Starting phenix.real_space_refine on Sat Aug 23 09:16:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j7u_36049/08_2025/8j7u_36049.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j7u_36049/08_2025/8j7u_36049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j7u_36049/08_2025/8j7u_36049.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j7u_36049/08_2025/8j7u_36049.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j7u_36049/08_2025/8j7u_36049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j7u_36049/08_2025/8j7u_36049.map" } resolution = 3.12 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 ------------------------------------------------------------------------------- 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= 0.013 sd= 0.057 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 45 5.16 5 C 7034 2.51 5 N 1839 2.21 5 O 2083 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11003 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2133 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 7, 'TRANS': 263} Chain breaks: 4 Chain: "E" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1638 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1672 Classifications: {'peptide': 215} Link IDs: {'PCIS': 4, 'PTRANS': 7, 'TRANS': 203} Chain: "D" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1672 Classifications: {'peptide': 215} Link IDs: {'PCIS': 4, 'PTRANS': 7, 'TRANS': 203} Chain: "F" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1638 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2248 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.42, per 1000 atoms: 0.22 Number of scatterers: 11003 At special positions: 0 Unit cell: (87.468, 113.472, 158.388, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 45 16.00 O 2083 8.00 N 1839 7.00 C 7034 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 200 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 145 " - pdb=" SG CYS F 200 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 445.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 240 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 240 " 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2664 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 26 sheets defined 32.1% alpha, 37.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 22 through 32 removed outlier: 4.027A pdb=" N PHE A 26 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG A 27 " --> pdb=" O SER A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 57 removed outlier: 3.775A pdb=" N PHE A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN A 45 " --> pdb=" O PHE A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 88 Processing helix chain 'A' and resid 102 through 132 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 143 through 159 removed outlier: 3.761A pdb=" N LEU A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 259 removed outlier: 4.077A pdb=" N GLN A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 294 Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 298 through 303 removed outlier: 4.343A pdb=" N ASN A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 314 Processing helix chain 'A' and resid 347 through 362 Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.633A pdb=" N ALA C 87 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 131 Processing helix chain 'C' and resid 187 through 192 Processing helix chain 'D' and resid 125 through 131 Processing helix chain 'D' and resid 187 through 193 removed outlier: 3.724A pdb=" N HIS D 193 " --> pdb=" O GLU D 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 65 No H-bonds generated for 'chain 'F' and resid 63 through 65' Processing helix chain 'F' and resid 86 through 90 Processing helix chain 'F' and resid 161 through 163 No H-bonds generated for 'chain 'F' and resid 161 through 163' Processing helix chain 'B' and resid 23 through 30 Processing helix chain 'B' and resid 32 through 57 Processing helix chain 'B' and resid 60 through 88 removed outlier: 4.049A pdb=" N LEU B 64 " --> pdb=" O ASN B 60 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 132 removed outlier: 4.469A pdb=" N VAL B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 159 removed outlier: 3.993A pdb=" N LEU B 143 " --> pdb=" O GLU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 259 removed outlier: 4.522A pdb=" N GLN B 235 " --> pdb=" O ARG B 231 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 237 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 294 Proline residue: B 284 - end of helix Processing helix chain 'B' and resid 298 through 303 removed outlier: 4.545A pdb=" N ASN B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 314 Processing helix chain 'B' and resid 347 through 362 removed outlier: 3.524A pdb=" N ALA B 362 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 329 removed outlier: 5.548A pdb=" N LEU A 321 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ILE A 341 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N GLU A 323 " --> pdb=" O LYS A 339 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS