Starting phenix.real_space_refine on Mon Jul 28 21:35:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vgz_31981/07_2025/7vgz_31981_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vgz_31981/07_2025/7vgz_31981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vgz_31981/07_2025/7vgz_31981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vgz_31981/07_2025/7vgz_31981.map" model { file = "/net/cci-nas-00/data/ceres_data/7vgz_31981/07_2025/7vgz_31981_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vgz_31981/07_2025/7vgz_31981_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2159 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 61 5.16 5 C 5631 2.51 5 N 1476 2.21 5 O 1622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8790 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2242 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1751 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2584 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 404 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1762 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Unusual residues: {'CLR': 1, 'JEV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.06, per 1000 atoms: 0.69 Number of scatterers: 8790 At special positions: 0 Unit cell: (90.47, 116.2, 125.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 61 16.00 O 1622 8.00 N 1476 7.00 C 5631 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 177 " distance=2.03 Simple disulfide: pdb=" SG CYS D 121 " - pdb=" SG CYS D 149 " distance=2.04 Simple disulfide: pdb=" SG CYS F 159 " - pdb=" SG CYS F 229 " 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: 2.41 Conformation dependent library (CDL) restraints added in 1.1 seconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 14 sheets defined 39.1% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'B' and resid 23 through 55 Processing helix chain 'B' and resid 63 through 75 Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 96 through 130 removed outlier: 3.754A pdb=" N SER B 103 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 105 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 139 Processing helix chain 'B' and resid 140 through 160 removed outlier: 3.614A pdb=" N LEU B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 166 Processing helix chain 'B' and resid 184 through 194 removed outlier: 3.550A pdb=" N THR B 188 " --> pdb=" O SER B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 220 removed outlier: 4.089A pdb=" N VAL B 203 " --> pdb=" O PRO B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 240 Processing helix chain 'B' and resid 240 through 245 Processing helix chain 'B' and resid 246 through 251 removed outlier: 3.790A pdb=" N CYS B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP B 251 " --> pdb=" O PHE B 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 246 through 251' Processing helix chain 'B' and resid 251 through 264 removed outlier: 3.833A pdb=" N LEU B 259 " --> pdb=" O ASN B 255 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 removed outlier: 3.960A pdb=" N VAL B 269 " --> pdb=" O PRO B 265 " (cutoff:3.500A) Proline residue: B 270 - end of helix Processing helix chain 'B' and resid 273 through 295 removed outlier: 3.524A pdb=" N PHE B 277 " --> pdb=" O PRO B 273 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N CYS B 289 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA B 292 " --> pdb=" O SER B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 313 removed outlier: 3.933A pdb=" N GLU B 305 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ARG B 307 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ARG B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 33 removed outlier: 3.510A pdb=" N ALA C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ARG C 24 " --> pdb=" O ASP C 20 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 55 removed outlier: 3.537A pdb=" N ILE C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.770A pdb=" N GLU C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.899A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 309 removed outlier: 3.551A pdb=" N ASP C 309 " --> pdb=" O CYS C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 352 Processing helix chain 'D' and resid 4 through 26 Processing helix chain 'D' and resid 29 through 35 Processing helix chain 'E' and resid 10 through 24 removed outlier: 3.736A pdb=" N ASN E 24 " --> pdb=" O LYS E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 