Starting phenix.real_space_refine on Wed Mar 4 06:58:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ru9_24700/03_2026/7ru9_24700.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ru9_24700/03_2026/7ru9_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_24700/03_2026/7ru9_24700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ru9_24700/03_2026/7ru9_24700.map" model { file = "/net/cci-nas-00/data/ceres_data/7ru9_24700/03_2026/7ru9_24700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ru9_24700/03_2026/7ru9_24700.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 6 5.49 5 Mg 2 5.21 5 S 64 5.16 5 C 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.47, per 1000 atoms: 0.21 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: 0.91 Conformation dependent library (CDL) restraints added in 458.4 milliseconds 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: 0.36 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: 1.73 Time building geometry restraints manager: 1.20 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 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: 4.320 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.340 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.260 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (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 ARG 0.014 0.001 ARG D1050 TYR 0.010 0.001 TYR A 250 PHE 0.008 0.001 PHE A 328 TRP 0.006 0.001 TRP C 132 HIS 0.005 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00347 (11836) covalent geometry : angle 0.59152 (16012) hydrogen bonds : bond 0.13487 ( 728) hydrogen bonds : angle 5.95885 ( 2160) metal coordination : bond 0.00163 ( 4) metal coordination : angle 4.42812 ( 6) 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 : 0.419 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: 0.5872 (ttt) REVERT: A 130 MET cc_start: 0.5085 (tpt) cc_final: 0.4106 (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: 0.6817 (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: 0.7036 (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: 0.5908 (ttt) REVERT: B 130 MET cc_start: 0.5037 (tpt) cc_final: 0.4096 (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: 0.6998 (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: 0.8015 (mmtm) REVERT: C 264 PRO cc_start: 0.8118 (Cg_exo) cc_final: 0.7868 (Cg_endo) REVERT: C 271 MET cc_start: 0.6371 (mmt) cc_final: 0.6148 (mmm) 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: 0.7116 (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: 0.7820 (mm-40) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.1125 time to fit residues: 38.9594 Evaluate side-chains 156 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 50.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 F 238 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.182642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.143183 restraints weight = 15940.565| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.78 r_work: 0.3435 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11842 Z= 0.203 Angle : 0.625 7.964 16018 Z= 0.319 Chirality : 0.043 0.165 1766 Planarity : 0.005 0.056 2072 Dihedral : 7.611 87.731 1630 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.04 % Allowed : 5.34 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.23), residues: 1424 helix: 1.94 (0.16), residues: 968 sheet: -0.32 (0.60), residues: 74 loop : -0.16 (0.34), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G1030 TYR 0.019 0.002 TYR B 250 PHE 0.015 0.002 PHE F 255 TRP 0.019 0.002 TRP D1010 HIS 0.005 0.002 HIS F 165 Details of bonding type rmsd covalent geometry : bond 0.00482 (11836) covalent geometry : angle 0.61421 (16012) hydrogen bonds : bond 0.04742 ( 728) hydrogen bonds : angle 4.32284 ( 2160) metal coordination : bond 0.00577 ( 4) metal coordination : angle 6.02477 ( 6) Misc. bond : bond 0.00631 ( 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 