Starting phenix.real_space_refine on Wed Jan 15 12:03:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dpf_27633/01_2025/8dpf_27633_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dpf_27633/01_2025/8dpf_27633.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dpf_27633/01_2025/8dpf_27633.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dpf_27633/01_2025/8dpf_27633.map" model { file = "/net/cci-nas-00/data/ceres_data/8dpf_27633/01_2025/8dpf_27633_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dpf_27633/01_2025/8dpf_27633_trim.cif" } resolution = 2.84 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= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 56 5.16 5 Cl 1 4.86 5 C 5236 2.51 5 N 1368 2.21 5 O 1499 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: 8160 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1939 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 9, 'TRANS': 254} Chain breaks: 4 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 80 Chain: "B" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1683 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 101 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 5, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 88 Chain: "C" Number of atoms: 2479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2479 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 84 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 9, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "D" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 284 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 39} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1734 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'CLR': 1, 'T4U': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.40, per 1000 atoms: 0.66 Number of scatterers: 8160 At special positions: 0 Unit cell: (90.09, 120.12, 134.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 56 16.00 O 1499 8.00 N 1368 7.00 C 5236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 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: 2.24 Conformation dependent library (CDL) restraints added in 1.0 seconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2048 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 38.8% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 61 through 80 removed outlier: 3.527A pdb=" N ILE A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 106 removed outlier: 5.138A pdb=" N PHE A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET A 93 " --> pdb=" O ASN A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 117 removed outlier: 3.692A pdb=" N SER A 110 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 111 " --> pdb=" O MET A 107 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 112 " --> pdb=" O PRO A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 158 removed outlier: 4.304A pdb=" N SER A 132 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 166 Processing helix chain 'A' and resid 167 through 185 removed outlier: 3.731A pdb=" N ALA A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET A 173 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL A 185 " --> pdb=" O ILE A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 194 removed outlier: 3.925A pdb=" N VAL A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 200 removed outlier: 6.928A pdb=" N GLU A 198 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 223 removed outlier: 4.456A pdb=" N ILE A 217 " --> pdb=" O ASN A 213 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N PHE A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 245 removed outlier: 3.506A pdb=" N THR A 228 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 337 removed outlier: 4.329A pdb=" N GLU A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS A 308 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER A 310 " --> pdb=" O GLU A 306 " (cutoff:3.500A) Proline residue: A 326 - end of helix removed outlier: 3.851A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 360 removed outlier: 3.603A pdb=" N VAL A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N TRP A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'B' and