Processing helix chain 'E' and resid 45 through 48 Processing helix chain 'F' and resid 53 through 56 removed outlier: 3.819A pdb=" N GLY F 56 " --> pdb=" O SER F 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 53 through 56' Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.509A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 168 through 171 removed outlier: 3.506A pdb=" N GLN B 169 " --> pdb=" O THR B 178 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 185 through 187 removed outlier: 6.600A pdb=" N LEU C 36 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU C 39 " --> pdb=" O CYS C 224 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ALA C 226 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 47 through 51 removed outlier: 6.834A pdb=" N ILE D 338 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR D 50 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU D 336 " --> pdb=" O THR D 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 58 through 63 removed outlier: 4.121A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU D 79 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA D 92 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE D 81 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 100 through 105 removed outlier: 6.939A pdb=" N GLY D 115 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N CYS D 103 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA D 113 " --> pdb=" O CYS D 103 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N TYR D 105 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N TYR D 111 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N CYS D 121 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N GLU D 138 " --> pdb=" O CYS D 121 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE D 123 " --> pdb=" O SER D 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 150 through 151 removed outlier: 3.756A pdb=" N ILE D 157 " --> pdb=" O TRP D 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.576A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE D 199 " --> pdb=" O TRP D 211 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER D 207 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN D 220 " --> pdb=" O LEU D 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 229 through 234 removed outlier: 3.501A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 273 through 276 removed outlier: 6.558A pdb=" N GLY D 288 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL D 276 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU D 286 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASP D 298 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG D 304 " --> pdb=" O ASP D 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.203A pdb=" N GLY F 10 " --> pdb=" O THR F 118 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU F 117 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA F 92 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N MET F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TYR F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.203A pdb=" N GLY F 10 " --> pdb=" O THR F 118 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU F 117 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA F 92 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE F 110 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 140 through 142 Processing sheet with id=AB5, first strand: chain 'F' and resid 146 through 148 removed outlier: 3.858A pdb=" N GLU F 246 " --> pdb=" O VAL F 147 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU F 174 " --> pdb=" O TYR F 190 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N TYR F 190 " --> pdb=" O LEU F 174 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP F 176 " --> pdb=" O LEU F 188 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1188 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: 2.48 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1419 1.31 - 1.44: 2495 1.44 - 1.56: 4981 1.56 - 1.69: 0 1.69 - 1.82: 87 Bond restraints: 8982 Sorted by residual: bond pdb=" CA TYR B 126 " pdb=" C TYR B 126 " ideal model delta sigma weight residual 1.523 1.437 0.087 1.30e-02 5.92e+03 4.45e+01 bond pdb=" C3 JEV B 401 " pdb=" N1 JEV B 401 " ideal model delta sigma weight residual 1.344 1.449 -0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" C15 JEV B 401 " pdb=" O1 JEV B 401 " ideal model delta sigma weight residual 1.439 1.351 