Starting phenix.real_space_refine on Sat Aug 3 16:29:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjn_33875/08_2024/7yjn_33875.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjn_33875/08_2024/7yjn_33875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjn_33875/08_2024/7yjn_33875.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjn_33875/08_2024/7yjn_33875.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjn_33875/08_2024/7yjn_33875.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjn_33875/08_2024/7yjn_33875.cif" } resolution = 3.4 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= 0.101 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 P 1 5.49 5 S 49 5.16 5 C 5476 2.51 5 N 1445 2.21 5 O 1557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A ASP 74": "OD1" <-> "OD2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A ASP 110": "OD1" <-> "OD2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 162": "NH1" <-> "NH2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ASP 265": "OD1" <-> "OD2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A ARG 291": "NH1" <-> "NH2" Residue "A ARG 294": "NH1" <-> "NH2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 361": "OD1" <-> "OD2" Residue "A ASP 386": "OD1" <-> "OD2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 443": "OD1" <-> "OD2" Residue "A ARG 446": "NH1" <-> "NH2" Residue "B TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 30": "NH1" <-> "NH2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 58": "NH1" <-> "NH2" Residue "B ASP 65": "OD1" <-> "OD2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 141": "OD1" <-> "OD2" Residue "B GLU 153": "OE1" <-> "OE2" Residue "B ARG 157": "NH1" <-> "NH2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 234": "NH1" <-> "NH2" Residue "B GLU 247": "OE1" <-> "OE2" Residue "B TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B ASP 276": "OD1" <-> "OD2" Residue "B ASP 301": "OD1" <-> "OD2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B ARG 366": "NH1" <-> "NH2" Residue "B ARG 373": "NH1" <-> "NH2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 382": "NH1" <-> "NH2" Residue "B PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B ASP 452": "OD1" <-> "OD2" Residue "B ARG 455": "NH1" <-> "NH2" Residue "B ASP 465": "OD1" <-> "OD2" Residue "B GLU 475": "OE1" <-> "OE2" Residue "D ARG 16": "NH1" <-> "NH2" Residue "D PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 6": "NH1" <-> "NH2" Residue "C TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8528 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3230 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 17, 'TRANS': 400} Chain: "B" Number of atoms: 3592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3592 Classifications: {'peptide': 465} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 21, 'TRANS': 443} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'TRP:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "D" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1122 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 131} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 186 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 24} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 383 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 46} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 6.13, per 1000 atoms: 0.72 Number of scatterers: 8528 At special positions: 0 Unit cell: (89.64, 82.08, 117.72, 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) S 49 16.00 P 1 15.00 O 1557 8.00 N 1445 7.00 C 5476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.39 Conformation dependent library (CDL) restraints added in 1.8 seconds 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2030 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 5 sheets defined 51.5% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 65 through 73 removed outlier: 3.857A pdb=" N ASP A 70 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU A 71 " --> pdb=" O GLN A 67 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 140 removed outlier: 3.546A pdb=" N LEU A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 168 removed outlier: 3.812A pdb=" N LEU A 157 " --> pdb=" O ILE A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.615A pdb=" N THR A 181 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N MET A 182 " --> pdb=" O GLY A 178 " (cutoff:3.500A) Proline residue: A 187 - end of helix removed outlier: 3.711A pdb=" N CYS A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.552A pdb=" N GLY A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 239 Processing helix chain 'A' and resid 263 through 275 removed outlier: 3.697A pdb=" N ILE A 267 " --> pdb=" O PRO A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 removed outlier: 3.777A pdb=" N HIS A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 349 through 365 removed outlier: 3.618A pdb=" N ALA A 353 " --> pdb=" O PRO A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 411 through 431 Processing helix chain 'A' and resid 460 through 480 removed outlier: 3.714A pdb=" N LEU A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 36 Processing helix chain 'B' and resid 54 through 63 Processing helix chain 'B' and resid 119 through 132 removed outlier: 3.913A pdb=" N ARG B 123 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 160 Processing helix chain 'B' and resid 169 through 182 Proline residue: B 179 - end of helix Processing helix chain 'B' and resid 195 through 204 Processing helix chain 'B' and resid 216 through 230 Processing helix chain 'B' and resid 258 through 267 Processing helix chain 'B' and resid 290 through 295 removed outlier: 3.792A pdb=" N LEU B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 314 removed outlier: 3.884A pdb=" N GLY B 314 " --> pdb=" O THR B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 334 removed outlier: 3.682A pdb=" N GLN B 328 " --> pdb=" O LYS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 369 through 389 removed outlier: 3.596A pdb=" N GLY B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 421 removed outlier: 3.553A pdb=" N ALA B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 468 Processing helix chain 'D' and resid 25 through 45 removed outlier: 3.791A pdb=" N MET D 31 " --> pdb=" O TRP D 27 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 71 Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 93 through 96 Processing helix chain 'D' and resid 99 through 119 Proline residue: D 109 - end of helix Processing helix chain 'D' and resid 124 through 141 removed outlier: 3.708A pdb=" N LYS D 141 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 54 removed outlier: 3.563A pdb=" N ARG E 54 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 15 Processing helix chain 'C' and resid 21 through 47 removed outlier: 3.845A pdb=" N VAL C 32 " --> pdb=" O PHE C 28 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL C 33 " --> pdb=" O ASN C 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 174 through 175 removed outlier: 6.648A pdb=" N VAL A 278 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N THR A 311 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU A 280 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N ALA A 313 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ARG A 247 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE A 279 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE A 249 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ASP A 281 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ALA A 251 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL A 195 " --> pdb=" O TYR A 248 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL A 250 " --> pdb=" O VAL A 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 390 through 392 removed outlier: 3.699A pdb=" N VAL A 435 " --> pdb=" O LYS A 452 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 82 through 85 removed outlier: 6.147A pdb=" N GLU B 83 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR B 96 " --> pdb=" O GLU B 83 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR B 85 " --> pdb=" O LYS B 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 163 through 167 removed outlier: 3.636A pdb=" N ALA B 163 " --> pdb=" O GLY B 322 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY B 318 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL B 304 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP B 191 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE B 212 " --> pdb=" O SER B 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 400 through 404 removed outlier: 3.501A pdb=" N MET B 401 " --> pdb=" O ILE B 442 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE B 442 " --> pdb=" O MET B 401 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1224 