A 339 " --> pdb=" O GLU A 323 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TYR A 334 " --> pdb=" O GLN A 366 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N TYR A 368 " --> pdb=" O TYR A 334 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLY A 336 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N GLN A 370 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU A 338 " --> pdb=" O GLN A 370 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ASP A 372 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU A 340 " --> pdb=" O ASP A 372 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.501A pdb=" N GLN E 77 " --> pdb=" O ASP E 72 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.575A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR E 107 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.575A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 125 through 129 removed outlier: 3.712A pdb=" N GLY E 144 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS E 145 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER E 184 " --> pdb=" O CYS E 145 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TYR E 180 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 125 through 129 removed outlier: 3.712A pdb=" N GLY E 144 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS E 145 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER E 184 " --> pdb=" O CYS E 145 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TYR E 180 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR E 181 " --> pdb=" O VAL E 174 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 156 through 159 removed outlier: 3.747A pdb=" N VAL E 211 " --> pdb=" O VAL E 202 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.261A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N MET C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N TYR C 53 " --> pdb=" O MET C 37 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP C 39 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.261A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR C 101 " --> pdb=" O GLN C 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AB3, first strand: chain 'C' and resid 118 through 122 removed outlier: 3.641A pdb=" N ASN C 141 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL C 137 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N TYR C 177 " --> pdb=" O ASN C 142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 149 through 153 removed outlier: 3.512A pdb=" N PHE C 213 " --> pdb=" O TYR C 196 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS C 198 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS C 211 " --> pdb=" O CYS C 198 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA C 200 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N HIS C 202 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N SER C 207 " --> pdb=" O HIS C 202 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 14 removed outlier: 6.818A pdb=" N MET D 37 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N TYR D 53 " --> pdb=" O MET D 37 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP D 39 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 14 removed outlier: 3.811A pdb=" N THR D 101 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AB9, first strand: chain 'D' and resid 120 through 122 removed outlier: 3.800A pdb=" N VAL D 137 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N TYR D 177 " --> pdb=" O ASN D 142 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 157 through 158 removed outlier: 3.584A pdb=" N ASN D 149 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE D 209 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N HIS D 202 " --> pdb=" O SER D 207 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER D 207 " --> pdb=" O HIS D 202 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AC3, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.682A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N SER F 40 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU F 45 " --> pdb=" O SER F 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.959A pdb=" N TYR F 107 " --> pdb=" O ARG F 97 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 125 through 129 removed outlier: 3.586A pdb=" N SER F 184 " --> pdb=" O CYS F 145 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY F 149 " --> pdb=" O TYR F 180 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR F 180 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 125 through 129 removed outlier: 3.586A pdb=" N SER F 184 " --> pdb=" O CYS F 145 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY F 149 " --> pdb=" O TYR F 180 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR F 180 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 156 through 159 removed outlier: 3.781A pdb=" N LYS F 213 " --> pdb=" O CYS F 200 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL F 211 " --> pdb=" O VAL F 202 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 318 through 329 removed outlier: 5.557A pdb=" N LEU B 321 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE B 341 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLU B 323 " --> pdb=" O LYS B 339 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS B 339 " --> pdb=" O GLU B 323 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TYR B 334 " --> pdb=" O VAL B 364 " (cutoff:3.500A) 624 hydrogen bonds defined for protein. 