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" CA TYR B 281 " pdb=" C TYR B 281 " ideal model delta sigma weight residual 1.522 1.464 0.058 1.38e-02 5.25e+03 1.79e+01 bond pdb=" N TYR B 282 " pdb=" CA TYR B 282 " ideal model delta sigma weight residual 1.457 1.404 0.053 1.27e-02 6.20e+03 1.74e+01 ... (remaining 8977 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 11879 1.88 - 3.76: 247 3.76 - 5.64: 54 5.64 - 7.51: 11 7.51 - 9.39: 2 Bond angle restraints: 12193 Sorted by residual: angle pdb=" N TYR B 126 " pdb=" CA TYR B 126 " pdb=" C TYR B 126 " ideal model delta sigma weight residual 111.28 101.89 9.39 1.09e+00 8.42e-01 7.43e+01 angle pdb=" N PHE B 237 " pdb=" CA PHE B 237 " pdb=" C PHE B 237 " ideal model delta sigma weight residual 111.28 104.76 6.52 1.09e+00 8.42e-01 3.58e+01 angle pdb=" C TYR B 282 " pdb=" CA TYR B 282 " pdb=" CB TYR B 282 " ideal model delta sigma weight residual 109.24 118.49 -9.25 1.75e+00 3.27e-01 2.80e+01 angle pdb=" N ARG B 235 " pdb=" CA ARG B 235 " pdb=" C ARG B 235 " ideal model delta sigma weight residual 111.28 106.09 5.19 1.09e+00 8.42e-01 2.27e+01 angle pdb=" N TYR B 282 " pdb=" CA TYR B 282 " pdb=" C TYR B 282 " ideal model delta sigma weight residual 113.41 107.63 5.78 1.22e+00 6.72e-01 2.24e+01 ... (remaining 12188 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.85: 5081 24.85 - 49.69: 249 49.69 - 74.54: 26 74.54 - 99.39: 3 99.39 - 124.23: 3 Dihedral angle restraints: 5362 sinusoidal: 2093 harmonic: 3269 Sorted by residual: dihedral pdb=" CB CYS D 121 " pdb=" SG CYS D 121 " pdb=" SG CYS D 149 " pdb=" CB CYS D 149 " ideal model delta sinusoidal sigma weight residual 93.00 167.31 -74.31 1 1.00e+01 1.00e-02 7.00e+01 dihedral pdb=" CB CYS B 100 " pdb=" SG CYS B 100 " pdb=" SG CYS B 177 " pdb=" CB CYS B 177 " ideal model delta sinusoidal sigma weight residual -86.00 -124.54 38.54 1 1.00e+01 1.00e-02 2.09e+01 dihedral pdb=" C1 CLR B 402 " pdb=" C2 CLR B 402 " pdb=" C3 CLR B 402 " pdb=" O1 CLR B 402 " ideal model delta sinusoidal sigma weight residual 180.04 55.81 124.23 1 3.00e+01 1.11e-03 1.67e+01 ... (remaining 5359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1255 0.076 - 0.152: 127 0.152 - 0.229: 3 0.229 - 0.305: 4 0.305 - 0.381: 2 Chirality restraints: 1391 Sorted by residual: chirality pdb=" CA CYS B 127 " pdb=" N CYS B 127 " pdb=" C CYS B 127 " pdb=" CB CYS B 127 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CA TYR B 282 " pdb=" N TYR B 282 " pdb=" C TYR B 282 " pdb=" CB TYR B 282 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CA TYR B 281 " pdb=" N TYR B 281 " pdb=" C TYR B 281 " pdb=" CB TYR B 281 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 1388 not shown) Planarity restraints: 1532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 279 " 0.027 2.00e-02 2.50e+03 5.49e-02 3.02e+01 pdb=" C ALA B 279 " -0.095 2.00e-02 2.50e+03 pdb=" O ALA B 279 " 0.036 2.00e-02 2.50e+03 pdb=" N SER B 280 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 193 " -0.019 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C VAL B 193 " 0.062 2.00e-02 2.50e+03 pdb=" O VAL B 193 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE B 194 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 150 " -0.043 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO F 151 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO F 151 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO F 151 " -0.036 5.00e-02 4.00e+02 ... (remaining 1529 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 217 2.69 - 3.24: 8642 3.24 - 3.79: 13989 3.79 - 4.35: 18367 4.35 - 4.90: 31157 Nonbonded interactions: 72372 Sorted by model distance: nonbonded pdb=" OG SER D 331 " pdb=" OD1 ASP D 333 " model vdw 2.137 3.040 nonbonded pdb=" OG1 THR D 274 " pdb=" O VAL D 315 " model vdw 2.184 3.040 nonbonded pdb=" OG SER D 74 " pdb=" OD1 ASP D 76 " model vdw 2.193 3.040 nonbonded pdb=" OH TYR C 290 " pdb=" OE1 GLU C 298 " model vdw 2.251 3.040 nonbonded pdb=" O SER D 67 " pdb=" OG SER D 67 " model vdw 2.272 3.040 ... (remaining 72367 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 9.