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: 2.21 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1363 1.27 - 1.40: 2196 1.40 - 1.54: 5003 1.54 - 1.67: 80 1.67 - 1.81: 76 Bond restraints: 8718 Sorted by residual: bond pdb=" CA THR D 64 " pdb=" C THR D 64 " ideal model delta sigma weight residual 1.522 1.396 0.126 1.37e-02 5.33e+03 8.46e+01 bond pdb=" C LEU B 103 " pdb=" N ASN B 104 " ideal model delta sigma weight residual 1.331 1.203 0.129 1.40e-02 5.10e+03 8.43e+01 bond pdb=" C LEU B 103 " pdb=" O LEU B 103 " ideal model delta sigma weight residual 1.234 1.130 0.105 1.15e-02 7.56e+03 8.31e+01 bond pdb=" CA LEU B 103 " pdb=" C LEU B 103 " ideal model delta sigma weight residual 1.520 1.414 0.107 1.20e-02 6.94e+03 7.89e+01 bond pdb=" C CYS B 102 " pdb=" O CYS B 102 " ideal model delta sigma weight residual 1.235 1.133 0.103 1.26e-02 6.30e+03 6.64e+01 ... (remaining 8713 not shown) Histogram of bond angle deviations from ideal: 95.02 - 102.85: 99 102.85 - 110.67: 2952 110.67 - 118.50: 3945 118.50 - 126.33: 4683 126.33 - 134.16: 137 Bond angle restraints: 11816 Sorted by residual: angle pdb=" N PHE A 189 " pdb=" CA PHE A 189 " pdb=" C PHE A 189 " ideal model delta sigma weight residual 113.16 130.33 -17.17 1.24e+00 6.50e-01 1.92e+02 angle pdb=" C ILE C 8 " pdb=" CA ILE C 8 " pdb=" CB ILE C 8 " ideal model delta sigma weight residual 111.97 98.11 13.86 1.28e+00 6.10e-01 1.17e+02 angle pdb=" C MET D 71 " pdb=" N LYS D 72 " pdb=" CA LYS D 72 " ideal model delta sigma weight residual 122.19 109.66 12.53 1.41e+00 5.03e-01 7.90e+01 angle pdb=" C PHE D 142 " pdb=" N PRO D 143 " pdb=" CA PRO D 143 " ideal model delta sigma weight residual 119.84 130.64 -10.80 1.25e+00 6.40e-01 7.46e+01 angle pdb=" C VAL B 223 " pdb=" CA VAL B 223 " pdb=" CB VAL B 223 " ideal model delta sigma weight residual 112.14 101.03 11.11 1.35e+00 5.49e-01 6.77e+01 ... (remaining 11811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4540 17.95 - 35.89: 499 35.89 - 53.83: 132 53.83 - 71.78: 17 71.78 - 89.72: 4 Dihedral angle restraints: 5192 sinusoidal: 2029 harmonic: 3163 Sorted by residual: dihedral pdb=" C PHE A 183 " pdb=" N PHE A 183 " pdb=" CA PHE A 183 " pdb=" CB PHE A 183 " ideal model delta harmonic sigma weight residual -122.60 -151.10 28.50 0 2.50e+00 1.60e-01 1.30e+02 dihedral pdb=" N PHE A 183 " pdb=" C PHE A 183 " pdb=" CA PHE A 183 " pdb=" CB PHE A 183 " ideal model delta harmonic sigma weight residual 122.80 150.73 -27.93 0 2.50e+00 1.60e-01 1.25e+02 dihedral pdb=" N LEU B 259 " pdb=" C LEU B 259 " pdb=" CA LEU B 259 " pdb=" CB LEU B 259 " ideal model delta harmonic sigma weight residual 122.80 143.93 -21.13 0 2.50e+00 1.60e-01 7.14e+01 ... (remaining 5189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.261: 1272 0.261 - 0.522: 51 0.522 - 0.782: 14 0.782 - 1.043: 0 1.043 - 1.304: 2 Chirality restraints: 1339 Sorted by residual: chirality pdb=" CA PHE A 183 " pdb=" N PHE A 183 " pdb=" C PHE A 183 " pdb=" CB PHE A 183 " both_signs ideal model delta sigma weight residual False 2.51 1.21 1.30 2.00e-01 2.50e+01 4.25e+01 chirality pdb=" CA LEU B 259 " pdb=" N LEU B 259 " pdb=" C LEU B 259 " pdb=" CB LEU B 259 " both_signs ideal model delta sigma weight residual False 2.51 1.38 1.13 2.00e-01 2.50e+01 3.18e+01 chirality pdb=" CG LEU D 129 " pdb=" CB LEU D 129 " pdb=" CD1 LEU D 129 " pdb=" CD2 LEU D 129 " both_signs ideal model delta sigma weight residual False -2.59 -1.84 -0.75 2.00e-01 2.50e+01 1.41e+01 ... (remaining 1336 not shown) Planarity restraints: 1486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 186 " -0.145 5.00e-02 4.00e+02 2.18e-01 7.59e+01 pdb=" N PRO A 187 " 0.377 5.00e-02 4.00e+02 pdb=" CA PRO A 187 " -0.121 5.00e-02 4.00e+02 pdb=" CD PRO A 187 " -0.110 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 68 " -0.026 2.00e-02 2.50e+03 5.02e-02 2.52e+01 pdb=" C PHE D 68 " 0.087 2.00e-02 2.50e+03 pdb=" O PHE D 68 " -0.033 2.00e-02 2.50e+03 pdb=" N HIS D 69 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 229 " -0.023 2.00e-02 2.50e+03 4.88e-02 2.38e+01 pdb=" C ALA B 229 " 0.084 2.00e-02 2.50e+03 pdb=" O ALA B 229 " -0.033 2.00e-02 2.50e+03 pdb=" N GLU B 230 " -0.028 2.00e-02 2.50e+03 ... (remaining 1483 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 45 2.40 - 3.03: 5810 3.03 - 3.65: 12168 3.65 - 4.28: 17359 4.28 - 4.90: 30608 Nonbonded interactions: 65990 Sorted by model distance: nonbonded pdb=" O GLY B 314 " pdb=" OE1 