Starting phenix.real_space_refine on Tue May 13 23:11:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j7u_36049/05_2025/8j7u_36049.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j7u_36049/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j7u_36049/05_2025/8j7u_36049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j7u_36049/05_2025/8j7u_36049.map" model { file = "/net/cci-nas-00/data/ceres_data/8j7u_36049/05_2025/8j7u_36049.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j7u_36049/05_2025/8j7u_36049.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.88, per 1000 atoms: 0.63 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: 2.66 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.56 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: 3.57 Time building geometry restraints manager: 3.12 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 \ 376 or resid 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 29.560 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.830 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.044 0.002 TRP C 167 HIS 0.023 0.002 HIS C 202 PHE 0.035 0.002 PHE A 120 TYR 0.014 0.001 TYR E 180 ARG 0.012 0.001 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.19916 ( 573) hydrogen bonds : angle 7.64977 ( 1704) metal coordination : bond 0.26843 ( 2) SS BOND : bond 0.00232 ( 8) SS BOND : angle 0.52231 ( 16) covalent geometry : bond 0.00410 (11262) covalent geometry : angle 0.83312 (15330) *********************** 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 : 1.235 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: 0.2930 time to fit residues: 77.5859 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 : 1.277 ------------------------------------------------------------------------------- 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 117 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 56 optimal weight: 20.0000 chunk 108 optimal weight: 30.0000 chunk 42 optimal weight: 50.0000 chunk 66 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 126 optimal weight: 20.0000 overall best weight: 9.9994 ------------------------------------------------------------------------------- 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 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 41 GLN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4568 r_free = 0.4568 target = 0.228411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.211461 restraints weight = 13432.778| |-----------------------------------------------------------------------------| r_work (start): 0.4402 rms_B_bonded: 0.88 r_work: 0.4276 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.4242 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.137 11272 Z= 0.558 Angle : 0.898 14.930 15346 Z= 0.458 Chirality : 0.055 0.235 1763 Planarity : 0.006 0.058 1938 Dihedral : 7.154 59.587 1550 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.89 % Allowed : 17.78 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.22), residues: 1399 helix: 0.72 (0.25), residues: 398 sheet: 0.77 (0.23), residues: 466 loop : -0.89 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP F 52 HIS 0.009 0.002 HIS C 202 PHE 0.038 0.004 PHE C 36 TYR 0.024 0.003 TYR C 32 ARG 0.010 0.001 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.05652 ( 573) hydrogen bonds : angle 5.54468 ( 1704) metal coordination : bond 0.00673 ( 2) SS BOND : bond 0.00388 ( 8) SS BOND : angle 1.17648 ( 16) covalent geometry : bond 0.01321 (11262) covalent geometry : angle 0.89725 (15330) *********************** 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 234 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 174 time to evaluate : 1.194 Fit side-chains REVERT: A 233 ILE cc_start: 0.6452 (OUTLIER) cc_final: 0.6069 (mp) REVERT: E 86 GLN cc_start: 0.7068 (mm110) cc_final: 0.6451 (mm-40) REVERT: D 179 MET cc_start: 0.5335 (tmm) cc_final: 0.4873 (tmm) REVERT: B 73 PHE cc_start: 0.5684 (OUTLIER) cc_final: 0.4509 (t80) REVERT: B 97 SER cc_start: 0.8678 (OUTLIER) cc_final: 0.8448 (m) outliers start: 60 outliers final: 35 residues processed: 210 average time/residue: 0.2792 time to fit residues: 78.5388 Evaluate side-chains 196 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 1.214 ------------------------------------------------------------------------------- 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 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 288 GLU 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 E residue 141 VAL 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 D residue 95 SER Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 6 GLU 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 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 Chi-restraints excluded: chain B residue 332 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 119 optimal weight: 0.9990 chunk 96 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 110 optimal weight: 20.0000 chunk 101 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 26 optimal weight: 0.0570 chunk 115 optimal weight: 50.0000 chunk 11 optimal weight: 6.