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.320 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 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 0.105 8985 Z= 0.299 Angle : 0.689 9.393 12199 Z= 0.395 Chirality : 0.048 0.381 1391 Planarity : 0.005 0.066 1532 Dihedral : 14.104 124.233 3247 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.21 % Allowed : 0.96 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.10 (0.26), residues: 1107 helix: 1.03 (0.28), residues: 386 sheet: -0.23 (0.32), residues: 276 loop : -0.85 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 275 HIS 0.007 0.001 HIS B 195 PHE 0.014 0.001 PHE B 196 TYR 0.019 0.002 TYR B 126 ARG 0.007 0.001 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.17918 ( 420) hydrogen bonds : angle 6.94945 ( 1188) SS BOND : bond 0.00388 ( 3) SS BOND : angle 0.97602 ( 6) covalent geometry : bond 0.00507 ( 8982) covalent geometry : angle 0.68926 (12193) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 1.105 Fit side-chains REVERT: B 169 GLN cc_start: 0.6863 (pp30) cc_final: 0.6415 (pp30) REVERT: B 287 ASN cc_start: 0.8591 (t0) cc_final: 0.8280 (t0) REVERT: C 26 ASP cc_start: 0.8306 (m-30) cc_final: 0.8041 (m-30) REVERT: D 226 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7732 (mt-10) REVERT: E 18 GLN cc_start: 0.8012 (tp40) cc_final: 0.7650 (tp40) outliers start: 2 outliers final: 1 residues processed: 131 average time/residue: 0.2416 time to fit residues: 42.7995 Evaluate side-chains 105 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 238 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 chunk 33 optimal weight: 0.1980 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.104165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.077142 restraints weight = 18563.446| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.19 r_work: 0.3016 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8985 Z= 0.141 Angle : 0.590 9.864 12199 Z= 0.306 Chirality : 0.043 0.161 1391 Planarity : 0.004 0.055 1532 Dihedral : 7.118 84.142 1305 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.85 % Allowed : 8.60 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.02 (0.26), residues: 1107 helix: 1.29 (0.27), residues: 391 sheet: -0.31 (0.32), residues: 273 loop : -0.86 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 82 HIS 0.004 0.001 HIS F 35 PHE 0.015 0.001 PHE C 354 TYR 0.015 0.001 TYR B 282 ARG 0.004 0.000 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.04053 ( 420) hydrogen bonds : angle 5.02751 ( 1188) SS BOND : bond 0.00392 ( 3) SS BOND : angle 1.44501 ( 6) covalent geometry : bond 0.00319 ( 8982) covalent geometry : angle 0.58886 (12193) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 1.004 Fit side-chains REVERT: B 169 GLN cc_start: 0.6665 (pp30) cc_final: 0.6289 (pp30) REVERT: B 171 ASP cc_start: 0.7460 (t70) cc_final: 0.7055 (t70) REVERT: B 287 ASN cc_start: 0.8576 (t0) cc_final: 0.8299 (t0) REVERT: C 26 ASP cc_start: 0.8672 (m-30) cc_final: 0.8364 (m-30) REVERT: D 226 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8398 (mt-10) REVERT: F 83 MET cc_start: 0.8721 (mtp) cc_final: 0.8484 (mtm) outliers start: 8 outliers final: 6 residues processed: 124 average time/residue: 0.2540 time to fit residues: 42.1648 Evaluate side-chains 112 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain F residue 17 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 106 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 23 optimal weight: 0.0040 chunk 60 optimal weight: 0.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.105704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.078965 restraints weight = 19148.803| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.19 r_work: 0.3073 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8985 Z= 0.120 Angle : 0.560 9.420 12199 Z= 0.291 Chirality : 0.042 0.165 1391 Planarity : 0.004 0.050 1532 Dihedral : 5.252 48.983 1305 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.17 % Allowed : 11.04 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.11 (0.26), residues: 1107 helix: 1.42 (0.27), residues: 389 sheet: -0.33 (0.32), residues: 276 loop : -0.81 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 82 HIS 0.003 0.001 HIS F 35 PHE 0.015 0.001 PHE C 354 TYR 0.016 0.001 TYR B 295 ARG 0.005 0.000 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.03487 ( 420) hydrogen bonds : angle 4.74422 ( 1188) SS BOND : bond 0.00498 ( 3) SS BOND : angle 1.44074 ( 6) covalent geometry : bond 0.00271 ( 8982) covalent geometry : angle 0.55962 (12193) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 1.023 Fit side-chains REVERT: B 169 GLN cc_start: 0.6784 (pp30) cc_final: 0.6401 (pp30) REVERT: B 171 ASP cc_start: 0.7476 (t70) cc_final: 0.7047 (t70) REVERT: B 281 TYR cc_start: 0.7480 (t80) cc_final: 0.6611 (t80) REVERT: B 287 ASN cc_start: 0.8617 (t0) cc_final: 0.8257 (t0) REVERT: C 26 ASP cc_start: 0.8611 (m-30) cc_final: 0.8343 (m-30) REVERT: C 304 GLN cc_start: 0.6234 (tt0) cc_final: 0.6033 (tt0) REVERT: D 226 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8368 (mt-10) outliers start: 11 outliers final: 6 residues processed: 123 average time/residue: 0.2357 time to fit residues: 39.5688 Evaluate side-chains 112 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 89 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 60 optimal weight: 0.2980 chunk 26 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.106160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.079127 restraints weight = 18908.981| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.18 r_work: 0.3073 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8985 Z= 0.116 Angle : 0.539 8.667 12199 Z= 0.280 Chirality : 0.042 0.152 1391 Planarity : 0.004 0.046 1532 Dihedral : 4.824 47.818 1304 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.91 % Allowed : 12.42 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.23 (0.26), residues: 1107 helix: 1.57 (0.27), residues: 389 sheet: -0.37 (0.32), residues: 267 loop : -0.71 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 82 HIS 0.003 0.001 HIS F 35 PHE 0.016 0.001 PHE C 354 TYR 0.016 0.001 TYR F 190 ARG 0.005 0.000 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.03184 ( 420) hydrogen bonds : angle 4.50068 ( 1188) SS BOND : bond 0.00687 ( 3) SS BOND : angle 1.30968 ( 6) covalent geometry : bond 0.00262 ( 8982) covalent geometry : angle 0.53801 (12193) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.960 Fit side-chains REVERT: B 169 GLN cc_start: 0.6855 (pp30) cc_final: 0.6437 (pp30) REVERT: B 287 ASN cc_start: 0.8610 (t0) cc_final: 0.8176 (t0) REVERT: C 26 ASP cc_start: 0.8614 (m-30) cc_final: 0.8309 (m-30) REVERT: C 304 GLN cc_start: 0.6235 (tt0) cc_final: 0.6006 (tt0) REVERT: C 306 GLN cc_start: 0.7656 (tm-30) cc_final: 0.7440 (pp30) REVERT: D 226 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8385 (mt-10) REVERT: E 18 GLN cc_start: 0.8350 (tp40) cc_final: 0.7649 (tp40) REVERT: E 21 MET cc_start: 0.8778 (tpp) cc_final: 0.8534 (ppp) outliers start: 18 outliers final: 10 residues processed: 131 average time/residue: 0.2272 time to fit residues: 40.6193 Evaluate side-chains 115 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 89 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 91 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 66 optimal weight: 0.0470 chunk 43 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.105170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.078129 restraints weight = 18907.249| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.17 r_work: 0.3050 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8985 Z= 0.146 Angle : 0.562 8.666 12199 Z= 0.291 Chirality : 0.042 0.156 1391 Planarity : 0.004 0.044 1532 Dihedral : 4.839 46.997 1304 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.12 % Allowed : 13.48 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.30 (0.26), residues: 1107 helix: 1.65 (0.27), residues: 389 sheet: -0.35 (0.32), residues: 266 loop : -0.67 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 82 HIS 0.004 0.001 HIS F 35 PHE 0.015 0.001 PHE C 354 TYR 0.015 0.001 TYR F 190 ARG 0.005 0.000 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.03257 ( 420) hydrogen bonds : angle 4.44052 ( 1188) SS BOND : bond 0.00868 ( 3) SS BOND : angle 1.65801 ( 6) covalent geometry : bond 0.00338 ( 8982) covalent geometry : angle 0.56122 (12193) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 1.045 Fit side-chains REVERT: B 169 GLN cc_start: 0.6860 (pp30) cc_final: 0.6419 (pp30) REVERT: B 287 ASN cc_start: 0.8675 (t0) cc_final: 0.8356 (t0) REVERT: C 26 ASP cc_start: 0.8601 (m-30) cc_final: 0.8303 (m-30) REVERT: D 226 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8402 (mt-10) REVERT: E 18 GLN cc_start: 0.8401 (tp40) cc_final: 0.8198 (tp40) outliers start: 20 outliers final: 13 residues processed: 121 average time/residue: 0.2917 time to fit residues: 47.4914 Evaluate side-chains 115 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 218 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 33 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 99 optimal weight: 0.0020 chunk 18 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 GLN ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.106230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.079282 restraints weight = 18866.970| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.16 