199 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.460 Fit side-chains REVERT: A 125 MET cc_start: 0.6166 (mmp) cc_final: 0.5939 (ttt) REVERT: A 130 MET cc_start: 0.5928 (tpt) cc_final: 0.4800 (mtt) REVERT: A 150 LYS cc_start: 0.7419 (mmtp) cc_final: 0.7081 (mmtt) REVERT: A 217 GLU cc_start: 0.7655 (tp30) cc_final: 0.7421 (pt0) REVERT: A 235 GLN cc_start: 0.8390 (mm-40) cc_final: 0.8097 (mm-40) REVERT: A 296 TYR cc_start: 0.8810 (m-80) cc_final: 0.8374 (m-80) REVERT: B 130 MET cc_start: 0.5928 (tpt) cc_final: 0.4807 (mtt) REVERT: B 217 GLU cc_start: 0.7644 (tp30) cc_final: 0.7426 (pt0) REVERT: B 235 GLN cc_start: 0.8404 (mm-40) cc_final: 0.8133 (mm-40) REVERT: B 296 TYR cc_start: 0.8827 (m-80) cc_final: 0.8430 (m-80) REVERT: C 58 LYS cc_start: 0.8757 (mtpp) cc_final: 0.8472 (mttp) REVERT: C 121 GLU cc_start: 0.7469 (mp0) cc_final: 0.6993 (mm-30) REVERT: C 131 LYS cc_start: 0.8481 (ttpp) cc_final: 0.8155 (ttpp) REVERT: C 173 GLU cc_start: 0.7388 (mp0) cc_final: 0.7144 (mt-10) REVERT: C 222 LYS cc_start: 0.8478 (mttm) cc_final: 0.8126 (mmtm) REVERT: C 253 THR cc_start: 0.7627 (t) cc_final: 0.7262 (m) REVERT: C 257 VAL cc_start: 0.7911 (t) cc_final: 0.7628 (m) REVERT: F 58 LYS cc_start: 0.8753 (mtpp) cc_final: 0.8472 (mttp) REVERT: F 95 LYS cc_start: 0.8965 (mmmm) cc_final: 0.8734 (mmmm) REVERT: F 121 GLU cc_start: 0.7465 (mp0) cc_final: 0.6968 (mm-30) REVERT: F 131 LYS cc_start: 0.8472 (ttpp) cc_final: 0.8147 (ttpp) REVERT: F 173 GLU cc_start: 0.7416 (mp0) cc_final: 0.7158 (mt-10) REVERT: F 253 THR cc_start: 0.7612 (t) cc_final: 0.7235 (m) REVERT: F 257 VAL cc_start: 0.7886 (t) cc_final: 0.7653 (m) outliers start: 26 outliers final: 8 residues processed: 197 average time/residue: 0.1126 time to fit residues: 31.2324 Evaluate side-chains 151 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 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 268 ASN 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 87 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 HIS A 331 GLN B 308 HIS D1060 GLN E 118 GLN F 238 ASN G1023 GLN G1060 GLN H 118 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.178880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.136768 restraints weight = 16082.291| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.91 r_work: 0.3344 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11842 Z= 0.170 Angle : 0.572 8.147 16018 Z= 0.290 Chirality : 0.041 0.158 1766 Planarity : 0.005 0.061 2072 Dihedral : 7.413 83.333 1630 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.02 % Allowed : 9.73 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.23), residues: 1424 helix: 2.01 (0.17), residues: 970 sheet: -0.35 (0.63), residues: 74 loop : -0.20 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G1030 TYR 0.018 0.002 TYR G1042 PHE 0.033 0.002 PHE C 255 TRP 0.012 0.002 TRP D1010 HIS 0.004 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00401 (11836) covalent geometry : angle 0.55942 (16012) hydrogen bonds : bond 0.04397 ( 728) hydrogen bonds : angle 4.16201 ( 2160) metal coordination : bond 0.00511 ( 4) metal coordination : angle 6.30934 ( 6) Misc. bond : bond 0.00137 ( 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 173 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.371 Fit side-chains REVERT: A 125 MET cc_start: 0.6163 (mmp) cc_final: 0.5937 (ttt) REVERT: A 126 MET cc_start: 0.6979 (mmp) cc_final: 0.6333 (mmp) REVERT: A 130 MET cc_start: 0.5718 (tpt) cc_final: 0.4595 (mtt) REVERT: A 150 LYS cc_start: 0.7414 (mmtp) cc_final: 0.6992 (mmtt) REVERT: A 235 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7897 (mm-40) REVERT: A 296 TYR cc_start: 0.8735 (m-80) cc_final: 0.8327 (m-80) REVERT: B 130 MET cc_start: 0.5747 (tpt) cc_final: 0.4634 (mtt) REVERT: B 235 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7943 (mm110) REVERT: B 296 TYR cc_start: 0.8754 (m-80) cc_final: 0.8342 (m-80) REVERT: C 58 LYS