resid 6 through 31 removed outlier: 3.831A pdb=" N GLU B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 30 " --> pdb=" O ASP B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.516A pdb=" N ILE B 49 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 101 removed outlier: 3.595A pdb=" N CYS B 99 " --> pdb=" O TRP B 96 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN B 101 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.593A pdb=" N LEU B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 164 through 170 Processing helix chain 'B' and resid 185 through 203 removed outlier: 3.810A pdb=" N ALA B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 201 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA B 203 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 removed outlier: 3.581A pdb=" N ARG B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 24 removed outlier: 3.606A pdb=" N GLU C 10 " --> pdb=" O GLN C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'D' and resid 17 through 24 removed outlier: 3.638A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 45 through 48 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.558A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 76 removed outlier: 3.623A pdb=" N PHE B 74 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N GLY B 40 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.714A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.784A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.002A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.769A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.850A pdb=" N SER C 189 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA C 203 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.942A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.960A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.817A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.302A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.302A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.767A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.767A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN E 219 " --> pdb=" O THR E 226 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR E 226 " --> pdb=" O GLN E 219 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1149 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: 2.65 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2618 1.34 - 1.46: 1981 1.46 - 1.58: 3645 1.58 - 1.70: 0 1.70 - 1.82: 84 Bond restraints: 8328 Sorted by residual: bond pdb=" N ILE A 156 " pdb=" CA ILE A 156 " ideal model delta sigma weight residual 1.460 1.507 -0.047 1.32e-02 5.74e+03 1.26e+01 bond pdb=" C ASN A 158 " pdb=" N PRO A 159 " ideal model delta sigma weight residual 1.335 1.369 -0.034 1.36e-02 5.41e+03 6.29e+00 bond pdb=" C08 T4U A 501 " pdb=" C11 T4U A 501 " ideal model delta sigma weight residual 1.520 1.563 -0.043 2.00e-02 2.50e+03 4.53e+00 bond pdb=" C04 T4U A 501 " pdb=" C09 T4U A 501 " ideal model delta sigma weight residual 1.508 1.548 -0.040 2.00e-02 2.50e+03 3.90e+00 bond pdb=" C GLU E 222 " pdb=" N TYR E 223 " ideal model delta sigma weight residual 1.331 1.290 0.041 2.07e-02 2.33e+03 3.85e+00 ... (remaining 8323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 11184 2.43 - 4.86: 145 4.86 - 7.29: 16 7.29 - 9.72: 2 9.72 - 12.15: 4 Bond angle restraints: 11351 Sorted by residual: angle pdb=" CA ASN A 158 " pdb=" C ASN A 158 " pdb=" N PRO A 159 " ideal model delta sigma weight residual 117.73 123.68 -5.95 1.04e+00 9.25e-01 3.28e+01 angle pdb=" O ALA A 155 " pdb=" C ALA A 155 " pdb=" N ILE A 156 " ideal model delta sigma weight residual 122.22 117.21 5.01 1.17e+00 7.31e-01 1.83e+01 angle pdb=" C07 T4U A 501 " pdb=" C08 T4U A 501 " pdb=" C11 T4U A 501 " ideal model delta sigma weight residual 111.70 123.85 -12.15 3.00e+00 1.11e-01 1.64e+01 angle pdb=" CA ASN A 158 " pdb=" C ASN A 158 " pdb=" O ASN A 158 " ideal model delta sigma weight residual 120.80 115.72 5.08 1.32e+00 5.74e-01 1.48e+01 angle pdb=" CA ALA A 155 " pdb=" C ALA A 155 " pdb=" N ILE A 156 " ideal model delta sigma weight residual 117.63 122.36 -4.73 1.25e+00 6.40e-01 1.43e+01 ... (remaining 11346 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.66: 4850 28.66 - 57.32: 56 57.32 - 85.98: 9 85.98 - 114.64: 2 114.64 - 143.30: 2 Dihedral angle restraints: 4919 sinusoidal: 1755 harmonic: 3164 Sorted by residual: dihedral pdb=" CA ALA E 131 " pdb=" C ALA E 131 " pdb=" N THR E 132 " pdb=" CA THR E 132 " ideal model delta harmonic sigma weight residual 180.00 135.65 44.35 0 5.00e+00 4.00e-02 7.87e+01 dihedral pdb=" C11 T4U A 501 " pdb=" C07 T4U A 501 " pdb=" C08 T4U A 501 " pdb=" N13 T4U A 501 " ideal model delta sinusoidal sigma weight residual -82.85 60.45 -143.30 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" CA PHE A 223 " pdb=" C PHE A 223 " pdb=" N PHE A 224 " pdb=" CA PHE A 224 " ideal model delta harmonic sigma weight residual -180.00 -158.42 -21.58 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 4916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.322: 1345 0.322 - 0.644: 0 0.644 - 0.965: 0 0.965 - 1.287: 0 1.287 - 1.609: 1 Chirality restraints: 1346 Sorted by residual: chirality pdb=" C08 T4U A 501 " pdb=" C01 T4U A 501 " pdb=" C07 T4U A 501 " pdb=" C11 T4U A 501 " both_signs ideal model delta sigma weight residual False -2.50 -0.89 -1.61 2.00e-01 2.50e+01 6.47e+01 chirality pdb=" CB ILE A 156 " pdb=" CA ILE A 156 " pdb=" CG1 ILE A 156 " pdb=" CG2 ILE A 156 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.77e-01 chirality pdb=" CA PRO C 236 " pdb=" N PRO C 236 " pdb=" C PRO C 236 " pdb=" CB PRO C 236 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.25e-01 ... (remaining 1343 not shown) Planarity restraints: 1424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 155 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.42e+00 pdb=" C ALA A 155 " -0.040 2.00e-02 2.50e+03 pdb=" O ALA A 155 " 0.014 2.00e-02 2.50e+03 pdb=" N ILE A 156 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 151 " 0.014 2.00e-02 2.50e+03 1.19e-02 2.47e+00 pdb=" CG PHE C 151 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE C 151 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE C 151 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 151 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 151 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 151 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 193 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.44e+00 pdb=" N PRO C 194 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 194 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 194 " -0.022 5.00e-02 4.00e+02 ... (remaining 1421 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 47 2.65 - 3.22: 7116 3.22 - 3.78: 11459 3.78 - 4.34: 15933 4.34 - 4.90: 27135 Nonbonded interactions: 61690 Sorted by model distance: nonbonded pdb=" OD2 ASP A 151 " pdb=" OH TYR B 243 " model vdw 2.093 3.040 nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.274 3.040 nonbonded pdb=" OG SER E 134 " pdb=" OE1 GLU E 234 " model vdw 2.328 3.040 nonbonded pdb=" NH2 ARG E 98 " pdb=" OD2 ASP E 109 " model vdw 2.346 3.120 nonbonded pdb=" OE1 GLN C 176 " pdb=" OG1 THR C 179 " model vdw 2.367 3.040 ... (remaining 61685 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 22.110 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 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 0.047 8328 Z= 0.296 Angle : 0.745 12.153 11351 Z= 0.410 Chirality : 0.064 1.609 1346 Planarity : 0.005 0.039 1424 Dihedral : 11.289 143.302 2865 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.12 % Allowed : 0.37 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 1.40 (0.25), residues: 1065 helix: 1.51 (0.29), residues: 326 sheet: 1.31 (0.30), residues: 271 loop : 0.40 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 63 HIS 0.008 0.002 HIS E 220 PHE 0.027 0.003 PHE C 151 TYR 0.017 0.002 TYR A 375 ARG 0.007 0.001 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 364 ASN cc_start: 0.7338 (m110) cc_final: 0.7025 (m110) REVERT: B 195 LYS cc_start: 0.7640 (tttt) cc_final: 0.6974 (tttm) REVERT: C 289 TYR cc_start: 0.8201 (m-80) cc_final: 0.8000 (m-80) REVERT: C 340 ASN cc_start: 0.7537 (t0) cc_final: 0.7296 (t0) REVERT: D 50 LEU cc_start: 0.8569 (mt) cc_final: 0.8174 (mt) outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.9966 