Starting phenix.real_space_refine on Fri Jul 19 23:06:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jil_36317/07_2024/8jil_36317_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jil_36317/07_2024/8jil_36317.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jil_36317/07_2024/8jil_36317.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jil_36317/07_2024/8jil_36317.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jil_36317/07_2024/8jil_36317_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jil_36317/07_2024/8jil_36317_neut.cif" } resolution = 3.5 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= 0.011 sd= 0.078 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 69 5.16 5 C 5765 2.51 5 N 1535 2.21 5 O 1659 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D ARG 205": "NH1" <-> "NH2" Residue "D GLU 216": "OE1" <-> "OE2" Residue "D GLU 276": "OE1" <-> "OE2" Residue "D GLU 298": "OE1" <-> "OE2" Residue "D GLU 308": "OE1" <-> "OE2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "S ARG 160": "NH1" <-> "NH2" Residue "S ARG 218": "NH1" <-> "NH2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A ARG 270": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 9028 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "D" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1796 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2364 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 9, 'TRANS': 278} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'CLR': 1, 'NIO': 1} Classifications: {'undetermined': 2, 'water': 1} Link IDs: {None: 2} Time building chain proxies: 5.31, per 1000 atoms: 0.59 Number of scatterers: 9028 At special positions: 0 Unit cell: (109.48, 135.24, 104.88, 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 69 16.00 O 1659 8.00 N 1535 7.00 C 5765 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.05 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.04 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 266 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.28 Conformation dependent library (CDL) restraints added in 1.6 seconds 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2134 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 34.3% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'B' and resid 1 through 25 removed outlier: 3.614A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.518A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.525A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 27 Processing helix chain 'D' and resid 45 through 53 Processing helix chain 'D' and resid 211 through 216 Processing helix chain 'D' and resid 241 through 254 removed outlier: 3.726A pdb=" N ALA D 245 " --> pdb=" O ASN D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 260 removed outlier: 6.118A pdb=" N TRP D 258 " --> pdb=" O ASN D 255 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR D 260 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 281 removed outlier: 3.945A pdb=" N GLU D 276 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 309 removed outlier: 3.691A pdb=" N ALA D 299 " --> pdb=" O THR D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 351 removed outlier: 3.816A pdb=" N GLN D 333 " --> pdb=" O THR D 329 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 342 " --> pdb=" O ALA D 338 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS D 351 " --> pdb=" O ASN D 347 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'A' and resid 25 through 55 removed outlier: 3.749A pdb=" N VAL A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) Proline residue: A 31 - end of helix removed outlier: 4.211A pdb=" N LEU A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 79 removed outlier: 3.948A pdb=" N LEU A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASN A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 89 removed outlier: 3.782A pdb=" N LEU A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 114 removed outlier: 4.251A pdb=" N PHE A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A 107 " --> pdb=" O MET A 103 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 removed outlier: 3.622A pdb=" N VAL A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 removed outlier: 4.231A pdb=" N TYR A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 4.144A pdb=" N ILE A 139 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 158 Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 187 through 215 removed