Starting phenix.real_space_refine on Wed Jan 15 05:49:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iyh_35822/01_2025/8iyh_35822.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iyh_35822/01_2025/8iyh_35822.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/8iyh_35822/01_2025/8iyh_35822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iyh_35822/01_2025/8iyh_35822.map" model { file = "/net/cci-nas-00/data/ceres_data/8iyh_35822/01_2025/8iyh_35822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iyh_35822/01_2025/8iyh_35822.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= 0.039 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 5108 2.51 5 N 1392 2.21 5 O 1487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8035 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2410 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 108 Chain: "B" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1538 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 4, 'TRANS': 201} Chain breaks: 2 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "D" Number of atoms: 2001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2001 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 380 Unresolved non-hydrogen angles: 485 Unresolved non-hydrogen dihedrals: 332 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 5, 'ASP:plan': 6, 'PHE:plan': 9, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 215 Chain: "G" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 400 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1658 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'FI7': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.96, per 1000 atoms: 0.62 Number of scatterers: 8035 At special positions: 0 Unit cell: (89.995, 117.432, 133.895, 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 48 16.00 O 1487 8.00 N 1392 7.00 C 5108 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS D 18 " - pdb=" SG CYS D 183 " distance=2.37 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 266 " distance=2.03 Simple disulfide: pdb=" SG CYS D 100 " - pdb=" SG CYS D 177 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 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: 2.25 Conformation dependent library (CDL) restraints added in 1.1 seconds 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2090 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 38.3% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 3 through 26 Processing helix chain 'A' and resid 29 through 35 Processing helix chain 'B' and resid 8 through 31 Processing helix chain 'B' and resid 45 through 53 Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 208 through 217 removed outlier: 3.712A pdb=" N LYS B 211 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N HIS B 214 " --> pdb=" O LYS B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 256 Processing helix chain 'B' and resid 257 through 261 removed outlier: 4.044A pdb=" N ILE B 261 " --> pdb=" O LYS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 279 Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 296 through 310 Processing helix chain 'B' and resid 330 through 351 Processing helix chain 'D' and resid 24 through 54 Proline residue: D 31 - end of helix removed outlier: 3.961A pdb=" N LEU D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 89 Proline residue: D 81 - end of helix Processing helix chain 'D' and resid 96 through 130 removed outlier: 3.502A pdb=" N PHE D 105 " --> pdb=" O ARG D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 139 removed outlier: 3.663A pdb=" N ILE D 139 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 158 Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 187 through 218 removed outlier: 3.980A pdb=" N ALA D 191 " --> pdb=" O GLN D 187 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Proline residue: D 200 - end of helix Processing helix chain 'D' and resid 224 through 229 Processing helix chain 'D' and resid 230 through 262 removed outlier: 3.905A pdb=" N VAL D 236 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA D 237 " --> pdb=" O ILE D 233 " (cutoff:3.500A) Proline residue: D 246 - end of helix Processing helix chain 'D' and resid 265 through 268 removed outlier: 4.228A pdb=" N VAL D 268 " --> pdb=" O ASN D 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 265 through 268' Processing helix chain 'D' and resid 269 through 280 Processing helix chain 'D' and resid 280 through 289 removed outlier: 3.745A pdb=" N TYR D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER D 287 " --> pdb=" O THR D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 295 removed outlier: 4.090A pdb=" N TYR D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.612A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 56 removed outlier: 3.814A pdb=" N GLY H 56 " --> pdb=" O SER H 