time to fit residues: 207.8330 Evaluate side-chains 172 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.0570 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.0980 chunk 84 optimal weight: 0.0270 chunk 32 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 0.0970 chunk 98 optimal weight: 3.9990 overall best weight: 0.1754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 223 ASN B 244 ASN C 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.129605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.115413 restraints weight = 12179.510| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.81 r_work: 0.3420 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8328 Z= 0.152 Angle : 0.561 6.140 11351 Z= 0.306 Chirality : 0.044 0.154 1346 Planarity : 0.004 0.046 1424 Dihedral : 8.870 150.163 1236 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.59 % Allowed : 7.68 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.63 (0.26), residues: 1065 helix: 2.07 (0.29), residues: 344 sheet: 1.29 (0.30), residues: 283 loop : 0.21 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 297 HIS 0.005 0.001 HIS B 209 PHE 0.016 0.001 PHE C 199 TYR 0.015 0.001 TYR E 178 ARG 0.006 0.001 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 366 LEU cc_start: 0.8022 (mt) cc_final: 0.7738 (mp) REVERT: B 22 ASN cc_start: 0.8285 (OUTLIER) cc_final: 0.7995 (OUTLIER) REVERT: C 189 SER cc_start: 0.8385 (p) cc_final: 0.8182 (t) REVERT: C 190 LEU cc_start: 0.7638 (mt) cc_final: 0.7429 (mp) REVERT: C 258 ASP cc_start: 0.6495 (t0) cc_final: 0.6235 (t0) REVERT: C 289 TYR cc_start: 0.8250 (m-80) cc_final: 0.7776 (m-80) REVERT: E 207 LEU cc_start: 0.8494 (tp) cc_final: 0.8292 (tp) outliers start: 13 outliers final: 6 residues processed: 171 average time/residue: 1.0470 time to fit residues: 191.7018 Evaluate side-chains 168 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 162 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 58 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 75 optimal weight: 0.1980 chunk 78 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 0.3980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 244 ASN C 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.126258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.111956 restraints weight = 12369.823| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.83 r_work: 0.3386 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8328 Z= 0.218 Angle : 0.572 7.008 11351 Z= 0.310 Chirality : 0.044 0.148 1346 Planarity : 0.004 0.051 1424 Dihedral : 8.307 153.950 1236 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.95 % Allowed : 9.27 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.57 (0.26), residues: 1065 helix: 2.24 (0.29), residues: 347 sheet: 1.24 (0.31), residues: 282 loop : -0.03 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 130 HIS 0.010 0.002 HIS B 209 PHE 0.016 0.002 PHE C 199 TYR 0.010 0.001 TYR E 178 ARG 0.006 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 366 LEU cc_start: 0.8199 (mt) cc_final: 0.7984 (mp) REVERT: B 22 ASN cc_start: 0.8252 (OUTLIER) cc_final: 0.7989 (m110) REVERT: B 32 ARG cc_start: 0.8236 (mtt180) cc_final: 0.7970 (mtt-85) REVERT: C 49 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8433 (tpp-160) REVERT: C 189 SER cc_start: 0.8453 (p) cc_final: 0.8245 (t) REVERT: C 190 LEU cc_start: 0.7811 (mt) cc_final: 0.7600 (mp) REVERT: C 258 ASP cc_start: 0.6603 (t0) cc_final: 0.6221 (t0) REVERT: C 289 TYR cc_start: 0.8381 (m-80) cc_final: 0.8041 (m-80) REVERT: E 132 THR cc_start: 0.8103 (t) cc_final: 0.7620 (m) REVERT: E 207 LEU cc_start: 0.8509 (tp) cc_final: 0.8303 (tp) outliers start: 16 outliers final: 7 residues processed: 174 average time/residue: 1.0791 time to fit residues: 200.4234 Evaluate side-chains 173 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 164 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 51 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 244 ASN C 75 GLN C 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.124910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.110648 restraints weight = 12324.182| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.82 