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- 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 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 138 HIS B 307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.230971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.210197 restraints weight = 13831.083| |-----------------------------------------------------------------------------| r_work (start): 0.4386 rms_B_bonded: 1.09 r_work: 0.4241 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.4207 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11272 Z= 0.228 Angle : 0.696 9.913 15346 Z= 0.358 Chirality : 0.046 0.142 1763 Planarity : 0.005 0.053 1938 Dihedral : 6.094 59.316 1530 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.49 % Allowed : 17.78 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.22), residues: 1399 helix: 1.22 (0.25), residues: 400 sheet: 0.81 (0.23), residues: 456 loop : -0.78 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 167 HIS 0.007 0.001 HIS B 240 PHE 0.026 0.002 PHE B 69 TYR 0.014 0.002 TYR F 94 ARG 0.005 0.001 ARG D 16 Details of bonding type rmsd hydrogen bonds : bond 0.04514 ( 573) hydrogen bonds : angle 5.12872 ( 1704) metal coordination : bond 0.00098 ( 2) SS BOND : bond 0.00230 ( 8) SS BOND : angle 0.73083 ( 16) covalent geometry : bond 0.00534 (11262) covalent geometry : angle 0.69632 (15330) *********************** 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 218 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 163 time to evaluate : 1.177 Fit side-chains REVERT: A 233 ILE cc_start: 0.6445 (OUTLIER) cc_final: 0.6000 (mp) REVERT: E 77 GLN cc_start: 0.7825 (mt0) cc_final: 0.7535 (mt0) REVERT: D 179 MET cc_start: 0.5477 (tmm) cc_final: 0.5146 (tmm) REVERT: F 51 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.8131 (tp) REVERT: B 73 PHE cc_start: 0.5749 (OUTLIER) cc_final: 0.4576 (t80) REVERT: B 332 ASP cc_start: 0.7561 (t70) cc_final: 0.7254 (t0) outliers start: 55 outliers final: 33 residues processed: 196 average time/residue: 0.2848 time to fit residues: 74.1926 Evaluate side-chains 192 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 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 E residue 160 ASN Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 192 ARG 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 321 LEU 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 75 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 108 optimal weight: 30.0000 chunk 120 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 43 optimal weight: 50.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 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 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.232671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.211732 restraints weight = 13802.779| |-----------------------------------------------------------------------------| r_work (start): 0.4398 rms_B_bonded: 1.06 r_work: 0.4259 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.4225 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11272 Z= 0.150 Angle : 0.642 8.223 15346 Z= 0.329 Chirality : 0.044 0.211 1763 Planarity : 0.004 0.052 1938 Dihedral : 5.795 59.239 1530 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.83 % Allowed : 18.52 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.22), residues: 1399 helix: 1.52 (0.26), residues: 403 sheet: 0.92 (0.23), residues: 454 loop : -0.80 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 167 HIS 0.007 0.001 HIS B 240 PHE 0.027 0.002 PHE B 69 TYR 0.013 0.001 TYR F 94 ARG 0.005 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 573) hydrogen bonds : angle 4.83504 ( 1704) metal coordination : bond 0.00237 ( 2) SS BOND : bond 0.00555 ( 8) SS BOND : angle 0.52941 ( 16) covalent geometry : bond 0.00340 (11262) covalent geometry : angle 0.64166 (15330) *********************** 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 217 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 170 time to evaluate : 1.178 Fit side-chains REVERT: A 233 ILE cc_start: 0.6471 (OUTLIER) cc_final: 0.6011 (mp) REVERT: F 51 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8116 (tp) REVERT: B 73 PHE cc_start: 0.5698 (OUTLIER) cc_final: 0.4563 (t80) REVERT: B 332 ASP cc_start: 0.7419 (t70) cc_final: 0.7094 (t0) outliers start: 47 outliers final: 33 residues processed: 198 average time/residue: 0.2934 time to fit residues: 77.3583 Evaluate side-chains 197 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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 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 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 181 THR 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 57 THR 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 22 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 71 optimal weight: 20.0000 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 131 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 70 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.233042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.208730 restraints weight = 13778.337| |-----------------------------------------------------------------------------| r_work (start): 0.4373 rms_B_bonded: 1.24 r_work: 0.4201 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4167 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.2258 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 : 0.644 10.626 15346 Z= 0.328 Chirality : 0.044 0.232 1763 Planarity : 0.004 0.049 1938 Dihedral : 5.533 58.215 1530 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.59 % Allowed : 19.00 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.22), residues: 1399 helix: 1.71 (0.26), residues: 403 sheet: 0.96 (0.24), residues: 458 loop : -0.78 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP C 167 HIS 0.005 0.001 HIS C 193 PHE 0.025 0.002 PHE B 69 TYR 0.012 0.001 TYR F 94 ARG 0.008 0.001 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.03745 ( 573) hydrogen bonds : angle 4.68500 ( 1704) metal coordination : bond 0.01000 ( 2) SS BOND : bond 0.00409 ( 8) SS BOND : angle 0.55527 ( 16) covalent geometry : bond 0.00314 (11262) covalent geometry : angle 0.64407 (15330) *********************** 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 206 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 162 time to evaluate : 1.180 Fit side-chains revert: symmetry clash REVERT: A 233 ILE cc_start: 0.6592 (OUTLIER) cc_final: 0.6148 (mp) REVERT: F 51 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8138 (tp) REVERT: B 73 PHE cc_start: 0.5822 (OUTLIER) cc_final: 0.4562 (t80) REVERT: B 332 ASP cc_start: 0.7468 (t70) cc_final: 0.7159 (t0) outliers start: 44 outliers final: 28 residues processed: 189 average time/residue: 0.2945 time to fit residues: 73.8419 Evaluate side-chains 190 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 1.266 ------------------------------------------------------------------------------- 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 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 92 ILE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 193 HIS 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 51 ILE Chi-restraints excluded: chain F residue 57 THR 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 282 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 328 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 115 optimal weight: 30.0000 chunk 49 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 126 optimal weight: 40.0000 chunk 18 optimal weight: 0.0270 chunk 129 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 42 optimal weight: 40.0000 overall best weight: 3.0046 ------------------------------------------------------------------------------- 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 86 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 240 HIS ** 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 = 0.4596 r_free = 0.4596 target = 0.232099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.208367 restraints weight = 13713.136| |-----------------------------------------------------------------------------| r_work (start): 0.4364 rms_B_bonded: 1.22 r_work: 0.4199 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.4163 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11272 Z= 0.203 Angle : 0.660 10.151 15346 Z= 0.336 Chirality : 0.045 0.267 1763 Planarity : 0.005 0.048 1938 Dihedral : 5.420 58.735 1527 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.67 % Allowed : 19.17 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.22), residues: 1399 helix: 1.73 (0.26), residues: 401 sheet: 0.97 (0.24), residues: 458 loop : -0.84 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 167 HIS 0.005 0.001 HIS C 193 PHE 0.025 0.002 PHE B 69 TYR 0.013 0.001 TYR F 94 ARG 0.008 0.001 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 573) hydrogen bonds : angle 4.63469 ( 1704) metal coordination : bond 0.00095 ( 2) SS BOND : bond 0.00244 ( 8) SS BOND : angle 0.57149 ( 16) covalent geometry : bond 0.00476 (11262) covalent geometry : angle 0.65989 (15330) *********************** 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 202 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 157 time to evaluate : 1.252 Fit side-chains REVERT: A 233 ILE cc_start: 0.6605 (OUTLIER) cc_final: 0.6187 (mp) REVERT: E 86 GLN cc_start: 0.7103 (mm110) cc_final: 0.6786 (mm-40) REVERT: F 51 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8152 (tp) REVERT: B 73 PHE cc_start: 0.5808 (OUTLIER) cc_final: 0.4605 (t80) REVERT: B 332 ASP cc_start: 0.7592 (t70) cc_final: 0.7273 (t0) outliers start: 45 outliers final: 34 residues processed: 185 average time/residue: 0.3040 time to fit residues: 74.3367 Evaluate side-chains 194 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 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 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 E residue 181 THR 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 138 CYS Chi-restraints excluded: chain D residue 172 SER 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 238 PHE Chi-restraints excluded: chain B residue 282 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 0 optimal weight: 60.0000 chunk 123 optimal weight: 6.9990 chunk 45 optimal weight: 40.0000 chunk 10 optimal weight: 0.0370 chunk 27 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 114 optimal weight: 0.4980 chunk 50 optimal weight: 8.9990 overall best weight: 2.4462 ------------------------------------------------------------------------------- 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 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 ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.232489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.207575 restraints weight = 13804.850| |-----------------------------------------------------------------------------| r_work (start): 0.4361 rms_B_bonded: 1.19 r_work: 0.4222 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.4189 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11272 Z= 0.178 Angle : 0.661 10.482 15346 Z= 0.337 Chirality : 0.045 0.244 1763 Planarity : 0.005 0.047 1938 Dihedral : 5.349 59.082 1527 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.59 % Allowed : 19.74 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.22), residues: 1399 helix: 1.72 (0.26), residues: 399 sheet: 1.00 (0.24), residues: 458 loop : -0.81 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 167 HIS 0.004 0.001 HIS C 193 PHE 0.025 0.002 PHE B 69 TYR 0.025 0.001 TYR C 144 ARG 0.008 0.001 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 573) hydrogen bonds : angle 4.59684 ( 1704) metal coordination : bond 0.00044 ( 2) SS BOND : bond 0.00219 ( 8) SS BOND : angle 0.54926 ( 16) covalent geometry : bond 0.00416 (11262) covalent geometry : angle 0.66125 (15330) *********************** 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 206 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 162 time to evaluate : 1.169 Fit side-chains REVERT: A 233 ILE cc_start: 0.6511 (OUTLIER) cc_final: 0.6107 (mp) REVERT: F 51 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8142 (tp) REVERT: B 73 PHE cc_start: 0.5741 (OUTLIER) cc_final: 0.4577 (t80) REVERT: B 332 ASP cc_start: 0.7535 (t70) cc_final: 0.7257 (t0) outliers start: 44 outliers final: 35 residues processed: 189 average time/residue: 0.2843 time to fit residues: 71.6903 Evaluate side-chains 195 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 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 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 E residue 181 THR Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 79 ILE 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 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 138 HIS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 288 GLU 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 108 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 20.0000 chunk 24 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 135 optimal weight: 4.9990 chunk 126 optimal weight: 30.0000 chunk 131 optimal weight: 0.8980 chunk 89 optimal weight: 50.0000 chunk 78 optimal weight: 0.3980 overall best weight: 2.0384 ------------------------------------------------------------------------------- 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 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 240 HIS ** 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 = 0.4600 r_free = 0.4600 target = 0.232642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.207462 restraints weight = 13682.143| |-----------------------------------------------------------------------------| r_work (start): 0.4357 rms_B_bonded: 1.17 r_work: 0.4165 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.4133 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11272 Z= 0.162 Angle : 0.663 10.815 15346 Z= 0.336 Chirality : 0.045 0.254 1763 Planarity : 0.005 0.047 1938 Dihedral : 5.242 58.013 1526 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.75 % Allowed : 19.98 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.22), residues: 1399 helix: 1.79 (0.26), residues: 401 sheet: 0.96 (0.24), residues: 460 loop : -0.84 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 167 HIS 0.004 0.001 HIS C 193 PHE 0.025 0.002 PHE B 69 TYR 0.024 0.001 TYR C 144 ARG 0.009 0.001 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 573) hydrogen bonds : angle 4.53125 ( 1704) metal coordination : bond 0.00063 ( 2) SS BOND : bond 0.00228 ( 8) SS BOND : angle 0.51773 ( 16) covalent geometry : bond 0.00377 (11262) covalent geometry : angle 0.66331 (15330) *********************** 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 214 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 168 time to evaluate : 1.230 Fit side-chains REVERT: A 233 ILE cc_start: 0.6605 (OUTLIER) cc_final: 0.6260 (mp) REVERT: E 86 GLN cc_start: 0.7222 (mm110) cc_final: 0.6901 (mm-40) REVERT: F 51 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.8090 (tp) REVERT: B 73 PHE cc_start: 0.5751 (OUTLIER) cc_final: 0.4539 (t80) REVERT: B 91 ARG cc_start: 0.6680 (OUTLIER) cc_final: 0.6397 (pmt170) REVERT: B 332 ASP cc_start: 0.7557 (t70) cc_final: 0.7280 (t0) outliers start: 46 outliers final: 36 residues processed: 195 average time/residue: 0.2827 time to fit residues: 73.5154 Evaluate side-chains 198 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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 97 SER 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 328 THR Chi-restraints excluded: chain E residue 24 VAL 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 E residue 160 ASN 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 79 ILE 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 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 138 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 324 GLN 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 5 optimal weight: 6.9990 chunk 125 optimal weight: 0.5980 chunk 114 optimal weight: 50.0000 chunk 89 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 107 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- 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 C 170 GLN ** 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 = 0.4591 r_free = 0.4591 target = 0.231635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.208312 restraints weight = 13684.359| |-----------------------------------------------------------------------------| r_work (start): 0.4369 rms_B_bonded: 1.23 r_work: 0.4157 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.4125 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11272 Z= 0.198 Angle : 0.709 13.305 15346 Z= 0.357 Chirality : 0.046 0.273 1763 Planarity : 0.005 0.073 1938 Dihedral : 5.264 57.796 1525 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.00 % Allowed : 20.