cc_start: 0.8644 (mtpp) cc_final: 0.8354 (mttp) REVERT: C 121 GLU cc_start: 0.7414 (mp0) cc_final: 0.6957 (mm-30) REVERT: C 131 LYS cc_start: 0.8384 (ttpp) cc_final: 0.8003 (ttpp) REVERT: C 173 GLU cc_start: 0.7253 (mp0) cc_final: 0.6993 (mt-10) REVERT: C 257 VAL cc_start: 0.7803 (t) cc_final: 0.7514 (m) REVERT: F 58 LYS cc_start: 0.8641 (mtpp) cc_final: 0.8358 (mttp) REVERT: F 121 GLU cc_start: 0.7404 (mp0) cc_final: 0.6958 (mm-30) REVERT: F 131 LYS cc_start: 0.8384 (ttpp) cc_final: 0.7999 (ttpp) REVERT: F 173 GLU cc_start: 0.7275 (mp0) cc_final: 0.7020 (mt-10) REVERT: F 257 VAL cc_start: 0.7873 (t) cc_final: 0.7617 (m) outliers start: 13 outliers final: 6 residues processed: 168 average time/residue: 0.0967 time to fit residues: 23.8322 Evaluate side-chains 154 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 148 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 B residue 64 ILE Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 157 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 40 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 97 optimal weight: 20.0000 chunk 42 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4118 r_free = 0.4118 target = 0.179435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.137843 restraints weight = 15978.610| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.97 r_work: 0.3346 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2526 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= 0.153 Angle : 0.539 7.837 16018 Z= 0.275 Chirality : 0.040 0.149 1766 Planarity : 0.005 0.064 2072 Dihedral : 7.129 77.295 1630 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.33 % Allowed : 10.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.23), residues: 1424 helix: 1.98 (0.17), residues: 972 sheet: -0.30 (0.65), residues: 74 loop : -0.11 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 278 TYR 0.016 0.001 TYR B 250 PHE 0.022 0.001 PHE F 255 TRP 0.011 0.002 TRP C 132 HIS 0.004 0.001 HIS F 168 Details of bonding type rmsd covalent geometry : bond 0.00359 (11836) covalent geometry : angle 0.52713 (16012) hydrogen bonds : bond 0.04137 ( 728) hydrogen bonds : angle 4.08801 ( 2160) metal coordination : bond 0.00426 ( 4) metal coordination : angle 5.85922 ( 6) Misc. bond : bond 0.00109 ( 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 177 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.382 Fit side-chains REVERT: A 125 MET cc_start: 0.6312 (mmp) cc_final: 0.6005 (ttt) REVERT: A 126 MET cc_start: 0.6992 (mmp) cc_final: 0.6370 (mmp) REVERT: A 130 MET cc_start: 0.6031 (tpt) cc_final: 0.4792 (mtt) REVERT: A 235 GLN cc_start: 0.8334 (mm-40) cc_final: 0.8047 (mm110) REVERT: A 296 TYR cc_start: 0.8778 (m-80) cc_final: 0.8429 (m-80) REVERT: B 126 MET cc_start: 0.7015 (mmp) cc_final: 0.6348 (mmp) REVERT: B 130 MET cc_start: 0.6100 (tpt) cc_final: 0.4874 (mtt) REVERT: B 235 GLN cc_start: 0.8329 (mm-40) cc_final: 0.8053 (mm110) REVERT: C 58 LYS cc_start: 0.8723 (mtpp) cc_final: 0.8407 (mttp) REVERT: C 121 GLU cc_start: 0.7692 (mp0) cc_final: 0.7268 (mm-30) REVERT: C 131 LYS cc_start: 0.8479 (ttpp) cc_final: 0.8095 (ttpp) REVERT: C 173 GLU cc_start: 0.7569 (mp0) cc_final: 0.7279 (mt-10) REVERT: C 257 VAL cc_start: 0.7833 (t) cc_final: 0.7534 (m) REVERT: F 58 LYS cc_start: 0.8719 (mtpp) cc_final: 0.8413 (mttp) REVERT: F 121 GLU cc_start: 0.7676 (mp0) cc_final: 0.7265 (mm-30) REVERT: F 131 LYS cc_start: 0.8489 (ttpp) cc_final: 0.8106 (ttpp) REVERT: F 155 LYS cc_start: 0.8378 (mptt) cc_final: 0.8128 (mptt) REVERT: F 173 GLU cc_start: 0.7525 (mp0) cc_final: 0.7238 (mt-10) REVERT: F 222 LYS cc_start: 0.8543 (mttm) cc_final: 0.8035 (mmtm) REVERT: F 257 VAL cc_start: 0.7904 (t) cc_final: 0.7600 (m) outliers start: 17 outliers final: 12 residues processed: 172 average time/residue: 0.1058 time to fit residues: 26.0703 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 : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 