1704 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: 1.70 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3053 1.33 - 1.45: 2113 1.45 - 1.57: 6031 1.57 - 1.69: 0 1.69 - 1.81: 65 Bond restraints: 11262 Sorted by residual: bond pdb=" N ASP C 74 " pdb=" CA ASP C 74 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.33e-02 5.65e+03 8.50e+00 bond pdb=" N VAL B 51 " pdb=" CA VAL B 51 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.17e+00 bond pdb=" CA SER F 40 " pdb=" CB SER F 40 " ideal model delta sigma weight residual 1.536 1.496 0.040 1.46e-02 4.69e+03 7.58e+00 bond pdb=" N VAL F 147 " pdb=" CA VAL F 147 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.27e-02 6.20e+03 7.43e+00 bond pdb=" N LYS F 148 " pdb=" CA LYS F 148 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.21e-02 6.83e+03 7.14e+00 ... (remaining 11257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 15086 2.72 - 5.45: 198 5.45 - 8.17: 37 8.17 - 10.90: 4 10.90 - 13.62: 5 Bond angle restraints: 15330 Sorted by residual: angle pdb=" CB MET D 179 " pdb=" CG MET D 179 " pdb=" SD MET D 179 " ideal model delta sigma weight residual 112.70 124.54 -11.84 3.00e+00 1.11e-01 1.56e+01 angle pdb=" CA GLU B 128 " pdb=" CB GLU B 128 " pdb=" CG GLU B 128 " ideal model delta sigma weight residual 114.10 121.92 -7.82 2.00e+00 2.50e-01 1.53e+01 angle pdb=" CA LEU D 129 " pdb=" CB LEU D 129 " pdb=" CG LEU D 129 " ideal model delta sigma weight residual 116.30 129.92 -13.62 3.50e+00 8.16e-02 1.52e+01 angle pdb=" CB MET A 258 " pdb=" CG MET A 258 " pdb=" SD MET A 258 " ideal model delta sigma weight residual 112.70 124.15 -11.45 3.00e+00 1.11e-01 1.46e+01 angle pdb=" C ARG C 72 " pdb=" CA ARG C 72 " pdb=" CB ARG C 72 " ideal model delta sigma weight residual 116.54 112.18 4.36 1.15e+00 7.56e-01 1.44e+01 ... (remaining 15325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 5938 17.72 - 35.44: 524 35.44 - 53.16: 154 53.16 - 70.88: 31 70.88 - 88.60: 10 Dihedral angle restraints: 6657 sinusoidal: 2530 harmonic: 4127 Sorted by residual: dihedral pdb=" CB CYS E 145 " pdb=" SG CYS E 145 " pdb=" SG CYS E 200 " pdb=" CB CYS E 200 " ideal model delta sinusoidal sigma weight residual 93.00 154.17 -61.17 1 1.00e+01 1.00e-02 4.97e+01 dihedral pdb=" CB CYS F 145 " pdb=" SG CYS F 145 " pdb=" SG CYS F 200 " pdb=" CB CYS F 200 " ideal model delta sinusoidal sigma weight residual 93.00 147.65 -54.65 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" CB CYS D 138 " pdb=" SG CYS D 138 " pdb=" SG CYS D 198 " pdb=" CB CYS D 198 " ideal model delta sinusoidal sigma weight residual 93.00 56.56 36.44 1 1.00e+01 1.00e-02 1.88e+01 ... (remaining 6654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1577 0.083 - 0.167: 178 0.167 - 0.250: 7 0.250 - 0.333: 0 0.333 - 0.416: 1 Chirality restraints: 1763 Sorted by residual: chirality pdb=" CG LEU F 129 " pdb=" CB LEU F 129 " pdb=" CD1 LEU F 129 " pdb=" CD2 LEU F 129 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" CB ILE B 122 " pdb=" CA ILE B 122 " pdb=" CG1 ILE B 122 " pdb=" CG2 ILE B 122 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CB THR B 245 " pdb=" CA THR B 245 " pdb=" OG1 THR B 245 " pdb=" CG2 THR B 245 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1760 not shown) Planarity restraints: 1938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 17 " 0.389 9.50e-02 1.11e+02 1.75e-01 1.87e+01 pdb=" NE ARG D 17 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG D 17 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG D 17 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 17 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 167 " 0.019 2.00e-02 2.50e+03 1.66e-02 6.90e+00 pdb=" CG TRP C 167 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP C 167 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C 167 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 167 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 167 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 167 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 167 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 167 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP C 167 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 159 " -0.012 2.00e-02 2.50e+03 1.53e-02 5.87e+00 pdb=" CG TRP E 159 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP E 159 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP E 159 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 159 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 159 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP E 159 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 159 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 159 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP E 159 " -0.001 2.00e-02 