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 53 through 56' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.673A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'H' and resid 220 through 224 removed outlier: 3.546A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 51 removed outlier: 3.566A pdb=" N LEU A 336 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 63 removed outlier: 3.935A pdb=" N LYS A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU A 79 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA A 92 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE A 81 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 105 removed outlier: 6.981A pdb=" N GLY A 115 " --> pdb=" O MET A 101 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N CYS A 103 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA A 113 " --> pdb=" O CYS A 103 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N TYR A 105 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N TYR A 111 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLY A 116 " --> pdb=" O ILE A 120 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ILE A 120 " --> pdb=" O GLY A 116 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG A 137 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ASN A 125 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL A 135 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 151 removed outlier: 5.896A pdb=" N ASP A 170 " --> pdb=" O GLN A 176 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLN A 176 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 192 removed outlier: 3.865A pdb=" N SER A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN A 220 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ASP A 212 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N CYS A 218 " --> pdb=" O ASP A 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 229 through 234 removed outlier: 6.822A pdb=" N CYS A 250 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N THR A 263 " --> pdb=" O CYS A 250 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU A 252 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A 259 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 273 through 278 removed outlier: 6.262A pdb=" N GLY A 288 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL A 276 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU A 286 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE A 278 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU A 284 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N CYS A 294 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL A 307 " --> pdb=" O CYS A 294 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 296 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 186 through 192 removed outlier: 3.643A pdb=" N VAL B 186 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL B 34 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N PHE B 200 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU B 36 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 9.483A pdb=" N ALA B 221 " --> pdb=" O ASP B 33 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LYS B 35 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE B 223 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU B 37 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N CYS B 225 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU B 39 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N ASP B 227 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE B 222 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N PHE B 268 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE B 224 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ASN B 270 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL B 226 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 11 through 13 removed outlier: 4.036A pdb=" N ILE D 182 " --> pdb=" O CYS D 19 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 169 through 171 Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.556A pdb=" N THR H 118 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 140 through 141 removed outlier: 3.898A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 146 through 149 removed outlier: 6.073A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) 435 hydrogen bonds defined for protein. 