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 110 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 139 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 98 optimal weight: 40.0000 chunk 88 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1023 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.177237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.135257 restraints weight = 15922.579| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.97 r_work: 0.3311 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11842 Z= 0.211 Angle : 0.590 8.901 16018 Z= 0.300 Chirality : 0.043 0.176 1766 Planarity : 0.005 0.062 2072 Dihedral : 7.300 84.810 1630 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.43 % Allowed : 10.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.23), residues: 1424 helix: 1.83 (0.17), residues: 970 sheet: -0.38 (0.63), residues: 74 loop : -0.27 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G1030 TYR 0.019 0.002 TYR A 250 PHE 0.019 0.002 PHE F 255 TRP 0.010 0.002 TRP C 132 HIS 0.006 0.002 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00510 (11836) covalent geometry : angle 0.57338 (16012) hydrogen bonds : bond 0.04462 ( 728) hydrogen bonds : angle 4.14096 ( 2160) metal coordination : bond 0.00684 ( 4) metal coordination : angle 7.20358 ( 6) Misc. bond : bond 0.00135 ( 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 176 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.367 Fit side-chains REVERT: A 125 MET cc_start: 0.6376 (mmp) cc_final: 0.6012 (ttt) REVERT: A 126 MET cc_start: 0.6946 (mmp) cc_final: 0.6319 (mmp) REVERT: A 130 MET cc_start: 0.6144 (tpt) cc_final: 0.4813 (mtp) REVERT: A 296 TYR cc_start: 0.8860 (m-80) cc_final: 0.8353 (m-80) REVERT: B 126 MET cc_start: 0.6972 (mmp) cc_final: 0.6310 (mmp) REVERT: B 130 MET cc_start: 0.6037 (tpt) cc_final: 0.4759 (mtp) REVERT: B 296 TYR cc_start: 0.8893 (m-80) cc_final: 0.8388 (m-80) REVERT: C 58 LYS cc_start: 0.8780 (mtpp) cc_final: 0.8433 (mttp) REVERT: C 121 GLU cc_start: 0.7818 (mp0) cc_final: 0.7368 (mm-30) REVERT: C 166 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.8374 (m-80) REVERT: C 173 GLU cc_start: 0.7474 (mp0) cc_final: 0.7217 (mt-10) REVERT: C 274 GLU cc_start: 0.7623 (mp0) cc_final: 0.7355 (mp0) REVERT: F 58 LYS cc_start: 0.8775 (mtpp) cc_final: 0.8433 (mttp) REVERT: F 121 GLU cc_start: 0.7785 (mp0) cc_final: 0.7348 (mm-30) REVERT: F 131 LYS cc_start: 0.8547 (ttpp) cc_final: 0.8118 (ttpp) REVERT: F 166 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8365 (m-80) REVERT: F 173 GLU cc_start: 0.7516 (mp0) cc_final: 0.7268 (mt-10) REVERT: G 1023 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7767 (mm110) outliers start: 31 outliers final: 14 residues processed: 168 average time/residue: 0.0989 time to fit residues: 24.3762 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 : 0.442 ------------------------------------------------------------------------------- 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 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 157 VAL Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain F residue 166 PHE Chi-restraints excluded: chain G residue 1023 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 65 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 chunk 138 optimal weight: 30.0000 chunk 111 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1023 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.179334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.137221 restraints weight = 15806.891| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.80 r_work: 0.3369 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11842 Z= 0.135 Angle : 0.528 7.811 16018 Z= 0.270 Chirality : 0.040 0.165 1766 Planarity : 0.005 0.064 2072 Dihedral : 6.960 73.995 1630 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.73 % Allowed : 11.