GLN B 350 " model vdw 1.776 3.040 nonbonded pdb=" OD1 ASP B 27 " pdb=" NH2 ARG B 58 " model vdw 1.869 3.120 nonbonded pdb=" OE1 GLN B 24 " pdb=" CE2 PHE B 54 " model vdw 1.908 3.340 nonbonded pdb=" O ALA B 229 " pdb=" N GLY B 231 " model vdw 1.910 3.120 nonbonded pdb=" O THR D 28 " pdb=" C THR D 29 " model vdw 1.946 3.270 ... (remaining 65985 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: 1.170 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 26.630 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: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 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 : 0.019 0.149 8718 Z= 1.235 Angle : 1.743 21.282 11816 Z= 1.050 Chirality : 0.133 1.304 1339 Planarity : 0.011 0.218 1486 Dihedral : 15.887 89.725 3162 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 26.04 Ramachandran Plot: Outliers : 1.94 % Allowed : 11.10 % Favored : 86.96 % Rotamer: Outliers : 8.37 % Allowed : 7.28 % Favored : 84.35 % Cbeta Deviations : 2.07 % Peptide Plane: Cis-proline : 0.00 % 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: -2.39 (0.25), residues: 1081 helix: -0.36 (0.22), residues: 543 sheet: -3.45 (0.48), residues: 80 loop : -2.75 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP D 70 HIS 0.019 0.003 HIS B 61 PHE 0.042 0.004 PHE B 20 TYR 0.029 0.003 TYR B 406 ARG 0.010 0.001 ARG B 26 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 126 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: A 89 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.6702 (mmt) REVERT: A 368 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7407 (t0) REVERT: A 388 LYS cc_start: 0.7788 (mttp) cc_final: 0.6983 (tttp) REVERT: A 473 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7825 (ttm170) REVERT: B 28 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: B 90 ASN cc_start: 0.7735 (OUTLIER) cc_final: 0.6954 (t0) REVERT: B 94 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8333 (ttpp) REVERT: B 113 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.8286 (m-80) REVERT: B 222 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7122 (ttm170) REVERT: D 24 PRO cc_start: 0.8738 (OUTLIER) cc_final: 0.8500 (Cg_endo) REVERT: D 30 TYR cc_start: 0.8213 (OUTLIER) cc_final: 0.7677 (t80) REVERT: D 72 LYS cc_start: 0.9003 (mtmm) cc_final: 0.8778 (mttt) REVERT: D 113 TYR cc_start: 0.8295 (t80) cc_final: 0.6948 (t80) REVERT: D 122 TYR cc_start: 0.7570 (OUTLIER) cc_final: 0.7336 (m-80) REVERT: D 128 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7547 (t80) REVERT: C 2 ASN cc_start: 0.6587 (OUTLIER) cc_final: 0.6230 (p0) outliers start: 77 outliers final: 39 residues processed: 191 average time/residue: 0.2238 time to fit residues: 57.7013 Evaluate side-chains 157 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 105 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain B residue 28 PHE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 239 TRP Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain D residue 24 PRO Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 61 PHE Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 122 TYR Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain C residue 2 ASN Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 GLN A 375 GLN B 61 HIS B 195 HIS B 200 ASN B 214 HIS B 227 GLN B 279 HIS D 84 ASN D 97 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8718 Z= 0.251 Angle : 0.751 9.946 11816 Z= 0.394 Chirality : 0.047 0.185 1339 Planarity : 0.006 0.061 1486 Dihedral : 9.161 58.991 1296 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.23 % Favored : 91.30 % Rotamer: Outliers : 4.67 % Allowed : 13.37 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.30 (0.26), residues: 1081 helix: 0.66 (0.22), residues: 561 sheet: -2.95 (0.52), residues: 80 loop : -2.53 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 239 HIS 0.006 0.001 HIS D 124 PHE 0.039 0.002 PHE A 183 TYR 0.019 0.002 TYR B 85 ARG 0.005 0.001 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 128 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 HIS cc_start: 0.7946 (OUTLIER) cc_final: 0.7324 (t-170) REVERT: A 368 ASP cc_start: 0.7129 (OUTLIER) cc_final: 0.6795 (t0) REVERT: A 473 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7929 (ttp80) REVERT: B 107 SER cc_start: 0.8868 (OUTLIER) cc_final: 0.8565 (p) REVERT: B 417 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7629 (mm-30) REVERT: D 30 TYR cc_start: 0.8505 (OUTLIER) cc_final: 0.7589 (t80) REVERT: D 92 MET cc_start: 0.7987 (mmm) cc_final: 0.7499 (tpt) outliers start: 43 outliers final: 20 residues processed: 158 average time/residue: 0.2010 time to fit residues: 43.6175 Evaluate side-chains 143 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 118 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain C residue 17 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 85 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 32 optimal weight: 0.0060 chunk 77 optimal weight: 4.