outlier: 4.223A pdb=" N ALA A 191 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Proline residue: A 200 - end of helix removed outlier: 4.390A pdb=" N PHE A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 261 removed outlier: 3.740A pdb=" N LYS A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) Proline residue: A 246 - end of helix removed outlier: 3.528A pdb=" N ARG A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 284 through 290 removed outlier: 3.550A pdb=" N MET A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 295 Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.555A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.860A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.857A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.685A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.563A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.634A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.496A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 185 through 190 removed outlier: 3.561A pdb=" N PHE D 189 " --> pdb=" O PHE D 196 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LYS D 35 " --> pdb=" O ALA D 220 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILE D 222 " --> pdb=" O LYS D 35 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU D 37 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N CYS D 224 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU D 39 " --> pdb=" O CYS D 224 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N ALA D 226 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 7.235A pdb=" N GLY S 16 " --> pdb=" O SER S 85 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N SER S 85 " --> pdb=" O GLY S 16 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.080A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.642A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR S 243 " --> pdb=" O TYR S 227 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR S 227 " --> pdb=" O THR S 243 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 155 through 160 Processing sheet with id=AB4, first strand: chain 'A' and resid 11 through 13 364 hydrogen bonds defined for protein. 1017 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: 2.42 Time building geometry restraints manager: 3.61 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: 2903 1.34 - 1.47: 2302 1.47 - 1.60: 3920 1.60 - 1.72: 0 1.72 - 1.85: 100 Bond restraints: 9225 Sorted by residual: bond pdb=" CA SER A 179 " pdb=" CB SER A 179 " ideal model delta sigma weight residual 1.537 1.480 0.057 1.38e-02 5.25e+03 1.70e+01 bond pdb=" N CYS A 183 " pdb=" CA CYS A 183 " ideal model delta sigma weight residual 1.453 1.496 -0.043 1.39e-02 5.18e+03 9.61e+00 bond pdb=" N PHE A 186 " pdb=" CA PHE A 186 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.22e-02 6.72e+03 9.25e+00 bond pdb=" N ILE A 77 " pdb=" CA ILE A 77 " ideal model delta sigma weight residual 1.462 1.495 -0.033 1.18e-02 7.18e+03 7.87e+00 bond pdb=" N SER A 179 " pdb=" CA SER A 179 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.31e-02 5.83e+03 7.82e+00 ... (remaining 9220 not shown) Histogram of bond angle deviations from ideal: 98.21 - 105.42: 126 105.42 - 112.62: 4777 112.62 - 119.83: 3112 119.83 - 127.04: 4361 127.04 - 134.24: 109 Bond angle restraints: 12485 Sorted by residual: angle pdb=" CB MET S 230 " pdb=" CG MET S 230 " pdb=" SD MET S 230 " ideal model delta sigma weight residual 112.70 126.87 -14.17 3.00e+00 1.11e-01 2.23e+01 angle pdb=" N SER A 178 " pdb=" CA SER A 178 " pdb=" C SER A 178 " ideal model delta sigma weight residual 108.96 114.78 -5.82 1.49e+00 4.50e-01 1.53e+01 angle pdb=" N SER A 179 " pdb=" CA SER A 179 " pdb=" C SER A 179 " ideal model delta sigma weight residual 114.31 109.31 5.00 1.29e+00 6.01e-01 1.50e+01 angle pdb=" CA MET C 21 " pdb=" CB MET C 21 " pdb=" CG MET C 21 " ideal model delta sigma weight residual 114.10 121.68 -7.58 2.00e+00 2.50e-01 1.44e+01 angle pdb=" C CYS A 183 " pdb=" CA CYS A 183 " pdb=" CB CYS A 183 " ideal model delta sigma weight residual 112.43 105.21 7.22 1.91e+00 2.74e-01 1.43e+01 ... (remaining 12480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.33: 4887 16.33 - 32.67: 506 32.67 - 49.00: 100 49.00 - 65.34: 10 65.34 - 81.67: 8 Dihedral angle restraints: 5511 sinusoidal: 2208 harmonic: 3303 Sorted by residual: dihedral pdb=" CA PHE S 239 " pdb=" C PHE S 239 " pdb=" N GLY S 240 " pdb=" CA GLY S 240 " ideal model delta harmonic sigma weight