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.22), residues: 1399 helix: 1.74 (0.26), residues: 403 sheet: 0.92 (0.24), residues: 460 loop : -0.87 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP C 167 HIS 0.004 0.001 HIS C 193 PHE 0.025 0.002 PHE B 69 TYR 0.021 0.002 TYR C 144 ARG 0.008 0.001 ARG D 215 Details of bonding type rmsd hydrogen bonds : bond 0.03830 ( 573) hydrogen bonds : angle 4.58898 ( 1704) metal coordination : bond 0.00125 ( 2) SS BOND : bond 0.00231 ( 8) SS BOND : angle 0.68165 ( 16) covalent geometry : bond 0.00467 (11262) covalent geometry : angle 0.70944 (15330) *********************** 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 209 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 160 time to evaluate : 1.266 Fit side-chains REVERT: A 233 ILE cc_start: 0.6641 (OUTLIER) cc_final: 0.6251 (mp) REVERT: F 51 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8115 (tp) REVERT: B 73 PHE cc_start: 0.5791 (OUTLIER) cc_final: 0.4598 (t80) REVERT: B 91 ARG cc_start: 0.6728 (OUTLIER) cc_final: 0.6453 (pmt170) REVERT: B 332 ASP cc_start: 0.7607 (t70) cc_final: 0.7329 (t0) outliers start: 49 outliers final: 38 residues processed: 191 average time/residue: 0.2887 time to fit residues: 74.3257 Evaluate side-chains 199 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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 97 SER 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 328 THR Chi-restraints excluded: chain E residue 24 VAL 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 E residue 160 ASN 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 79 ILE Chi-restraints excluded: chain D residue 138 CYS Chi-restraints excluded: chain D residue 172 SER 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 138 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 328 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 119 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 chunk 86 optimal weight: 20.0000 chunk 77 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 122 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 130 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 D 96 ASN ** 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 = 0.4609 r_free = 0.4609 target = 0.233403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.210231 restraints weight = 13678.669| |-----------------------------------------------------------------------------| r_work (start): 0.4385 rms_B_bonded: 1.22 r_work: 0.4226 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.4185 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11272 Z= 0.133 Angle : 0.691 13.813 15346 Z= 0.349 Chirality : 0.045 0.254 1763 Planarity : 0.005 0.053 1938 Dihedral : 5.104 56.066 1525 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.94 % Allowed : 22.19 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.22), residues: 1399 helix: 1.85 (0.26), residues: 405 sheet: 0.95 (0.24), residues: 456 loop : -0.90 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP C 167 HIS 0.006 0.001 HIS C 193 PHE 0.024 0.001 PHE B 69 TYR 0.017 0.001 TYR C 144 ARG 0.008 0.001 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 573) hydrogen bonds : angle 4.49427 ( 1704) metal coordination : bond 0.00016 ( 2) SS BOND : bond 0.00249 ( 8) SS BOND : angle 0.55779 ( 16) covalent geometry : bond 0.00303 (11262) covalent geometry : angle 0.69090 (15330) ********************** 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 199 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 1.227 Fit side-chains REVERT: A 233 ILE cc_start: 0.6471 (OUTLIER) cc_final: 0.6089 (mp) REVERT: E 86 GLN cc_start: 0.7032 (mm110) cc_final: 0.6786 (mm-40) REVERT: F 51 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8088 (tp) REVERT: B 73 PHE cc_start: 0.5675 (OUTLIER) cc_final: 0.4490 (t80) REVERT: B 91 ARG cc_start: 0.6713 (OUTLIER) cc_final: 0.6360 (pmt170) REVERT: B 332 ASP cc_start: 0.7510 (t70) cc_final: 0.7257 (t0) outliers start: 36 outliers final: 26 residues processed: 182 average time/residue: 0.2818 time to fit residues: 68.4077 Evaluate side-chains 186 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 322 GLN Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 138 CYS Chi-restraints excluded: chain D residue 172 SER 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 97 SER Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 328 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 0.8980 chunk 121 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 37 optimal weight: 0.3980 chunk 45 optimal weight: 20.0000 chunk 33 optimal weight: 7.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- 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 57 ASN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 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 = 0.4587 r_free = 0.4587 target = 0.231216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.206102 restraints weight = 13535.294| |-----------------------------------------------------------------------------| r_work (start): 0.4343 rms_B_bonded: 1.30 r_work: 0.4170 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.4132 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 11272 Z= 0.235 Angle : 0.750 13.511 15346 Z= 0.377 Chirality : 0.047 0.255 1763 Planarity : 0.005 0.048 1938 Dihedral : 5.308 57.006 1525 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.34 % Allowed : 21.94 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.22), residues: 1399 helix: 1.67 (0.26), residues: 403 sheet: 0.79 (0.24), residues: 462 loop : -0.86 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP C 167 HIS 0.006 0.001 HIS C 193 PHE 0.024 0.002 PHE C 36 TYR 0.022 0.002 TYR C 144 ARG 0.023 0.001 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.03922 ( 573) hydrogen bonds : angle 4.64298 ( 1704) metal coordination : bond 0.00117 ( 2) SS BOND : bond 0.00240 ( 8) SS BOND : angle 0.72392 ( 16) covalent geometry : bond 0.00558 (11262) covalent geometry : angle 0.75025 (15330) =============================================================================== Job complete usr+sys time: 5669.34 seconds wall clock time: 98 minutes 59.70 seconds (5939.70 seconds total)