2.50e+03 ... (remaining 1935 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 109 2.57 - 3.15: 8684 3.15 - 3.73: 17704 3.73 - 4.32: 24673 4.32 - 4.90: 40978 Nonbonded interactions: 92148 Sorted by model distance: nonbonded pdb=" OD2 ASP B 74 " pdb="ZN ZN B 501 " model vdw 1.982 2.230 nonbonded pdb=" OD1 ASP A 74 " pdb="ZN ZN A 501 " model vdw 1.985 2.230 nonbonded pdb=" OD2 ASP A 74 " pdb="ZN ZN A 501 " model vdw 1.990 2.230 nonbonded pdb=" OD1 ASP B 244 " pdb="ZN ZN B 501 " model vdw 1.995 2.230 nonbonded pdb=" OD2 ASP B 244 " pdb="ZN ZN B 501 " model vdw 2.004 2.230 ... (remaining 92143 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' selection = (chain 'B' and (resid 22 through 57 or resid 70 through 132 or resid 136 through \ 501)) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.040 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 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 : 0.005 0.269 11272 Z= 0.255 Angle : 0.833 13.623 15346 Z= 0.464 Chirality : 0.049 0.416 1763 Planarity : 0.007 0.175 1938 Dihedral : 15.326 88.599 3969 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.88 % Allowed : 19.74 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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 aren not related in a simple way. whole: 0.27 (0.22), residues: 1399 helix: 0.71 (0.26), residues: 395 sheet: 0.90 (0.24), residues: 450 loop : -0.76 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 24 TYR 0.014 0.001 TYR E 180 PHE 0.035 0.002 PHE A 120 TRP 0.044 0.002 TRP C 167 HIS 0.023 0.002 HIS C 202 Details of bonding type rmsd covalent geometry : bond 0.00410 (11262) covalent geometry : angle 0.83312 (15330) SS BOND : bond 0.00232 ( 8) SS BOND : angle 0.52231 ( 16) hydrogen bonds : bond 0.19916 ( 573) hydrogen bonds : angle 7.64977 ( 1704) metal coordination : bond 0.26843 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 40 SER cc_start: 0.6503 (OUTLIER) cc_final: 0.6087 (p) REVERT: E 75 LYS cc_start: 0.8889 (ptpp) cc_final: 0.8571 (ptmm) REVERT: C 32 TYR cc_start: 0.6870 (m-80) cc_final: 0.6592 (m-80) REVERT: C 203 LYS cc_start: 0.8743 (tmmm) cc_final: 0.8494 (pttt) REVERT: D 46 GLN cc_start: 0.7845 (mp10) cc_final: 0.7498 (pm20) REVERT: D 59 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7196 (tp30) REVERT: B 36 ARG cc_start: 0.7383 (ptp-110) cc_final: 0.6909 (ptp-110) REVERT: B 52 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7559 (pt0) REVERT: B 73 PHE cc_start: 0.7180 (OUTLIER) cc_final: 0.6311 (t80) outliers start: 23 outliers final: 13 residues processed: 200 average time/residue: 0.1207 time to fit residues: 32.0479 Evaluate side-chains 180 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 322 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 40.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.0670 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 50.0000 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 overall best weight: 5.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 310 GLN ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 HIS A 357 ASN A 366 GLN ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 ASN ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 HIS ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 ASN B 37 ASN B 138 HIS B 307 GLN B 325 HIS B 366 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.231470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.214013 restraints weight = 13615.685| |-----------------------------------------------------------------------------| r_work (start): 0.4425 rms_B_bonded: 0.89 r_work: 0.4311 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.4269 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 11272 Z= 0.344 Angle : 0.770 10.916 15346 Z= 0.393 Chirality : 0.049 0.245 1763 Planarity : 0.005 0.056 1938 Dihedral : 6.655 58.877 1550 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.92 % Allowed : 17.70 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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 aren not related in a simple way. whole: 0.44 (0.22), residues: 1399 helix: 1.02 (0.25), residues: 398 sheet: 0.88 (0.23), residues: 470 loop : -0.77 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 102 TYR 0.017 0.002 TYR C 32 PHE 0.028 0.003 PHE C 36 TRP 0.027 0.002 TRP F 52 HIS 0.009 0.001 HIS C 202 Details of bonding type rmsd covalent geometry : bond 0.00809 (11262) covalent geometry : angle 0.76977 (15330) SS BOND : bond 0.00393 ( 8) SS BOND : angle 0.97365 ( 16) hydrogen bonds : bond 0.05125 ( 573) hydrogen bonds : angle 5.48039 ( 1704) metal coordination : bond 0.00559 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 174 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 233 ILE cc_start: 0.6293 (OUTLIER) cc_final: 0.5779 (mp) REVERT: D 179 MET cc_start: 0.5265 (tmm) cc_final: 0.4800 (tmm) REVERT: F 51 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8120 (tp) REVERT: B 73 PHE cc_start: 0.5511 (OUTLIER) cc_final: 0.4485 (t80) outliers start: 48 outliers final: 32 residues processed: 202 average time/residue: 0.1121 time to fit residues: 