r_work: 0.3072 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8985 Z= 0.116 Angle : 0.543 8.445 12199 Z= 0.281 Chirality : 0.041 0.153 1391 Planarity : 0.003 0.042 1532 Dihedral : 4.691 45.938 1304 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.91 % Allowed : 14.33 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.38 (0.26), residues: 1107 helix: 1.68 (0.27), residues: 388 sheet: -0.25 (0.32), residues: 263 loop : -0.62 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 82 HIS 0.003 0.001 HIS F 35 PHE 0.017 0.001 PHE C 354 TYR 0.016 0.001 TYR F 190 ARG 0.006 0.000 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.03014 ( 420) hydrogen bonds : angle 4.35532 ( 1188) SS BOND : bond 0.00603 ( 3) SS BOND : angle 1.37493 ( 6) covalent geometry : bond 0.00264 ( 8982) covalent geometry : angle 0.54185 (12193) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.128 Fit side-chains REVERT: B 169 GLN cc_start: 0.6869 (pp30) cc_final: 0.6438 (pp30) REVERT: B 287 ASN cc_start: 0.8641 (t0) cc_final: 0.8200 (t0) REVERT: C 26 ASP cc_start: 0.8605 (m-30) cc_final: 0.8306 (m-30) REVERT: D 226 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8364 (mt-10) REVERT: E 18 GLN cc_start: 0.8434 (tp40) cc_final: 0.7668 (tp40) REVERT: E 21 MET cc_start: 0.8788 (tpp) cc_final: 0.8416 (ppp) outliers start: 18 outliers final: 12 residues processed: 124 average time/residue: 0.2289 time to fit residues: 38.4976 Evaluate side-chains 118 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 139 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.5264 > 50: distance: 74 - 211: 22.539 distance: 109 - 215: 23.661 distance: 112 - 212: 20.373 distance: 131 - 197: 20.632 distance: 134 - 194: 16.949 distance: 147 - 178: 28.846 distance: 150 - 175: 11.804 distance: 173 - 175: 8.978 distance: 175 - 176: 15.983 distance: 176 - 177: 49.367 distance: 176 - 179: 16.055 distance: 177 - 178: 48.573 distance: 177 - 182: 42.285 distance: 179 - 180: 18.097 distance: 179 - 181: 22.086 distance: 182 - 183: 25.451 distance: 182 - 313: 15.338 distance: 183 - 184: 15.411 distance: 183 - 186: 23.638 distance: 184 - 185: 14.671 distance: 184 - 194: 18.602 distance: 185 - 310: 19.551 distance: 186 - 187: 16.531 distance: 187 - 188: 7.327 distance: 187 - 189: 11.488 distance: 188 - 190: 13.106 distance: 189 - 191: 12.492 distance: 190 - 192: 4.732 distance: 191 - 192: 7.129 distance: 192 - 193: 10.059 distance: 194 - 195: 13.877 distance: 195 - 196: 23.304 distance: 195 - 198: 12.519 distance: 196 - 197: 11.601 distance: 196 - 206: 24.828 distance: 198 - 199: 10.081 distance: 199 - 200: 9.549 distance: 199 - 201: 8.616 distance: 200 - 202: 14.932 distance: 201 - 203: 25.114 distance: 202 - 204: 12.616 distance: 203 - 204: 10.424 distance: 204 - 205: 9.648 distance: 206 - 207: 13.425 distance: 207 - 208: 22.152 distance: 207 - 210: 19.513 distance: 208 - 209: 13.760 distance: 208 - 212: 7.531 distance: 210 - 211: 33.643 distance: 212 - 213: 20.379 distance: 213 - 214: 17.786 distance: 213 - 216: 22.371 distance: 214 - 215: 9.824 distance: 214 - 220: 16.821 distance: 216 - 217: 24.216 distance: 217 - 218: 17.717 distance: 218 - 219: 34.194 distance: 220 - 221: 10.896 distance: 221 - 222: 10.214 distance: 221 - 224: 8.390 distance: 222 - 223: 13.576 distance: 222 - 229: 6.519 distance: 224 - 225: 8.996 distance: 225 - 226: 9.715 distance: 226 - 227: 17.631 distance: 226 - 228: 21.802 distance: 229 - 230: 6.606 distance: 230 - 231: 4.628 distance: 230 - 233: 9.997 distance: 231 - 232: 33.266 distance: 231 - 239: 18.039 distance: 233 - 234: 5.861 distance: 234 - 235: 9.598 distance: 234 - 236: 13.618 distance: 235 - 237: 12.586 distance: 236 - 238: 6.707 distance: 237 - 238: 13.022 distance: 239 - 240: 15.650 distance: 240 - 241: 25.070 distance: 240 - 243: 11.442 distance: 241 - 242: 14.924 distance: 241 - 247: 27.918 distance: 243 - 244: 19.112 distance: 244 - 245: 11.721 distance: 244 - 246: 13.573 distance: 247 - 248: 20.039 distance: 248 - 249: 20.393 distance: 248 - 251: 22.759 distance: 249 - 250: 25.338 distance: 249 - 256: 13.078 distance: 251 - 252: 25.879 distance: 252 - 253: 19.967 distance: 253 - 254: 3.007 distance: 256 - 257: 22.785 distance: 257 - 258: 14.874 distance: 257 - 260: 27.604 distance: 258 - 259: 7.448 distance: 258 - 268: 7.290 distance: 260 - 261: 32.832 distance: 261 - 262: 12.428 distance: 261 - 263: 17.361 distance: 262 - 264: 19.767 distance: 263 - 265: 10.873 distance: 264 - 266: 15.031 distance: 265 - 266: 25.330