1212 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: 2.60 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1399 1.32 - 1.45: 2223 1.45 - 1.57: 4518 1.57 - 1.69: 1 1.69 - 1.81: 64 Bond restraints: 8205 Sorted by residual: bond pdb=" N PHE D 186 " pdb=" CA PHE D 186 " ideal model delta sigma weight residual 1.455 1.528 -0.073 1.23e-02 6.61e+03 3.50e+01 bond pdb=" CA PHE D 186 " pdb=" C PHE D 186 " ideal model delta sigma weight residual 1.522 1.581 -0.060 1.22e-02 6.72e+03 2.39e+01 bond pdb=" C20 FI7 D 401 " pdb=" N19 FI7 D 401 " ideal model delta sigma weight residual 1.396 1.327 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C22 FI7 D 401 " pdb=" O23 FI7 D 401 " ideal model delta sigma weight residual 1.269 1.203 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C LYS B 24 " pdb=" O LYS B 24 " ideal model delta sigma weight residual 1.236 1.201 0.036 1.15e-02 7.56e+03 9.75e+00 ... (remaining 8200 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 10882 1.96 - 3.91: 253 3.91 - 5.87: 42 5.87 - 7.82: 10 7.82 - 9.78: 4 Bond angle restraints: 11191 Sorted by residual: angle pdb=" CA PHE D 186 " pdb=" C PHE D 186 " pdb=" O PHE D 186 " ideal model delta sigma weight residual 120.70 112.56 8.14 1.08e+00 8.57e-01 5.68e+01 angle pdb=" N HIS D 184 " pdb=" CA HIS D 184 " pdb=" C HIS D 184 " ideal model delta sigma weight residual 113.19 120.64 -7.45 1.19e+00 7.06e-01 3.92e+01 angle pdb=" N PHE D 186 " pdb=" CA PHE D 186 " pdb=" C PHE D 186 " ideal model delta sigma weight residual 109.40 119.18 -9.78 1.63e+00 3.76e-01 3.60e+01 angle pdb=" O LEU B 23 " pdb=" C LEU B 23 " pdb=" N LYS B 24 " ideal model delta sigma weight residual 122.07 116.90 5.17 1.03e+00 9.43e-01 2.52e+01 angle pdb=" CA LEU B 23 " pdb=" C LEU B 23 " pdb=" N LYS B 24 " ideal model delta sigma weight residual 117.07 122.14 -5.07 1.14e+00 7.69e-01 1.98e+01 ... (remaining 11186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 4372 17.56 - 35.11: 339 35.11 - 52.67: 70 52.67 - 70.22: 10 70.22 - 87.78: 3 Dihedral angle restraints: 4794 sinusoidal: 1561 harmonic: 3233 Sorted by residual: dihedral pdb=" CB CYS D 18 " pdb=" SG CYS D 18 " pdb=" SG CYS D 183 " pdb=" CB CYS D 183 " ideal model delta sinusoidal sigma weight residual 93.00 53.07 39.93 1 1.00e+01 1.00e-02 2.24e+01 dihedral pdb=" CA ARG H 191 " pdb=" C ARG H 191 " pdb=" N MET H 192 " pdb=" CA MET H 192 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA VAL D 29 " pdb=" C VAL D 29 " pdb=" N LEU D 30 " pdb=" CA LEU D 30 " ideal model delta harmonic sigma weight residual -180.00 -162.14 -17.86 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 4791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 938 0.044 - 0.088: 263 0.088 - 0.132: 91 0.132 - 0.177: 8 0.177 - 0.221: 3 Chirality restraints: 1303 Sorted by residual: chirality pdb=" CA ILE D 182 " pdb=" N ILE D 182 " pdb=" C ILE D 182 " pdb=" CB ILE D 182 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA ILE D 242 " pdb=" N ILE D 242 " pdb=" C ILE D 242 " pdb=" CB ILE D 242 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ILE D 13 " pdb=" N ILE D 13 " pdb=" C ILE D 13 " pdb=" CB ILE D 13 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.42e-01 ... (remaining 1300 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C04 FI7 D 401 " 0.064 2.00e-02 2.50e+03 5.71e-02 5.72e+01 pdb=" C05 FI7 D 401 " -0.021 2.00e-02 2.50e+03 pdb=" C07 FI7 D 401 " -0.063 2.00e-02 2.50e+03 pdb=" C08 FI7 D 401 " 0.091 2.00e-02 2.50e+03 pdb=" N06 FI7 D 401 " -0.075 2.00e-02 2.50e+03 pdb=" N15 FI7 D 401 " -0.013 2.00e-02 2.50e+03 pdb=" O16 FI7 D 401 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C07 FI7 D 401 " 0.081 2.00e-02 2.50e+03 4.11e-02 3.38e+01 pdb=" C08 FI7 D 401 " -0.040 2.00e-02 2.50e+03 pdb=" C09 FI7 D 401 " -0.032 2.00e-02 2.50e+03 pdb=" C10 FI7 D 401 " -0.010 2.00e-02 2.50e+03 pdb=" C11 FI7 D 401 " -0.001 2.00e-02 2.50e+03 pdb=" C13 FI7 D 401 " -0.014 2.00e-02 2.50e+03 pdb=" N14 FI7 D 401 " -0.036 2.00e-02 2.50e+03 pdb=" O12 FI7 D 401 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 232 " -0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C PHE D 232 " 0.063 2.00e-02 2.50e+03 pdb=" O PHE D 232 " -0.023 2.00e-02 2.50e+03 pdb=" N ILE D 233 " -0.022 2.00e-02 2.50e+03 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 744 2.74 - 3.28: 8075 3.28 - 3.82: 13000 3.82 - 4.36: 15067 4.36 - 4.90: 27511 Nonbonded interactions: 64397 Sorted by model distance: nonbonded pdb=" OD1 ASP A 27 " pdb=" OG SER G 31 " model vdw 2.204 3.040 nonbonded pdb=" O ALA B 41 " pdb=" OG SER B 44 " model vdw 2.212 3.040 nonbonded pdb=" O GLY D 44 " pdb=" OH TYR D 295 " model vdw 2.213 3.040 nonbonded pdb=" NZ LYS G 32 " pdb=" OD2 ASP G 36 " model vdw 2.273 3.120 nonbonded pdb=" OG SER A 281 " pdb=" OD2 ASP G 48 " model vdw 2.278 3.040 ... (remaining 64392 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: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.470 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 21.800 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 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 : 0.004 0.073 8205 Z= 0.287 Angle : 0.723 9.780 11191 Z= 0.432 Chirality : 0.046 0.221 1303 Planarity : 0.005 0.075 1440 Dihedral : 13.480 87.775 2689 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.08 % Allowed : 15.16 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.53 (0.26), residues: 1099 helix: 0.81 (0.28), residues: 372 sheet: 0.26 (0.31), residues: 273 loop : 0.21 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 82 HIS 0.004 0.001 HIS D 184 PHE 0.015 0.001 PHE D 232 TYR 0.010 0.001 TYR H 190 ARG 0.006 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.918 Fit side-chains REVERT: A 46 ARG cc_start: 0.7274 (mtm110) cc_final: 0.7028 (ttp80) REVERT: B 24 LYS cc_start: 0.7064 (OUTLIER) cc_final: 0.6812 (pttm) REVERT: B 26 ASP cc_start: 0.8047 (t0) cc_final: 0.7726 (t0) REVERT: B 210 LYS cc_start: 0.7393 (ptmm) cc_final: 0.6892 (pttm) REVERT: B 273 ASP cc_start: 0.7963 (m-30) cc_final: 0.7631 (p0) REVERT: D 84 MET cc_start: 0.6521 (tpt) cc_final: 0.6267 (tpt) REVERT: D 225 LYS cc_start: 0.6333 (mmtp) cc_final: 0.6041 (mttt) outliers start: 8 outliers final: 1 residues processed: 136 average time/residue: 0.2257 time to fit residues: 40.8925 Evaluate side-chains 110 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 LYS Chi-restraints excluded: chain D residue 232 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.0270 chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN B 189 HIS ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN G 24 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.191887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.147072 restraints weight = 8911.052| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.08 r_work: 0.3231 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8205 Z= 0.242 Angle : 0.583 7.319 11191 Z= 0.309 Chirality : 0.045 0.164 1303 Planarity : 0.005 0.051 1440 Dihedral : 6.430 56.595 1217 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.25 % Allowed : 13.80 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.61 (0.26), residues: 1099 helix: 1.15 (0.27), residues: 374 sheet: -0.03 (0.30), residues: 300 loop : 0.26 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 169 HIS 0.004 0.001 HIS A 91 PHE 0.022 0.002 PHE H 68 TYR 0.018 0.001 TYR H 190 ARG 0.005 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 1.261 Fit side-chains REVERT: A 46 ARG cc_start: 0.7743 (mtm110) cc_final: 0.7368 (ttp80) REVERT: A 160 SER cc_start: 0.9003 (p) cc_final: 0.8681 (p) REVERT: B 53 MET cc_start: 0.6627 (OUTLIER) cc_final: 0.6385 (ptp) REVERT: B 210 LYS cc_start: 0.7403 (ptmm) cc_final: 0.6932 (pttm) REVERT: B 273 ASP cc_start: 0.8051 (m-30) cc_final: 0.7454 (p0) REVERT: D 232 PHE cc_start: 0.7513 (OUTLIER) cc_final: 0.7094 (t80) outliers start: 24 outliers final: 13 residues processed: 131 average time/residue: 0.2059 time to fit residues: 36.9148 Evaluate side-chains 123 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 71 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 46 optimal weight: 0.0870 chunk 2 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 90 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN G 24 ASN H 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.181070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.126213 restraints weight = 9045.293| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.60 r_work: 0.3174 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8205 Z= 0.211 Angle : 0.530 8.394 11191 Z= 0.282 Chirality : 0.043 0.161 1303 Planarity : 0.004 0.040 1440 Dihedral : 5.983 51.000 1213 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.25 % Allowed : 14.61 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.69 (0.26), residues: 1099 helix: 1.47 (0.28), residues: 369 sheet: -0.11 (0.30), residues: 299 loop : 0.17 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 169 HIS 0.004 0.001 HIS H 35 PHE 0.017 0.001 PHE H 68 TYR 0.017 0.001 TYR H 190 ARG 0.004 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.852 Fit side-chains REVERT: A 160 SER cc_start: 0.9098 (p) cc_final: 0.8790 (p) REVERT: B 210 LYS cc_start: 0.7217 (ptmm) cc_final: 0.6667 (pttm) REVERT: B 258 LYS cc_start: 0.8146 (ttpt) cc_final: 0.7213 (ptpp) REVERT: B 273 ASP cc_start: 0.7975 (m-30) cc_final: 0.7315 (p0) REVERT: D 111 ARG cc_start: 0.6341 (ttm-80) cc_final: 0.6094 (ttm110) REVERT: D 232 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.7089 (t80) REVERT: H 21 SER cc_start: 0.8928 (p) cc_final: 0.8676 (t) outliers start: 24 outliers final: 14 residues processed: 127 average time/residue: 0.2065 time to fit residues: 35.8953 Evaluate side-chains 125 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 29 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 100 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.180018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.119854 restraints weight = 9012.259| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.62 r_work: 0.3094 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8205 Z= 0.364 Angle : 0.577 7.053 11191 Z= 0.310 Chirality : 0.045 0.182 1303 Planarity : 0.004 0.044 