30.3795 Evaluate side-chains 195 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 328 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 126 optimal weight: 40.0000 chunk 6 optimal weight: 0.9990 chunk 136 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 chunk 61 optimal weight: 40.0000 chunk 43 optimal weight: 50.0000 chunk 98 optimal weight: 9.9990 chunk 128 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 324 GLN A 366 GLN ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 HIS B 307 GLN ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.232387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.208404 restraints weight = 13827.807| |-----------------------------------------------------------------------------| r_work (start): 0.4365 rms_B_bonded: 1.22 r_work: 0.4207 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.4170 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11272 Z= 0.182 Angle : 0.672 9.006 15346 Z= 0.343 Chirality : 0.045 0.144 1763 Planarity : 0.005 0.052 1938 Dihedral : 5.630 58.480 1530 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.00 % Allowed : 17.13 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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 aren not related in a simple way. whole: 0.60 (0.22), residues: 1399 helix: 1.36 (0.25), residues: 399 sheet: 0.90 (0.24), residues: 456 loop : -0.73 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 16 TYR 0.014 0.001 TYR F 94 PHE 0.027 0.002 PHE B 69 TRP 0.026 0.002 TRP C 167 HIS 0.006 0.001 HIS C 202 Details of bonding type rmsd covalent geometry : bond 0.00421 (11262) covalent geometry : angle 0.67214 (15330) SS BOND : bond 0.00300 ( 8) SS BOND : angle 0.73158 ( 16) hydrogen bonds : bond 0.04346 ( 573) hydrogen bonds : angle 5.05989 ( 1704) metal coordination : bond 0.00098 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 167 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 233 ILE cc_start: 0.6500 (OUTLIER) cc_final: 0.5983 (mp) REVERT: E 77 GLN cc_start: 0.7850 (mt0) cc_final: 0.7606 (mt0) REVERT: D 179 MET cc_start: 0.5518 (tmm) cc_final: 0.5212 (tmm) REVERT: F 51 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8159 (tp) REVERT: B 73 PHE cc_start: 0.5797 (OUTLIER) cc_final: 0.4662 (t80) REVERT: B 91 ARG cc_start: 0.6616 (OUTLIER) cc_final: 0.6402 (pmt170) outliers start: 49 outliers final: 28 residues processed: 195 average time/residue: 0.1123 time to fit residues: 29.2934 Evaluate side-chains 192 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 71 LYS Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 328 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 3 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 43 optimal weight: 50.0000 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 133 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 44 optimal weight: 30.0000 chunk 82 optimal weight: 9.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 366 GLN ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.231944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.207786 restraints weight = 13840.918| |-----------------------------------------------------------------------------| r_work (start): 0.4353 rms_B_bonded: 1.26 r_work: 0.4159 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.4122 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11272 Z= 0.211 Angle : 0.663 9.238 15346 Z= 0.338 Chirality : 0.045 0.207 1763 Planarity : 0.005 0.051 1938 Dihedral : 5.642 58.287 1530 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.83 % Allowed : 18.03 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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 aren not related in a simple way. whole: 0.66 (0.22), residues: 1399 helix: 1.51 (0.25), residues: 401 sheet: 0.89 (0.23), residues: 460 loop : -0.75 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 18 TYR 0.015 0.002 TYR F 94 PHE 0.027 0.002 PHE B 69 TRP 0.035 0.002 TRP C 167 HIS 0.004 0.001 HIS C 193 Details of bonding type rmsd covalent geometry : bond 0.00494 (11262) covalent geometry : angle 0.66341 (15330) SS BOND : bond 0.00234 ( 8) SS BOND : angle 0.61831 ( 16) hydrogen bonds : bond 0.04167 ( 573) hydrogen bonds : angle 4.84057 ( 1704) metal coordination : bond 0.00090 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 164 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 233 ILE cc_start: 0.6582 (OUTLIER) cc_final: 0.6060 (mp) REVERT: E 51 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8434 (tp) REVERT: F 51 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8142 (tp) REVERT: B 73 PHE cc_start: 0.5855 (OUTLIER) cc_final: 0.4612 (t80) REVERT: B 91 ARG cc_start: 0.6710 (OUTLIER) cc_final: 0.6509 (pmt170) outliers start: 47 outliers final: 35 residues processed: 192 average time/residue: 0.1181 time to fit residues: 30.4048 Evaluate side-chains 196 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 71 LYS Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 328 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 43 optimal weight: 50.0000 chunk 101 optimal weight: 20.0000 chunk 23 