residual 180.00 154.39 25.61 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA ASP A 14 " pdb=" C ASP A 14 " pdb=" N LYS A 15 " pdb=" CA LYS A 15 " ideal model delta harmonic sigma weight residual 180.00 156.94 23.06 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA GLU D 8 " pdb=" C GLU D 8 " pdb=" N ASP D 9 " pdb=" CA ASP D 9 " ideal model delta harmonic sigma weight residual 180.00 159.14 20.86 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 5508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 837 0.037 - 0.075: 371 0.075 - 0.112: 146 0.112 - 0.150: 39 0.150 - 0.187: 10 Chirality restraints: 1403 Sorted by residual: chirality pdb=" CA VAL S 37 " pdb=" N VAL S 37 " pdb=" C VAL S 37 " pdb=" CB VAL S 37 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.76e-01 chirality pdb=" CA LEU A 76 " pdb=" N LEU A 76 " pdb=" C LEU A 76 " pdb=" CB LEU A 76 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.08e-01 chirality pdb=" CA CYS A 177 " pdb=" N CYS A 177 " pdb=" C CYS A 177 " pdb=" CB CYS A 177 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.28e-01 ... (remaining 1400 not shown) Planarity restraints: 1574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 182 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" C ILE A 182 " 0.051 2.00e-02 2.50e+03 pdb=" O ILE A 182 " -0.019 2.00e-02 2.50e+03 pdb=" N CYS A 183 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " -0.045 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO C 49 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.038 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO S 75 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.033 5.00e-02 4.00e+02 ... (remaining 1571 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1058 2.75 - 3.29: 8595 3.29 - 3.82: 14216 3.82 - 4.36: 17102 4.36 - 4.90: 30046 Nonbonded interactions: 71017 Sorted by model distance: nonbonded pdb=" O ALA C 56 " pdb=" NH1 ARG C 62 " model vdw 2.209 2.520 nonbonded pdb=" NH1 ARG B 49 " pdb=" O PHE C 61 " model vdw 2.216 2.520 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.241 2.440 nonbonded pdb=" NH2 ARG B 22 " pdb=" O THR B 221 " model vdw 2.254 2.520 nonbonded pdb=" OG SER S 30 " pdb=" OD1 ASP S 74 " model vdw 2.279 2.440 ... (remaining 71012 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue 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: 1.070 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.370 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 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 : 0.006 0.061 9225 Z= 0.362 Angle : 0.876 14.172 12485 Z= 0.502 Chirality : 0.050 0.187 1403 Planarity : 0.005 0.069 1574 Dihedral : 13.683 81.670 3365 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.10 % Allowed : 0.41 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.81 (0.24), residues: 1127 helix: -0.21 (0.29), residues: 325 sheet: -0.34 (0.30), residues: 273 loop : -2.35 (0.24), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 169 HIS 0.010 0.002 HIS A 189 PHE 0.023 0.002 PHE A 105 TYR 0.022 0.002 TYR S 50 ARG 0.005 0.001 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 1.116 Fit side-chains REVERT: A 167 MET cc_start: 0.5256 (tpt) cc_final: 0.5011 (tpp) REVERT: A 217 GLN cc_start: 0.7802 (pp30) cc_final: 0.7594 (pp30) outliers start: 1 outliers final: 1 residues processed: 116 average time/residue: 0.2740 time to fit residues: 41.7525 Evaluate side-chains 98 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 45 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS C 18 GLN D 188 HIS A 45 ASN A 184 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9225 Z= 0.253 Angle : 0.683 10.349 12485 Z= 0.347 Chirality : 0.046 0.147 1403 Planarity : 0.005 0.058 1574 Dihedral : 6.147 53.482 1300 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.92 % Allowed : 7.32 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.48 (0.24), residues: 1127 helix: 0.26 (0.29), residues: 329 sheet: -0.26 (0.30), residues: 280 loop : -2.27 (0.24), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 169 HIS 0.008 0.002 HIS A 184 PHE 0.020 0.002 PHE A 105 TYR 0.016 0.002 TYR B 105 ARG 0.003 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: S 230 MET cc_start: 0.6714 (tpp) cc_final: 0.6434 (tpp) REVERT: A 101 ARG cc_start: 0.7879 (ttp-170) cc_final: 0.7677 (ttp-110) REVERT: A 167 MET cc_start: 0.5084 (tpt) cc_final: 0.4848 (tpp) outliers start: 9 outliers final: 4 residues processed: 108 average time/residue: 0.2713 time to fit residues: 38.8921 Evaluate side-chains 101 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain A residue 143 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 84 optimal weight: 0.0470 chunk 69 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 90 optimal weight: 0.1980 chunk 34 optimal weight: 9.9990 chunk 81 optimal weight: 0.0570 chunk 100 optimal weight: 10.0000 overall best weight: 0.