r_work: 0.3351 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8328 Z= 0.239 Angle : 0.588 7.460 11351 Z= 0.317 Chirality : 0.044 0.156 1346 Planarity : 0.004 0.054 1424 Dihedral : 7.595 138.493 1236 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.56 % Allowed : 10.73 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.40 (0.26), residues: 1065 helix: 2.27 (0.29), residues: 347 sheet: 1.16 (0.32), residues: 271 loop : -0.27 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 130 HIS 0.011 0.002 HIS B 209 PHE 0.018 0.002 PHE C 151 TYR 0.010 0.002 TYR E 50 ARG 0.005 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 323 MET cc_start: 0.7412 (mmm) cc_final: 0.7022 (mtm) REVERT: B 22 ASN cc_start: 0.8270 (m-40) cc_final: 0.8003 (m110) REVERT: B 83 MET cc_start: 0.8903 (ttp) cc_final: 0.8696 (ttp) REVERT: B 126 LYS cc_start: 0.8733 (ttpt) cc_final: 0.8529 (ttmm) REVERT: C 49 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8423 (tpp-160) REVERT: C 98 SER cc_start: 0.8473 (p) cc_final: 0.8157 (t) REVERT: C 258 ASP cc_start: 0.6857 (t0) cc_final: 0.6426 (t0) REVERT: C 289 TYR cc_start: 0.8420 (m-80) cc_final: 0.8096 (m-80) REVERT: E 132 THR cc_start: 0.8246 (t) cc_final: 0.7832 (m) outliers start: 21 outliers final: 8 residues processed: 176 average time/residue: 1.0345 time to fit residues: 194.6936 Evaluate side-chains 172 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 117 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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: 63.0893 > 50: distance: 28 - 43: 25.592 distance: 33 - 49: 32.828 distance: 39 - 43: 26.715 distance: 43 - 44: 5.263 distance: 44 - 45: 28.207 distance: 44 - 47: 26.236 distance: 45 - 46: 10.350 distance: 45 - 49: 29.380 distance: 47 - 48: 37.338 distance: 49 - 50: 12.545 distance: 50 - 51: 8.625 distance: 50 - 53: 51.785 distance: 51 - 52: 7.775 distance: 51 - 60: 30.059 distance: 53 - 54: 15.535 distance: 54 - 55: 32.170 distance: 54 - 56: 22.608 distance: 55 - 57: 8.111 distance: 57 - 59: 20.108 distance: 58 - 59: 14.229 distance: 60 - 61: 16.382 distance: 60 - 292: 32.610 distance: 61 - 62: 8.804 distance: 62 - 63: 13.383 distance: 62 - 64: 28.360 distance: 63 - 289: 26.032 distance: 64 - 65: 17.632 distance: 65 - 66: 7.535 distance: 65 - 68: 22.155 distance: 66 - 67: 16.578 distance: 66 - 72: 33.263 distance: 68 - 69: 41.624 distance: 69 - 70: 38.167 distance: 70 - 71: 20.782 distance: 72 - 73: 48.530 distance: 72 - 276: 24.646 distance: 73 - 74: 21.682 distance: 73 - 76: 18.227 distance: 74 - 75: 8.506 distance: 74 - 82: 10.314 distance: 75 - 273: 35.145 distance: 76 - 77: 14.648 distance: 77 - 78: 18.790 distance: 77 - 79: 47.951 distance: 78 - 80: 37.516 distance: 82 - 83: 13.803 distance: 83 - 84: 32.081 distance: 83 - 86: 42.107 distance: 84 - 85: 15.898 distance: 84 - 96: 25.850 distance: 85 - 171: 24.465 distance: 86 - 87: 31.024 distance: 87 - 88: 29.501 distance: 87 - 89: 20.349 distance: 88 - 90: 4.531 distance: 89 - 91: 11.378 distance: 89 - 92: 17.990 distance: 90 - 91: 8.201 distance: 91 - 93: 9.932 distance: 92 - 94: 22.824 distance: 93 - 95: 11.710 distance: 94 - 95: 18.345 distance: 96 - 97: 21.883 distance: 96 - 260: 22.106 distance: 97 - 98: 22.540 distance: 97 - 100: 36.564 distance: 98 - 99: 11.554 distance: 98 - 103: 30.725 distance: 99 - 257: 27.282 distance: 100 - 101: 21.239 distance: 100 - 102: 13.129 distance: 103 - 104: 44.159 distance: 103 - 157: 27.493 distance: 104 - 105: 25.864 distance: 104 - 107: 40.863 distance: 105 - 106: 18.834 distance: 105 - 114: 9.293 distance: 106 - 154: 20.587 distance: 107 - 108: 30.537 distance: 108 - 109: 39.961 distance: 109 - 110: 12.719 distance: 110 - 111: 8.010 distance: 111 - 112: 13.514 distance: 111 - 113: 10.730 distance: 114 - 115: 27.061 distance: 114 - 244: 33.788 distance: 115 - 116: 45.483 distance: 115 - 118: 62.030 distance: 116 - 117: 21.423 distance: 116 - 123: 40.292 distance: 117 - 241: 30.638 distance: 118 - 119: 3.217 distance: 119 - 120: 34.307 distance: 120 - 121: 35.825 distance: 120 - 122: 23.893 distance: 123 - 124: 31.530 distance: 123 - 145: 22.062 distance: 124 - 125: 7.318 distance: 124 - 127: 41.454 distance: 125 - 126: 34.864 distance: 125 - 128: 22.048