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 61 optimal weight: 30.0000 chunk 80 optimal weight: 30.0000 chunk 2 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 324 GLN A 366 GLN ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.230493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.207302 restraints weight = 13853.402| |-----------------------------------------------------------------------------| r_work (start): 0.4350 rms_B_bonded: 1.19 r_work: 0.4207 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.4168 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 11272 Z= 0.326 Angle : 0.725 10.468 15346 Z= 0.368 Chirality : 0.048 0.232 1763 Planarity : 0.005 0.055 1938 Dihedral : 5.980 59.959 1530 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.40 % Allowed : 18.11 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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 aren not related in a simple way. whole: 0.54 (0.22), residues: 1399 helix: 1.36 (0.26), residues: 401 sheet: 0.82 (0.23), residues: 460 loop : -0.79 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 18 TYR 0.018 0.002 TYR C 32 PHE 0.029 0.002 PHE C 36 TRP 0.044 0.003 TRP F 193 HIS 0.005 0.001 HIS C 193 Details of bonding type rmsd covalent geometry : bond 0.00773 (11262) covalent geometry : angle 0.72464 (15330) SS BOND : bond 0.00257 ( 8) SS BOND : angle 0.82858 ( 16) hydrogen bonds : bond 0.04448 ( 573) hydrogen bonds : angle 4.87296 ( 1704) metal coordination : bond 0.00125 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 159 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 233 ILE cc_start: 0.6537 (OUTLIER) cc_final: 0.6113 (mp) REVERT: E 51 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8433 (tp) REVERT: E 77 GLN cc_start: 0.7925 (mt0) cc_final: 0.7360 (mt0) REVERT: F 51 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8147 (tp) REVERT: B 73 PHE cc_start: 0.5845 (OUTLIER) cc_final: 0.4640 (t80) outliers start: 54 outliers final: 38 residues processed: 192 average time/residue: 0.1117 time to fit residues: 28.6046 Evaluate side-chains 196 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 138 CYS Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 332 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 127 optimal weight: 30.0000 chunk 115 optimal weight: 50.0000 chunk 10 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 366 GLN E 86 GLN E 160 ASN C 96 ASN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.232125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.206851 restraints weight = 13753.827| |-----------------------------------------------------------------------------| r_work (start): 0.4350 rms_B_bonded: 1.32 r_work: 0.4183 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4145 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11272 Z= 0.189 Angle : 0.665 9.976 15346 Z= 0.339 Chirality : 0.046 0.262 1763 Planarity : 0.005 0.051 1938 Dihedral : 5.796 59.667 1530 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.16 % Allowed : 19.00 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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 aren not related in a simple way. whole: 0.68 (0.22), residues: 1399 helix: 1.62 (0.26), residues: 401 sheet: 0.87 (0.23), residues: 458 loop : -0.79 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 18 TYR 0.013 0.001 TYR F 94 PHE 0.025 0.002 PHE B 69 TRP 0.049 0.002 TRP C 167 HIS 0.006 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00441 (11262) covalent geometry : angle 0.66482 (15330) SS BOND : bond 0.00222 ( 8) SS BOND : angle 0.56718 ( 16) hydrogen bonds : bond 0.03965 ( 573) hydrogen bonds : angle 4.72372 ( 1704) metal coordination : bond 0.00159 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 158 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 233 ILE cc_start: 0.6631 (OUTLIER) cc_final: 0.6198 (mp) REVERT: E 51 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8421 (tp) REVERT: F 51 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8168 (tp) REVERT: B 73 PHE cc_start: 0.5844 (OUTLIER) cc_final: 0.4584 (t80) REVERT: B 332 ASP cc_start: 0.7647 (t70) cc_final: 0.7275 (t0) outliers start: 51 outliers final: 36 residues processed: 189 average time/residue: 0.1148 time to fit residues: 28.7200 Evaluate side-chains 196 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 71 LYS Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 328 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 95 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 110 optimal weight: 50.0000 chunk 13 optimal weight: 6.9990 chunk 88 optimal weight: 50.