tpt) cc_final: 0.4632 (ttt) REVERT: A 167 THR cc_start: 0.8105 (m) cc_final: 0.7798 (m) REVERT: A 184 LEU cc_start: 0.7262 (mt) cc_final: 0.6958 (tp) REVERT: A 296 TYR cc_start: 0.8184 (m-80) cc_final: 0.7618 (m-80) REVERT: B 19 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7046 (tp30) REVERT: B 87 LYS cc_start: 0.8363 (tttt) cc_final: 0.7995 (mtpp) REVERT: B 89 LYS cc_start: 0.7754 (ttmm) cc_final: 0.7453 (tmtt) REVERT: B 125 MET cc_start: 0.5996 (mmp) cc_final: 0.5781 (ttt) REVERT: B 130 MET cc_start: 0.5439 (tpt) cc_final: 0.4632 (ttt) REVERT: B 167 THR cc_start: 0.8117 (m) cc_final: 0.7822 (m) REVERT: B 296 TYR cc_start: 0.8197 (m-80) cc_final: 0.7619 (m-80) REVERT: C 24 GLN cc_start: 0.8044 (tp40) cc_final: 0.7808 (tm-30) REVERT: C 58 LYS cc_start: 0.8201 (mtpp) cc_final: 0.7717 (mttp) REVERT: C 121 GLU cc_start: 0.7697 (mp0) cc_final: 0.7060 (mm-30) REVERT: F 24 GLN cc_start: 0.8040 (tp40) cc_final: 0.7803 (tm-30) REVERT: F 58 LYS cc_start: 0.8206 (mtpp) cc_final: 0.7718 (mttp) REVERT: F 121 GLU cc_start: 0.7677 (mp0) cc_final: 0.7150 (mm-30) REVERT: G 1023 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7821 (mm-40) outliers start: 27 outliers final: 18 residues processed: 166 average time/residue: 0.2274 time to fit residues: 55.0035 Evaluate side-chains 162 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 1.310 ------------------------------------------------------------------------------- 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 156 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain G residue 1023 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11836 Z= 0.268 Angle : 0.536 7.644 16012 Z= 0.275 Chirality : 0.040 0.151 1766 Planarity : 0.005 0.055 2072 Dihedral : 6.748 78.619 1630 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.81 % Allowed : 11.46 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.52 (0.23), residues: 1424 helix: 1.70 (0.17), residues: 946 sheet: -0.45 (0.58), residues: 74 loop : -0.26 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D1010 HIS 0.004 0.001 HIS C 165 PHE 0.014 0.001 PHE F 255 TYR 0.017 0.002 TYR A 250 ARG 0.003 0.000 ARG C 278 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 143 time to evaluate : 1.208 Fit side-chains REVERT: A 19 GLU cc_start: 0.7367 (mm-30) cc_final: 0.7036 (tp30) REVERT: A 89 LYS cc_start: 0.7747 (ttmm) cc_final: 0.7455 (tmtt) REVERT: A 125 MET cc_start: 0.6080 (mmp) cc_final: 0.5826 (ttt) REVERT: A 130 MET cc_start: 0.5351 (tpt) cc_final: 0.4576 (ttt) REVERT: A 167 THR cc_start: 0.8109 (m) cc_final: 0.7803 (m) REVERT: A 184 LEU cc_start: 0.7266 (mt) cc_final: 0.6956 (tp) REVERT: A 296 TYR cc_start: 0.8210 (m-80) cc_final: 0.7616 (m-80) REVERT: B 19 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7050 (tp30) REVERT: B 89 LYS cc_start: 0.7754 (ttmm) cc_final: 0.7460 (tmtt) REVERT: B 130 MET cc_start: 0.5350 (tpt) cc_final: 0.4579 (ttt) REVERT: B 167 THR cc_start: 0.8114 (m) cc_final: 0.7819 (m) REVERT: B 296 TYR cc_start: 0.8223 (m-80) cc_final: 0.7623 (m-80) REVERT: C 24 GLN cc_start: 0.8033 (tp40) cc_final: 0.7798 (tm-30) REVERT: C 58 LYS cc_start: 0.8215 (mtpp) cc_final: 0.7723 (mttp) REVERT: C 121 GLU cc_start: 0.7696 (mp0) cc_final: 0.7060 (mm-30) REVERT: C 271 MET cc_start: 0.6764 (mmt) cc_final: 0.6482 (mmt) REVERT: F 24 GLN cc_start: 0.8028 (tp40) cc_final: 0.7793 (tm-30) REVERT: F 58 LYS cc_start: 0.8219 (mtpp) cc_final: 0.7726 (mttp) REVERT: F 121 GLU cc_start: 0.7681 (mp0) cc_final: 0.7062 (mm-30) REVERT: G 1023 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7772 (mm-40) outliers start: 23 outliers final: 19 residues processed: 161 average time/residue: 0.2201 time to fit residues: 51.9053 Evaluate side-chains 159 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 140 time to evaluate : 1.315 ------------------------------------------------------------------------------- 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 156 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 200 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 129 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 98 optimal weight: 40.0000 chunk 38 optimal weight: 0.9990 chunk 113 optimal weight: 0.0070 chunk 118 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 GLN C 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11836 Z= 0.187 Angle : 0.506 7.767 16012 Z= 0.259 Chirality : 0.038 0.150 1766 Planarity : 0.005 0.055 2072 Dihedral : 6.444 70.897 1630 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.33 % Allowed : 11.85 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.23), residues: 1424 helix: 1.80 (0.17), residues: 950 sheet: -0.48 (0.60), residues: 74 loop : -0.25 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D1010 HIS 0.004 0.001 HIS F 43 PHE 0.014 0.001 PHE C 255 TYR 0.014 0.001 TYR B 250 ARG 0.003 0.000 ARG G1030 *********************** 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 161 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 144 time to evaluate : 1.314 Fit side-chains REVERT: A 19 GLU cc_start: 0.7372 (mm-30) cc_final: 0.7062 (tp30) REVERT: A 89 LYS cc_start: 0.7722 (ttmm) cc_final: 0.7441 (tmtt) REVERT: A 125 MET cc_start: 0.6128 (mmp) cc_final: 0.5871 (ttt) REVERT: A 130 MET cc_start: 0.5298 (tpt) cc_final: 0.4522 (ttt) REVERT: A 167 THR cc_start: 0.8105 (m) cc_final: 0.7803 (m) REVERT: A 296 TYR cc_start: 0.8128 (m-80) cc_final: 0.7635 (m-80) REVERT: B 19 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7067 (tp30) REVERT: B 89 LYS cc_start: 0.7723 (ttmm) cc_final: 0.7450 (tmtt) REVERT: B 130 MET cc_start: 0.5304 (tpt) cc_final: 0.4527 (ttt) REVERT: B 167 THR cc_start: 0.8103 (m) cc_final: 0.7813 (m) REVERT: B 296 TYR cc_start: 0.8138 (m-80) cc_final: 0.7628 (m-80) REVERT: C 24 GLN cc_start: 0.8003 (tp40) cc_final: 0.7772 (tm-30) REVERT: C 58 LYS cc_start: 0.8212 (mtpp) cc_final: 0.7719 (mttp) REVERT: C 121 GLU cc_start: 0.7669 (mp0) cc_final: 0.7135 (mm-30) REVERT: C 166 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.7870 (m-80) REVERT: C 271 MET cc_start: 0.6764 (mmt) cc_final: 0.6489 (mmt) REVERT: F 24 GLN cc_start: 0.8001 (tp40) cc_final: 0.7769 (tm-30) REVERT: F 58 LYS cc_start: 0.8217 (mtpp) cc_final: 0.7721 (mttp) REVERT: F 121 GLU cc_start: 0.7648 (mp0) cc_final: 0.7137 (mm-30) REVERT: F 166 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7846 (m-80) REVERT: F 271 MET cc_start: 0.6942 (mmt) cc_final: 0.6672 (mmt) REVERT: G 1023 GLN cc_start: 0.8014 (mt0) cc_final: 0.7748 (mm-40) outliers start: 17 outliers final: 12 residues processed: 159 average time/residue: 0.2127 time to fit residues: 50.3541 Evaluate side-chains 157 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 143 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 278 ASP 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 156 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain F residue 166 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.0770 chunk 63 optimal weight: 0.9980 chunk 92 optimal weight: 7.9990 chunk 139 optimal weight: 20.0000 chunk 128 optimal weight: 0.0770 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 