1440 Dihedral : 6.177 53.452 1213 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.19 % Allowed : 15.56 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.50 (0.26), residues: 1099 helix: 1.48 (0.27), residues: 369 sheet: -0.43 (0.30), residues: 291 loop : 0.04 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 82 HIS 0.005 0.001 HIS H 35 PHE 0.021 0.002 PHE A 235 TYR 0.017 0.002 TYR H 190 ARG 0.003 0.001 ARG B 198 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 0.862 Fit side-chains REVERT: A 160 SER cc_start: 0.9177 (p) cc_final: 0.8866 (p) REVERT: A 270 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8687 (pt) REVERT: B 210 LYS cc_start: 0.7187 (ptmm) cc_final: 0.6711 (pttm) REVERT: B 254 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8598 (tp) REVERT: B 258 LYS cc_start: 0.8091 (ttpt) cc_final: 0.7288 (ptpp) REVERT: B 273 ASP cc_start: 0.7975 (m-30) cc_final: 0.7329 (p0) outliers start: 31 outliers final: 21 residues processed: 137 average time/residue: 0.2073 time to fit residues: 38.6198 Evaluate side-chains 140 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.184232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.126564 restraints weight = 8925.330| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.55 r_work: 0.3059 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8205 Z= 0.239 Angle : 0.523 6.462 11191 Z= 0.279 Chirality : 0.043 0.170 1303 Planarity : 0.004 0.051 1440 Dihedral : 5.792 50.740 1211 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.92 % Allowed : 15.83 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.57 (0.26), residues: 1099 helix: 1.61 (0.28), residues: 372 sheet: -0.45 (0.30), residues: 295 loop : 0.05 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 169 HIS 0.004 0.001 HIS H 35 PHE 0.015 0.001 PHE A 235 TYR 0.017 0.001 TYR H 190 ARG 0.005 0.000 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.875 Fit side-chains REVERT: A 160 SER cc_start: 0.9137 (p) cc_final: 0.8860 (p) REVERT: A 270 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8721 (pt) REVERT: B 210 LYS cc_start: 0.7191 (ptmm) cc_final: 0.6694 (pttm) REVERT: B 254 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8618 (tp) REVERT: B 258 LYS cc_start: 0.8084 (ttpt) cc_final: 0.7312 (ptpp) REVERT: B 273 ASP cc_start: 0.8019 (m-30) cc_final: 0.7348 (p0) REVERT: D 198 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6443 (m-10) REVERT: D 232 PHE cc_start: 0.7882 (m-80) cc_final: 0.7430 (t80) REVERT: H 19 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7123 (tptp) outliers start: 29 outliers final: 20 residues processed: 131 average time/residue: 0.2022 time to fit residues: 36.2862 Evaluate side-chains 136 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 53.9114 > 50: distance: 47 - 130: 34.243 distance: 56 - 66: 20.071 distance: 66 - 67: 21.239 distance: 67 - 68: 7.231 distance: 67 - 70: 19.869 distance: 68 - 69: 9.297 distance: 68 - 74: 8.117 distance: 70 - 71: 22.418 distance: 71 - 72: 10.603 distance: 71 - 73: 9.043 distance: 74 - 75: 13.260 distance: 75 - 76: 18.776 distance: 75 - 78: 7.544 distance: 76 - 77: 17.142 distance: 76 - 81: 11.678 distance: 78 - 79: 15.289 distance: 78 - 80: 16.046 distance: 81 - 82: 5.540 distance: 82 - 83: 18.062 distance: 82 - 85: 12.748 distance: 83 - 84: 11.120 distance: 83 - 92: 19.191 distance: 85 - 86: 4.473 distance: 86 - 87: 11.780 distance: 87 - 88: 16.306 distance: 89 - 90: 9.314 distance: 89 - 91: 12.262 distance: 92 - 93: 4.202 distance: 93 - 94: 6.020 distance: 93 - 96: 13.672 distance: 94 - 95: 3.591 distance: 94 - 101: 16.636 distance: 96 - 97: 12.667 distance: 97 - 98: 22.550 distance: 98 - 99: 11.775 distance: 98 - 100: 19.813 distance: 101 - 102: 15.017 distance: 102 - 103: 13.538 distance: 103 - 104: 18.390 distance: 103 - 105: 14.273 distance: 105 - 106: 5.211 distance: 106 - 107: 13.581 distance: 106 - 109: 16.591 distance: 107 - 108: 11.036 distance: 107 - 110: 14.321 distance: 110 - 111: 23.193 distance: 111 - 112: 27.883 distance: 111 - 114: 10.289 distance: 112 - 113: 13.781 distance: 112 - 116: 7.519 distance: 114 - 115: 7.598 distance: 116 - 117: 29.742 distance: 117 - 118: 26.560 distance: 117 - 120: 8.841 distance: 118 - 119: 17.695 distance: 118 - 127: 7.847 distance: 120 - 121: 13.938 distance: 121 - 122: 16.919 distance: 122 - 123: 7.207 distance: 123 - 124: 13.586 distance: 124 - 125: 15.924 distance: 124 - 126: 23.635 distance: 127 - 128: 6.975 distance: 128 - 129: 20.261 distance: 128 - 131: 9.901 distance: 129 - 130: 23.752 distance: 129 - 136: 25.413 distance: 131 - 132: 5.158 distance: 132 - 133: 8.352 distance: 133 - 134: 36.317 distance: 133 - 135: 15.882 distance: 136 - 137: 13.641 distance: 137 - 138: 25.957 distance: 137 - 140: 19.303 distance: 138 - 139: 6.757 distance: 138 - 143: 30.446 distance: 140 - 141: 15.962 distance: 140 - 142: 12.044