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.23), residues: 1424 helix: 1.94 (0.17), residues: 972 sheet: -0.58 (0.63), residues: 74 loop : -0.20 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G1030 TYR 0.015 0.001 TYR B 250 PHE 0.015 0.001 PHE F 255 TRP 0.011 0.001 TRP F 132 HIS 0.004 0.001 HIS F 43 Details of bonding type rmsd covalent geometry : bond 0.00309 (11836) covalent geometry : angle 0.51644 (16012) hydrogen bonds : bond 0.04000 ( 728) hydrogen bonds : angle 4.06079 ( 2160) metal coordination : bond 0.00457 ( 4) metal coordination : angle 5.60885 ( 6) Misc. bond : bond 0.00079 ( 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 166 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.435 Fit side-chains REVERT: A 125 MET cc_start: 0.6369 (mmp) cc_final: 0.6012 (ttt) REVERT: A 126 MET cc_start: 0.6946 (mmp) cc_final: 0.6338 (mmp) REVERT: A 130 MET cc_start: 0.5956 (tpt) cc_final: 0.4628 (mtp) REVERT: A 220 LEU cc_start: 0.8141 (tt) cc_final: 0.7932 (tp) REVERT: A 296 TYR cc_start: 0.8780 (m-80) cc_final: 0.8370 (m-80) REVERT: B 130 MET cc_start: 0.5959 (tpt) cc_final: 0.4702 (mtt) REVERT: B 296 TYR cc_start: 0.8789 (m-80) cc_final: 0.8396 (m-80) REVERT: C 58 LYS cc_start: 0.8727 (mtpp) cc_final: 0.8368 (mttp) REVERT: C 121 GLU cc_start: 0.7638 (mp0) cc_final: 0.7256 (mm-30) REVERT: C 166 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.8190 (m-80) REVERT: C 173 GLU cc_start: 0.7555 (mp0) cc_final: 0.7289 (mt-10) REVERT: F 58 LYS cc_start: 0.8730 (mtpp) cc_final: 0.8378 (mttp) REVERT: F 121 GLU cc_start: 0.7655 (mp0) cc_final: 0.7275 (mm-30) REVERT: F 131 LYS cc_start: 0.8516 (ttpp) cc_final: 0.8100 (ttpp) REVERT: F 166 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.8274 (m-80) REVERT: F 173 GLU cc_start: 0.7505 (mp0) cc_final: 0.7254 (mt-10) outliers start: 22 outliers final: 12 residues processed: 160 average time/residue: 0.1022 time to fit residues: 23.9957 Evaluate side-chains 151 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 10 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 14 optimal weight: 0.0980 chunk 25 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.179303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.138113 restraints weight = 15814.701| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.18 r_work: 0.3324 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11842 Z= 0.141 Angle : 0.533 7.823 16018 Z= 0.272 Chirality : 0.040 0.142 1766 Planarity : 0.005 0.062 2072 Dihedral : 6.810 72.383 1630 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.73 % Allowed : 12.17 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.23), residues: 1424 helix: 2.01 (0.17), residues: 972 sheet: -0.63 (0.63), residues: 74 loop : -0.16 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 278 TYR 0.015 0.001 TYR A 250 PHE 0.014 0.001 PHE F 255 TRP 0.010 0.001 TRP F 132 HIS 0.004 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00328 (11836) covalent geometry : angle 0.52324 (16012) hydrogen bonds : bond 0.03934 ( 728) hydrogen bonds : angle 4.01775 ( 2160) metal coordination : bond 0.00532 ( 4) metal coordination : angle 5.39272 ( 6) Misc. bond : bond 0.00085 ( 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 166 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.569 Fit side-chains REVERT: A 125 MET cc_start: 0.6491 (mmp) cc_final: 0.6112 (ttt) REVERT: A 126 MET cc_start: 0.7086 (mmp) cc_final: 0.6438 (mmp) REVERT: A 130 MET cc_start: 0.6229 (tpt) cc_final: 0.4903 (mtt) REVERT: A 234 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8276 (mt-10) REVERT: A 296 TYR cc_start: 0.8809 (m-80) cc_final: 0.8457 (m-80) REVERT: B 130 MET cc_start: 0.6283 (tpt) cc_final: 0.4989 (mtt) REVERT: B 234 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8286 (mt-10) REVERT: B 296 TYR cc_start: 0.8831 (m-80) cc_final: 0.8464 (m-80) REVERT: C 58 LYS cc_start: 0.8787 (mtpp) cc_final: 0.8464 (mttp) REVERT: C 121 GLU cc_start: 0.7723 (mp0) cc_final: 0.7344 (mm-30) REVERT: C 131 LYS cc_start: 0.8463 (ttpp) cc_final: 0.8074 (ttpp) REVERT: C 166 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.8090 (m-80) REVERT: C 173 GLU cc_start: 0.7566 (mp0) cc_final: 0.7313 (mt-10) REVERT: F 58 LYS cc_start: 0.8778 (mtpp) cc_final: 0.8461 (mttp) REVERT: F 121 GLU cc_start: 0.7738 (mp0) cc_final: 0.7360 (mm-30) REVERT: F 131 LYS cc_start: 0.8459 (ttpp) cc_final: 0.8063 (ttpp) REVERT: F 166 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.8097 (m-80) REVERT: F 173 GLU cc_start: 0.7608 (mp0) cc_final: 0.7355 (mt-10) outliers start: 22 outliers final: 16 residues processed: 161 average time/residue: 0.1035 time to fit residues: 24.5263 Evaluate side-chains 156 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 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 156 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain F residue 166 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 45 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 70 optimal weight: 0.0470 chunk 36 optimal weight: 0.3980 chunk 17 optimal weight: 0.0370 chunk 5 optimal weight: 0.5980 chunk 92 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 116 optimal weight: 0.0050 chunk 99 optimal weight: 7.9990 overall best weight: 0.2170 ------------------------------------------------------------------------------- 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** D1095 GLN G1023 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.181795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.140434 restraints weight = 15800.048| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.76 r_work: 0.3420 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11842 Z= 0.114 Angle : 0.515 8.742 16018 Z= 0.262 Chirality : 0.039 0.155 1766 Planarity : 0.004 0.063 2072 Dihedral : 6.366 61.515 1630 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.02 % Allowed : 12.87 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.23), residues: 1424 helix: 2.16 (0.17), residues: 970 sheet: -0.66 (0.63), residues: 74 loop : -0.02 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 278 TYR 0.012 0.001 TYR A 250 PHE 0.043 0.001 PHE F 255 TRP 0.010 0.001 TRP F 132 HIS 0.004 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00244 (11836) covalent geometry : angle 0.50718 (16012) hydrogen bonds : bond 0.03565 ( 728) hydrogen bonds : angle 3.92859 ( 2160) metal coordination : bond 0.00301 ( 4) metal coordination : angle 4.70787 ( 6) Misc. bond : bond 0.00068 ( 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 179 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.472 Fit side-chains REVERT: A 125 MET cc_start: 0.6474 (mmp) cc_final: 0.6102 (ttt) REVERT: A 130 MET cc_start: 0.5842 (tpt) cc_final: 0.4614 (mtt) REVERT: A 234 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8290 (mt-10) REVERT: A 296 TYR cc_start: 0.8698 (m-80) cc_final: 0.8425 (m-80) REVERT: B 130 MET cc_start: 0.5900 (tpt) cc_final: 0.4655 (mtt) REVERT: B 234 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8297 (mt-10) REVERT: B 296 TYR cc_start: 0.8696 (m-80) cc_final: 0.8366 (m-80) REVERT: C 58 LYS cc_start: 0.8693 (mtpp) cc_final: 0.8348 (mttp) REVERT: C 121 GLU cc_start: 0.7539 (mp0) cc_final: 0.7208 (mm-30) REVERT: C 123 VAL cc_start: 0.8688 (t) cc_final: 0.8450 (p) REVERT: C 131 LYS cc_start: 0.8338 (ttpp) cc_final: 0.7877 (ttpp) REVERT: C 166 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.7932 (m-80) REVERT: C 173 GLU cc_start: 0.7593 (mp0) cc_final: 0.7323 (mt-10) REVERT: F 58 LYS cc_start: 0.8694 (mtpp) cc_final: 0.8358 (mttp) REVERT: F 121 GLU cc_start: 0.7543 (mp0) cc_final: 0.7209 (mm-30) REVERT: F 123 VAL cc_start: 0.8669 (t) cc_final: 0.8421 (p) REVERT: F 131 LYS cc_start: 0.8365 (ttpp) cc_final: 0.7901 (ttpp) REVERT: F 166 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8032 (m-80) REVERT: F 173 GLU cc_start: 0.7565 (mp0) cc_final: 0.7286 (mt-10) REVERT: F 