118 optimal weight: 0.7980 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11836 Z= 0.185 Angle : 0.505 8.496 16012 Z= 0.257 Chirality : 0.038 0.154 1766 Planarity : 0.005 0.055 2072 Dihedral : 6.363 70.056 1630 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.02 % Allowed : 12.09 % Favored : 86.89 % 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: 1.68 (0.23), residues: 1424 helix: 1.85 (0.17), residues: 950 sheet: -0.56 (0.60), residues: 74 loop : -0.28 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D1010 HIS 0.004 0.001 HIS C 43 PHE 0.014 0.001 PHE C 255 TYR 0.015 0.001 TYR D1042 ARG 0.004 0.000 ARG D1030 ********************** 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 157 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 144 time to evaluate : 1.209 Fit side-chains REVERT: A 19 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7065 (tp30) REVERT: A 89 LYS cc_start: 0.7738 (ttmm) cc_final: 0.7447 (tmtt) REVERT: A 125 MET cc_start: 0.6109 (mmp) cc_final: 0.5848 (ttt) REVERT: A 130 MET cc_start: 0.5626 (tpt) cc_final: 0.4751 (mtp) REVERT: A 167 THR cc_start: 0.8111 (m) cc_final: 0.7810 (m) REVERT: A 296 TYR cc_start: 0.8105 (m-80) cc_final: 0.7558 (m-80) REVERT: B 19 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7071 (tp30) REVERT: B 89 LYS cc_start: 0.7717 (ttmm) cc_final: 0.7430 (tmtt) REVERT: B 130 MET cc_start: 0.5627 (tpt) cc_final: 0.4743 (mtp) REVERT: B 167 THR cc_start: 0.8104 (m) cc_final: 0.7813 (m) REVERT: B 296 TYR cc_start: 0.8119 (m-80) cc_final: 0.7582 (m-80) REVERT: C 24 GLN cc_start: 0.7984 (tp40) cc_final: 0.7753 (tm-30) REVERT: C 58 LYS cc_start: 0.8215 (mtpp) cc_final: 0.7723 (mttp) REVERT: C 121 GLU cc_start: 0.7678 (mp0) cc_final: 0.7133 (mm-30) REVERT: C 166 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.7761 (m-80) REVERT: C 271 MET cc_start: 0.6720 (mmt) cc_final: 0.6469 (mmt) REVERT: F 24 GLN cc_start: 0.7981 (tp40) cc_final: 0.7748 (tm-30) REVERT: F 58 LYS cc_start: 0.8221 (mtpp) cc_final: 0.7725 (mttp) REVERT: F 121 GLU cc_start: 0.7634 (mp0) cc_final: 0.7023 (mm-30) REVERT: F 166 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.7749 (m-80) REVERT: G 1023 GLN cc_start: 0.8022 (mt0) cc_final: 0.7754 (mm-40) outliers start: 13 outliers final: 10 residues processed: 155 average time/residue: 0.2153 time to fit residues: 49.6451 Evaluate side-chains 151 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain F residue 166 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 97 optimal weight: 20.0000 chunk 6 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1023 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.177837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.137800 restraints weight = 15647.322| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.10 r_work: 0.3315 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11836 Z= 0.255 Angle : 0.532 7.900 16012 Z= 0.272 Chirality : 0.039 0.154 1766 Planarity : 0.005 0.055 2072 Dihedral : 6.586 77.635 1630 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.26 % Allowed : 12.24 % Favored : 86.50 % 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: 1.59 (0.23), residues: 1424 helix: 1.78 (0.17), residues: 946 sheet: -0.56 (0.59), residues: 74 loop : -0.27 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D1010 HIS 0.004 0.001 HIS C 165 PHE 0.043 0.001 PHE F 255 TYR 0.029 0.002 TYR D1042 ARG 0.004 0.000 ARG C 278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2418.75 seconds wall clock time: 44 minutes 59.93 seconds (2699.93 seconds total)