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 324 GLN A 366 GLN E 86 GLN E 160 ASN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.232852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.210150 restraints weight = 13702.868| |-----------------------------------------------------------------------------| r_work (start): 0.4382 rms_B_bonded: 1.17 r_work: 0.4230 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.4194 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11272 Z= 0.151 Angle : 0.653 10.400 15346 Z= 0.333 Chirality : 0.045 0.268 1763 Planarity : 0.005 0.049 1938 Dihedral : 5.622 58.547 1530 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.67 % Allowed : 19.41 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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 aren not related in a simple way. whole: 0.80 (0.22), residues: 1399 helix: 1.74 (0.26), residues: 399 sheet: 0.98 (0.24), residues: 458 loop : -0.77 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 18 TYR 0.026 0.001 TYR C 144 PHE 0.024 0.002 PHE B 69 TRP 0.046 0.002 TRP C 167 HIS 0.005 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00348 (11262) covalent geometry : angle 0.65305 (15330) SS BOND : bond 0.00235 ( 8) SS BOND : angle 0.52909 ( 16) hydrogen bonds : bond 0.03751 ( 573) hydrogen bonds : angle 4.60463 ( 1704) metal coordination : bond 0.00063 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 233 ILE cc_start: 0.6531 (OUTLIER) cc_final: 0.6102 (mp) REVERT: F 51 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8141 (tp) REVERT: B 73 PHE cc_start: 0.5656 (OUTLIER) cc_final: 0.4513 (t80) REVERT: B 332 ASP cc_start: 0.7586 (t70) cc_final: 0.7245 (t0) outliers start: 45 outliers final: 35 residues processed: 191 average time/residue: 0.1355 time to fit residues: 34.6898 Evaluate side-chains 200 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 71 LYS Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 328 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 63 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 89 optimal weight: 50.0000 chunk 68 optimal weight: 40.0000 chunk 136 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 324 GLN A 366 GLN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.230906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.206062 restraints weight = 13740.051| |-----------------------------------------------------------------------------| r_work (start): 0.4344 rms_B_bonded: 1.30 r_work: 0.4146 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.4112 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 11272 Z= 0.305 Angle : 0.729 10.612 15346 Z= 0.371 Chirality : 0.048 0.258 1763 Planarity : 0.005 0.052 1938 Dihedral : 5.756 59.469 1527 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.92 % Allowed : 20.23 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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 aren not related in a simple way. whole: 0.64 (0.22), residues: 1399 helix: 1.59 (0.26), residues: 399 sheet: 0.89 (0.24), residues: 458 loop : -0.86 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 18 TYR 0.019 0.002 TYR C 144 PHE 0.028 0.002 PHE C 36 TRP 0.048 0.002 TRP C 167 HIS 0.004 0.001 HIS B 325 Details of bonding type rmsd covalent geometry : bond 0.00725 (11262) covalent geometry : angle 0.72955 (15330) SS BOND : bond 0.00213 ( 8) SS BOND : angle 0.68100 ( 16) hydrogen bonds : bond 0.04235 ( 573) hydrogen bonds : angle 4.74385 ( 1704) metal coordination : bond 0.00613 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 159 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 233 ILE cc_start: 0.6670 (OUTLIER) cc_final: 0.6333 (mp) REVERT: F 51 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.8128 (tp) REVERT: B 73 PHE cc_start: 0.5969 (OUTLIER) cc_final: 0.4688 (t80) REVERT: B 332 ASP cc_start: 0.7778 (t70) cc_final: 0.7430 (t0) outliers start: 48 outliers final: 40 residues processed: 188 average time/residue: 0.1412 time to fit residues: 35.4638 Evaluate side-chains 197 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 71 LYS Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 328 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 95 optimal weight: 0.5980 chunk 76 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 86 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 11 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 324 GLN A 366 GLN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.233455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.209339 restraints weight = 13607.709| |-----------------------------------------------------------------------------| r_work (start): 0.4379 rms_B_bonded: 1.21 r_work: 0.4232 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.4184 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11272 Z= 0.138 Angle : 0.669 13.291 15346 Z= 0.339 Chirality : 0.045 0.294 1763 Planarity : 0.005 0.049 1938 Dihedral : 5.438 57.788 1527 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.43 % Allowed : 20.80 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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 aren not related in a simple way. whole: 0.74 (0.22), residues: 1399 helix: 1.81 (0.26), residues: 401 sheet: 0.80 (0.23), residues: 470 loop : -0.81 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 215 TYR 0.017 0.001 TYR C 144 PHE 0.024 0.001 PHE B 69 TRP 0.048 0.002 TRP C 167 HIS 0.007 0.001 HIS C 193 Details of bonding type rmsd covalent geometry : bond 0.00314 (11262) covalent geometry : angle 0.66904 (15330) SS BOND : bond 0.00231 ( 8) SS BOND : angle 