257 VAL cc_start: 0.7895 (t) cc_final: 0.7545 (m) outliers start: 13 outliers final: 8 residues processed: 176 average time/residue: 0.0964 time to fit residues: 24.9803 Evaluate side-chains 151 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 157 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 109 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 138 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 96 optimal weight: 50.0000 chunk 50 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 70 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.179849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.138096 restraints weight = 15668.631| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.72 r_work: 0.3392 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11842 Z= 0.141 Angle : 0.538 7.893 16018 Z= 0.272 Chirality : 0.040 0.140 1766 Planarity : 0.005 0.060 2072 Dihedral : 6.476 66.689 1630 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.41 % Allowed : 13.03 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.23), residues: 1424 helix: 2.12 (0.17), residues: 972 sheet: -0.62 (0.61), residues: 74 loop : -0.09 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 59 TYR 0.016 0.001 TYR B 250 PHE 0.045 0.001 PHE C 255 TRP 0.014 0.002 TRP C 241 HIS 0.004 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00331 (11836) covalent geometry : angle 0.52648 (16012) hydrogen bonds : bond 0.03764 ( 728) hydrogen bonds : angle 3.95591 ( 2160) metal coordination : bond 0.00348 ( 4) metal coordination : angle 5.75884 ( 6) Misc. bond : bond 0.00092 ( 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 171 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.422 Fit side-chains REVERT: A 125 MET cc_start: 0.6501 (mmp) cc_final: 0.6098 (ttt) REVERT: A 130 MET cc_start: 0.5832 (tpt) cc_final: 0.4604 (mtt) REVERT: A 234 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8235 (mt-10) REVERT: A 296 TYR cc_start: 0.8721 (m-80) cc_final: 0.8388 (m-80) REVERT: B 130 MET cc_start: 0.5920 (tpt) cc_final: 0.4708 (mtt) REVERT: B 234 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8255 (mt-10) REVERT: B 296 TYR cc_start: 0.8693 (m-80) cc_final: 0.8296 (m-80) REVERT: C 58 LYS cc_start: 0.8725 (mtpp) cc_final: 0.8412 (mttp) REVERT: C 121 GLU cc_start: 0.7506 (mp0) cc_final: 0.7200 (mm-30) REVERT: C 131 LYS cc_start: 0.8412 (ttpp) cc_final: 0.8035 (ttpp) REVERT: C 166 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.7993 (m-80) REVERT: C 173 GLU cc_start: 0.7671 (mp0) cc_final: 0.7386 (mt-10) REVERT: C 257 VAL cc_start: 0.7903 (t) cc_final: 0.7529 (m) REVERT: F 58 LYS cc_start: 0.8727 (mtpp) cc_final: 0.8412 (mttp) REVERT: F 121 GLU cc_start: 0.7577 (mp0) cc_final: 0.7243 (mm-30) REVERT: F 131 LYS cc_start: 0.8422 (ttpp) cc_final: 0.8048 (ttpp) REVERT: F 166 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.8005 (m-80) REVERT: F 173 GLU cc_start: 0.7692 (mp0) cc_final: 0.7390 (mt-10) REVERT: F 257 VAL cc_start: 0.7937 (t) cc_final: 0.7564 (m) outliers start: 18 outliers final: 14 residues processed: 168 average time/residue: 0.0907 time to fit residues: 22.9207 Evaluate side-chains 166 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL 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 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 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 107 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 121 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 128 optimal weight: 0.3980 chunk 38 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.179511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.138571 restraints weight = 15858.521| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.92 r_work: 0.3374 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3194 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= 0.133 Angle : 0.529 7.868 16018 Z= 0.268 Chirality : 0.040 0.139 1766 Planarity : 0.005 0.062 2072 Dihedral : 6.457 65.563 1630 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.33 % Allowed : 13.50 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.23), residues: 1424 helix: 2.09 (0.17), residues: 976 sheet: -0.88 (0.59), residues: 74 loop : -0.06 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 278 TYR 0.015 0.001 TYR A 250 PHE 0.039 0.001 PHE C 255 TRP 0.013 0.002 TRP C 241 HIS 0.004 0.001 HIS F 43 Details of bonding type rmsd covalent geometry : bond 0.00308 (11836) covalent geometry : angle 0.51712 (16012) hydrogen bonds : bond 0.03718 ( 728) hydrogen bonds : angle 3.93848 ( 2160) metal coordination : bond 0.00405 ( 4) metal coordination : angle 5.70484 ( 6) Misc. bond : bond 0.00084 ( 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 173 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.310 Fit side-chains REVERT: A 125 MET cc_start: 0.6558 (mmp) cc_final: 0.6087 (ttt) REVERT: A 130 MET cc_start: 0.5789 (tpt) cc_final: 0.4517 (mtt) REVERT: A 234 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8219 (mt-10) REVERT: A 296 TYR cc_start: 0.8708 (m-80) cc_final: 0.8303 (m-80) REVERT: B 130 MET cc_start: 0.5851 (tpt) cc_final: 0.4580 (mtt) REVERT: B 234 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8222 (mt-10) REVERT: B 296 TYR cc_start: 0.8712 (m-80) cc_final: 0.8386 (m-80) REVERT: C 58 LYS cc_start: 0.8718 (mtpp) cc_final: 0.8377 (mttp) REVERT: C 121 GLU cc_start: 0.7692 (mp0) cc_final: 0.7288 (mm-30) REVERT: C 131 LYS cc_start: 0.8466 (ttpp) cc_final: 0.8054 (ttpp) REVERT: C 166 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.7990 (m-80) REVERT: C 173 GLU cc_start: 0.7628 (mp0) cc_final: 0.7318 (mt-10) REVERT: C 257 VAL cc_start: 0.7855 (t) cc_final: 0.7492 (m) REVERT: F 58 LYS cc_start: 0.8724 (mtpp) cc_final: 0.8387 (mttp) REVERT: F 121 GLU cc_start: 0.7662 (mp0) cc_final: 0.7280 (mm-30) REVERT: F 131 LYS cc_start: 0.8471 (ttpp) cc_final: 0.8056 (ttpp) REVERT: F 166 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.8018 (m-80) REVERT: F 173 GLU cc_start: 0.7675 (mp0) cc_final: 0.7378 (mt-10) REVERT: F 257 VAL cc_start: 0.7919 (t) cc_final: 0.7551 (m) outliers start: 17 outliers final: 13 residues processed: 169 average time/residue: 0.0960 time to fit residues: 24.1417 Evaluate side-chains 163 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 156 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 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 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 7 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.0870 chunk 129 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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** G1095 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.179953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.138119 restraints weight = 15819.797| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.79 r_work: 0.3387 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11842 Z= 0.132 Angle : 0.539 7.850 16018 Z= 0.272 Chirality : 0.040 0.193 1766 Planarity : 0.005 0.060 2072 Dihedral : 6.428 65.023 1630 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.26 % Allowed : 13.19 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.23), residues: 1424 helix: 2.12 (0.17), residues: 972 sheet: -0.95 (0.59), residues: 74 loop : -0.11 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 59 TYR 0.015 0.001 TYR B 250 PHE 0.038 0.001 PHE C 255 TRP 0.012 0.002 TRP F 241 HIS 0.005 0.001 HIS F 43 Details of bonding type rmsd covalent geometry : bond 0.00304 (11836) covalent geometry : angle 0.52748 (16012) hydrogen bonds : bond 0.03706 ( 728) hydrogen bonds : angle 3.93000 ( 2160) metal coordination : bond 0.00455 ( 4) metal coordination : angle 5.74249 ( 6) Misc. bond : bond 0.00074 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3157.10 seconds wall clock time: 54 minutes 52.84 seconds (3292.84 seconds total)