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 GLN B 195 HIS D 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8718 Z= 0.221 Angle : 0.660 7.316 11816 Z= 0.348 Chirality : 0.044 0.192 1339 Planarity : 0.005 0.056 1486 Dihedral : 7.401 59.715 1229 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.85 % Favored : 92.78 % Rotamer: Outliers : 3.91 % Allowed : 16.09 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.26), residues: 1081 helix: 1.19 (0.22), residues: 560 sheet: -2.70 (0.53), residues: 80 loop : -2.47 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 239 HIS 0.005 0.001 HIS B 214 PHE 0.032 0.001 PHE A 183 TYR 0.015 0.001 TYR D 83 ARG 0.005 0.000 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 118 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 125 HIS cc_start: 0.7944 (OUTLIER) cc_final: 0.7414 (t-170) REVERT: A 368 ASP cc_start: 0.7296 (OUTLIER) cc_final: 0.7058 (t0) REVERT: A 413 LYS cc_start: 0.8110 (mmtm) cc_final: 0.7583 (tmtt) REVERT: D 30 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.7521 (t80) outliers start: 36 outliers final: 25 residues processed: 144 average time/residue: 0.2153 time to fit residues: 42.9439 Evaluate side-chains 137 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 109 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 GLN D 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8718 Z= 0.262 Angle : 0.656 8.874 11816 Z= 0.342 Chirality : 0.045 0.162 1339 Planarity : 0.005 0.056 1486 Dihedral : 6.711 59.296 1217 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.77 % Favored : 91.95 % Rotamer: Outliers : 4.13 % Allowed : 17.39 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.26), residues: 1081 helix: 1.30 (0.22), residues: 563 sheet: -2.52 (0.54), residues: 80 loop : -2.31 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 239 HIS 0.005 0.001 HIS B 214 PHE 0.032 0.002 PHE A 183 TYR 0.015 0.002 TYR C 9 ARG 0.005 0.000 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 121 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 125 HIS cc_start: 0.7863 (OUTLIER) cc_final: 0.7408 (t-170) REVERT: A 182 MET cc_start: 0.7776 (mmm) cc_final: 0.6908 (mmt) REVERT: A 338 SER cc_start: 0.8780 (t) cc_final: 0.8557 (t) REVERT: A 407 LYS cc_start: 0.8484 (mmtp) cc_final: 0.8094 (mttt) REVERT: A 413 LYS cc_start: 0.8202 (mmtm) cc_final: 0.7681 (tmtt) REVERT: A 422 MET cc_start: 0.7409 (ttt) cc_final: 0.7147 (ttt) REVERT: D 30 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.7511 (t80) REVERT: D 86 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8286 (mp) outliers start: 38 outliers final: 27 residues processed: 150 average time/residue: 0.2133 time to fit residues: 44.5795 Evaluate side-chains 145 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 115 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 76 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 87 optimal weight: 0.0040 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 25 optimal weight: 0.4980 chunk 34 optimal weight: 5.9990 overall best weight: 1.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 GLN D 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8718 Z= 0.220 Angle : 0.622 8.357 11816 Z= 0.323 Chirality : 0.043 0.157 1339 Planarity : 0.005 0.055 1486 Dihedral : 6.428 57.195 1214 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.66 % Favored : 93.06 % Rotamer: Outliers : 5.22 % Allowed : 17.07 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.26), residues: 1081 helix: 1.48 (0.22), residues: 560 sheet: -2.03 (0.53), residues: 93 loop : -2.22 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 239 HIS 0.005 0.001 HIS B 214 PHE 0.028 0.001 PHE A 183 TYR 0.014 0.001 TYR D 83 ARG 0.005 0.000 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 123 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 125 HIS cc_start: 0.7855 (OUTLIER) cc_final: 0.7491 (t-170) REVERT: A 182 MET cc_start: 0.7751 (mmm) cc_final: 0.6848 (mmt) REVERT: A 388 LYS cc_start: 0.7946 (mttm) cc_final: 0.7211 (tttp) REVERT: A 407 LYS cc_start: 0.8463 (mmtp) cc_final: 0.8191 (mttt) REVERT: A 413 LYS cc_start: 0.8099 (mmtm) cc_final: 0.7713 (tmtt) REVERT: B 299 THR cc_start: 0.8406 (p) cc_final: 0.8054 (p) REVERT: B 400 VAL cc_start: 0.8698 (OUTLIER) cc_final: 0.8486 (m) REVERT: D 30 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.7672 (t80) REVERT: D 86 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8240 (mp) outliers start: 48 outliers final: 34 residues processed: 159 average time/residue: 0.1959 time to fit residues: 43.1623 Evaluate side-chains 153 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 115 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.7980 chunk 20 optimal weight: 0.0770 chunk 60 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 102 optimal weight: 0.0020 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.5346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 GLN A 375 GLN D 84 ASN D 94 ASN ** D 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 144 ASN C 2 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8718 Z= 0.160 Angle : 0.581 8.551 11816 Z= 0.299 Chirality : 0.042 0.166 1339 Planarity : 0.005 0.054 1486 Dihedral : 6.069 53.825 1214 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.83 % Favored : 93.89 % Rotamer: Outliers : 4.35 % Allowed : 19.02 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.27), residues: 1081 helix: 1.62 (0.23), residues: 562 sheet: -1.88 (0.50), residues: 103 loop : -1.99 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 126 HIS 0.003 0.001 HIS B 214 PHE 0.027 0.001 PHE A 183 TYR 0.014 0.001 TYR D 83 ARG 0.004 0.000 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 126 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.6988 (pm20) REVERT: A 125 HIS cc_start: 0.7797 (OUTLIER) cc_final: 0.7456 (t-170) REVERT: A 182 MET cc_start: 0.7793 (mmm) cc_final: 0.7585 (mmt) REVERT: A 388 LYS cc_start: 0.7859 (mttm) cc_final: 0.7127 (tttp) REVERT: A 413 LYS cc_start: 0.8075 (mmtm) cc_final: 0.7740 (tmtt) REVERT: B 299 THR cc_start: 0.8333 (OUTLIER) cc_final: 0.7973 (p) REVERT: B 400 VAL cc_start: 0.8632 (OUTLIER) cc_final: 0.8387 (m) outliers start: 40 outliers final: 27 residues processed: 155 average time/residue: 0.2240 time to fit residues: 47.3628 Evaluate side-chains 145 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 114 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 234 ARG Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.3057 > 50: distance: 4 - 48: 3.519 distance: 49 - 52: 3.771 distance: 50 - 51: 3.273 distance: 50 - 59: 3.738 distance: 52 - 53: 4.845 distance: 53 - 54: 5.569 distance: 54 - 55: 5.090 distance: 55 - 56: 5.259 distance: 56 - 57: 3.003 distance: 59 - 60: 3.713 distance: 60 - 63: 3.347 distance: 61 - 62: 3.806 distance: 67 - 68: 3.907 distance: 67 - 70: 3.747 distance: 68 - 69: 4.668 distance: 70 - 71: 4.160 distance: 71 - 72: 3.057 distance: 73 - 75: 3.236 distance: 74 - 76: 3.681 distance: 78 - 81: 5.278 distance: 79 - 80: 3.863 distance: 79 - 86: 4.378 distance: 81 - 82: 4.455 distance: 83 - 84: 3.607 distance: 86 - 87: 3.033 distance: 87 - 88: 3.281 distance: 87 - 90: 3.834 distance: 88 - 89: 3.591 distance: 88 - 96: 3.807 distance: 90 - 91: 4.800 distance: 91 - 93: 6.425 distance: 92 - 94: 4.199 distance: 93 - 95: 3.593 distance: 94 - 95: 3.011 distance: 96 - 97: 3.438 distance: 97 - 100: 3.005 distance: 98 - 99: 5.530 distance: 98 - 104: 7.699 distance: 100 - 101: 5.757 distance: 101 - 102: 7.965 distance: 101 - 103: 3.823 distance: 104 - 105: 4.874 distance: 105 - 106: 4.337 distance: 105 - 108: 4.510 distance: 106 - 107: 6.640 distance: 106 - 111: 7.289 distance: 107 - 134: 5.247 distance: 108 - 109: 5.244 distance: 108 - 110: 9.048 distance: 111 - 112: 8.943 distance: 111 - 117: 14.475 distance: 112 - 113: 8.257 distance: 112 - 115: 11.588 distance: 113 - 114: 12.360 distance: 113 - 118: 17.015 distance: 114 - 142: 12.797 distance: 115 - 116: 12.597 distance: 116 - 117: 3.796 distance: 118 - 119: 21.498 distance: 119 - 120: 4.617 distance: 119 - 122: 15.209 distance: 120 - 121: 5.793 distance: 120 - 124: 7.017 distance: 122 - 123: 20.669 distance: 125 - 128: 3.272 distance: 127 - 158: 4.573 distance: 129 - 131: 4.591 distance: 132 - 133: 4.047 distance: 137 - 164: 3.440