0.50283 ( 16) hydrogen bonds : bond 0.03640 ( 573) hydrogen bonds : angle 4.58886 ( 1704) metal coordination : bond 0.00054 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 170 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 233 ILE cc_start: 0.6581 (OUTLIER) cc_final: 0.6243 (mp) REVERT: F 51 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8113 (tp) REVERT: B 73 PHE cc_start: 0.5886 (OUTLIER) cc_final: 0.4545 (t80) REVERT: B 91 ARG cc_start: 0.6667 (OUTLIER) cc_final: 0.6430 (pmt170) REVERT: B 332 ASP cc_start: 0.7585 (t70) cc_final: 0.7305 (t0) outliers start: 42 outliers final: 30 residues processed: 190 average time/residue: 0.1515 time to fit residues: 38.0202 Evaluate side-chains 190 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain E residue 71 LYS Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 322 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 97 optimal weight: 0.1980 chunk 21 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 104 optimal weight: 50.0000 chunk 28 optimal weight: 9.9990 chunk 123 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 98 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 366 GLN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 ASN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN B 324 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.233907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.208593 restraints weight = 13747.034| |-----------------------------------------------------------------------------| r_work (start): 0.4369 rms_B_bonded: 1.32 r_work: 0.4196 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4160 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11272 Z= 0.133 Angle : 0.694 13.951 15346 Z= 0.349 Chirality : 0.045 0.275 1763 Planarity : 0.005 0.048 1938 Dihedral : 5.257 57.310 1526 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.94 % Allowed : 21.45 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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 aren not related in a simple way. whole: 0.74 (0.22), residues: 1399 helix: 1.86 (0.26), residues: 401 sheet: 0.77 (0.23), residues: 470 loop : -0.82 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 18 TYR 0.011 0.001 TYR F 94 PHE 0.024 0.002 PHE B 69 TRP 0.059 0.002 TRP C 167 HIS 0.007 0.001 HIS C 193 Details of bonding type rmsd covalent geometry : bond 0.00306 (11262) covalent geometry : angle 0.69451 (15330) SS BOND : bond 0.00240 ( 8) SS BOND : angle 0.58397 ( 16) hydrogen bonds : bond 0.03559 ( 573) hydrogen bonds : angle 4.49417 ( 1704) metal coordination : bond 0.00023 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ILE cc_start: 0.6590 (OUTLIER) cc_final: 0.6227 (mp) REVERT: F 51 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.8078 (tp) REVERT: B 73 PHE cc_start: 0.5862 (OUTLIER) cc_final: 0.4554 (t80) REVERT: B 91 ARG cc_start: 0.6678 (OUTLIER) cc_final: 0.6410 (pmt170) REVERT: B 332 ASP cc_start: 0.7598 (t70) cc_final: 0.7316 (t0) outliers start: 36 outliers final: 26 residues processed: 180 average time/residue: 0.1375 time to fit residues: 33.4198 Evaluate side-chains 189 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TYR Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 324 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 92 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 137 optimal weight: 0.6980 chunk 131 optimal weight: 0.9990 chunk 42 optimal weight: 20.0000 chunk 63 optimal weight: 50.0000 chunk 10 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 366 GLN E 73 ASN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN B 324 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.233183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.207059 restraints weight = 13740.075| |-----------------------------------------------------------------------------| r_work (start): 0.4344 rms_B_bonded: 1.27 r_work: 0.4169 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.4137 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11272 Z= 0.159 Angle : 0.712 13.820 15346 Z= 0.355 Chirality : 0.045 0.265 1763 Planarity : 0.005 0.048 1938 Dihedral : 5.260 57.074 1526 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.77 % Allowed : 21.94 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % 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 aren not related in a simple way. whole: 0.75 (0.22), residues: 1399 helix: 1.83 (0.26), residues: 401 sheet: 0.84 (0.24), residues: 458 loop : -0.83 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 18 TYR 0.015 0.001 TYR F 180 PHE 0.024 0.002 PHE B 69 TRP 0.059 0.002 TRP C 167 HIS 0.005 0.001 HIS B 325 Details of bonding type rmsd covalent geometry : bond 0.00371 (11262) covalent geometry : angle 0.71258 (15330) SS BOND : bond 0.00246 ( 8) SS BOND : angle 0.60464 ( 16) hydrogen bonds : bond 0.03627 ( 573) hydrogen bonds : angle 4.51160 ( 1704) metal coordination : bond 0.00056 ( 2) =============================================================================== Job complete usr+sys time: 2668.11 seconds wall clock time: 46 minutes 30.14 seconds (2790.14 seconds total)