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN A 131 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 9225 Z= 0.150 Angle : 0.576 10.239 12485 Z= 0.294 Chirality : 0.042 0.195 1403 Planarity : 0.004 0.052 1574 Dihedral : 5.584 47.017 1300 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.22 % Allowed : 10.38 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.06 (0.25), residues: 1127 helix: 0.76 (0.30), residues: 341 sheet: -0.15 (0.30), residues: 275 loop : -2.10 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 169 HIS 0.007 0.001 HIS A 133 PHE 0.011 0.001 PHE A 105 TYR 0.009 0.001 TYR S 95 ARG 0.005 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: B 172 GLU cc_start: 0.6876 (pm20) cc_final: 0.6622 (pm20) REVERT: D 227 LEU cc_start: 0.5149 (OUTLIER) cc_final: 0.4751 (pp) REVERT: D 276 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6703 (mp0) outliers start: 12 outliers final: 4 residues processed: 119 average time/residue: 0.2506 time to fit residues: 39.8674 Evaluate side-chains 106 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 100 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 143 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 90 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 9225 Z= 0.186 Angle : 0.582 9.493 12485 Z= 0.297 Chirality : 0.043 0.219 1403 Planarity : 0.004 0.050 1574 Dihedral : 5.526 42.383 1300 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.53 % Allowed : 10.99 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.97 (0.25), residues: 1127 helix: 0.86 (0.30), residues: 340 sheet: -0.08 (0.30), residues: 274 loop : -2.06 (0.24), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 169 HIS 0.006 0.001 HIS A 133 PHE 0.015 0.001 PHE A 105 TYR 0.012 0.001 TYR B 105 ARG 0.005 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 172 GLU cc_start: 0.7059 (pm20) cc_final: 0.6566 (pm20) REVERT: D 227 LEU cc_start: 0.5142 (OUTLIER) cc_final: 0.4771 (pp) REVERT: D 272 ASP cc_start: 0.5390 (m-30) cc_final: 0.3943 (m-30) REVERT: D 276 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6702 (mp0) outliers start: 15 outliers final: 7 residues processed: 118 average time/residue: 0.2310 time to fit residues: 37.3900 Evaluate side-chains 110 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 241 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.4723 > 50: distance: 4 - 9: 16.046 distance: 9 - 10: 16.877 distance: 10 - 11: 22.943 distance: 10 - 13: 36.790 distance: 11 - 12: 17.676 distance: 11 - 15: 14.359 distance: 13 - 14: 32.698 distance: 15 - 16: 18.316 distance: 16 - 17: 7.981 distance: 16 - 19: 21.433 distance: 17 - 18: 9.114 distance: 17 - 21: 25.470 distance: 19 - 20: 16.455 distance: 21 - 22: 26.550 distance: 21 - 118: 11.358 distance: 22 - 23: 20.338 distance: 22 - 25: 24.491 distance: 23 - 24: 33.232 distance: 23 - 28: 19.689 distance: 25 - 26: 43.718 distance: 25 - 27: 7.103 distance: 28 - 29: 18.243 distance: 28 - 34: 37.275 distance: 29 - 30: 43.021 distance: 30 - 31: 38.063 distance: 30 - 35: 30.489 distance: 33 - 34: 31.435 distance: 35 - 36: 31.170 distance: 36 - 37: 21.146 distance: 36 - 39: 22.728 distance: 37 - 42: 22.945 distance: 39 - 40: 3.134 distance: 39 - 41: 10.798 distance: 42 - 43: 10.671 distance: 43 - 44: 17.541 distance: 43 - 46: 30.588 distance: 44 - 45: 40.926 distance: 44 - 49: 7.399 distance: 46 - 47: 35.412 distance: 46 - 48: 4.140 distance: 49 - 50: 7.094 distance: 49 - 55: 23.353 distance: 50 - 51: 19.476 distance: 50 - 53: 45.907 distance: 51 - 52: 36.144 distance: 51 - 56: 25.724 distance: 53 - 54: 42.163 distance: 54 - 55: 32.444 distance: 56 - 57: 11.517 distance: 57 - 58: 3.372 distance: 58 - 59: 31.349 distance: 58 - 60: 12.640 distance: 60 - 61: 5.665 distance: 61 - 62: 41.632 distance: 61 - 64: 18.393 distance: 62 - 63: 42.527 distance: 62 - 69: 7.135 distance: 64 - 65: 5.134 distance: 65 - 66: 49.450 distance: 66 - 68: 6.372 distance: 69 - 70: 16.457 distance: 70 - 71: 22.579 distance: 70 - 73: 42.805 distance: 71 - 72: 21.950 distance: 71 - 75: 22.520 distance: 73 - 74: 35.827