Starting phenix.real_space_refine on Mon Aug 5 00:42:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c21_16387/08_2024/8c21_16387.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c21_16387/08_2024/8c21_16387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c21_16387/08_2024/8c21_16387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c21_16387/08_2024/8c21_16387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c21_16387/08_2024/8c21_16387.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c21_16387/08_2024/8c21_16387.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.028 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 32 5.16 5 C 7918 2.51 5 N 1927 2.21 5 O 2077 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 32": "OD1" <-> "OD2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A ASP 81": "OD1" <-> "OD2" Residue "A ASP 91": "OD1" <-> "OD2" Residue "A ASP 97": "OD1" <-> "OD2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A ASP 105": "OD1" <-> "OD2" Residue "A TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "B ASP 238": "OD1" <-> "OD2" Residue "B PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C GLU 209": "OE1" <-> "OE2" Residue "C TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 327": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 11954 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 3014 Classifications: {'peptide': 365} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 344} Chain breaks: 3 Chain: "B" Number of atoms: 3033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 3033 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 346} Chain breaks: 1 Chain: "C" Number of atoms: 3033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 3033 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 346} Chain breaks: 1 Chain: "D" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2848 Classifications: {'peptide': 342} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 324} Chain breaks: 4 Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'SRO': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'SRO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.47, per 1000 atoms: 0.62 Number of scatterers: 11954 At special positions: 0 Unit cell: (89.559, 88.722, 130.572, 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 32 16.00 O 2077 8.00 N 1927 7.00 C 7918 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " 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: 4.40 Conformation dependent library (CDL) restraints added in 2.1 seconds 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2806 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 17 sheets defined 41.9% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 removed outlier: 4.741A pdb=" N ASN A 22 " --> pdb=" O HIS A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 80 Processing helix chain 'A' and resid 170 through 176 removed outlier: 3.798A pdb=" N SER A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 225 removed outlier: 4.445A pdb=" N VAL A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 244 Processing helix chain 'A' and resid 251 through 273 Processing helix chain 'A' and resid 281 through 311 removed outlier: 4.015A pdb=" N VAL A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 328 Processing helix chain 'A' and resid 422 through 462 removed outlier: 4.097A pdb=" N TRP A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 453 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 21 Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.623A pdb=" N ILE B 93 " --> pdb=" O THR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 176 Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 227 through 241 removed outlier: 3.976A pdb=" N MET B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing helix chain 'B' and resid 249 through 273 removed outlier: 3.616A pdb=" N SER B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 309 removed outlier: 3.847A pdb=" N VAL B 285 " --> pdb=" O PRO B 281 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 307 " --> pdb=" O PHE B 303 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 423 through 462 Processing helix chain 'C' and resid 11 through 20 Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.560A pdb=" N ILE C 93 " --> pdb=" O THR C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 176 removed outlier: 3.789A pdb=" N SER C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 244 removed outlier: 4.409A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Proline residue: C 230 - end of helix removed outlier: 4.035A pdb=" N CYS C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 273 removed outlier: 3.751A pdb=" N ILE C 256 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR C 272 " --> pdb=" O ILE C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 305 Processing helix chain 'C' and resid 320 through 333 removed outlier: 4.110A pdb=" N ASP C 327 " --> pdb=" O HIS C 323 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE C 329 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ALA C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 461 Processing helix chain 'D' and resid 14 through 22 removed outlier: 4.071A pdb=" N ASN D 22 " --> pdb=" O HIS D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 4.334A pdb=" N VAL D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASP D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS D 178 " --> pdb=" O VAL D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 227 Processing helix chain 'D' and resid 227 through 242 removed outlier: 3.529A pdb=" N PHE D 233 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP D 238 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 273 removed outlier: 3.997A pdb=" N ILE D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE D 268 " --> pdb=" O VAL D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 308 removed outlier: 3.960A pdb=" N TYR D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL D 288 " --> pdb=" O GLY D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 330 removed outlier: 3.698A pdb=" N HIS D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 462 removed outlier: 3.790A pdb=" N ARG D 428 " --> pdb=" O ARG D 424 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL D 429 " --> pdb=" O ASP D 425 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER D 462 " --> pdb=" O ILE D 458 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 105 removed outlier: 7.172A pdb=" N VAL A 132 " --> pdb=" O VAL A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 105 removed outlier: 7.172A pdb=" N VAL A 132 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N TYR A 61 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE A 48 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N TRP A 63 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N TYR A 46 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ARG A 65 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ILE A 44 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N TYR A 67 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N ASP A 42 " --> pdb=" O TYR A 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 99 through 100 removed outlier: 3.550A pdb=" N LEU A 99 " --> pdb=" O THR A 154 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 99 through 100 removed outlier: 3.550A pdb=" N LEU A 99 " --> pdb=" O THR A 154 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ASN A 205 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N SER A 200 " --> pdb=" O ASN A 205 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR A 207 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU A 198 " --> pdb=" O TYR A 207 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N GLU A 209 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N PHE A 196 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LYS A 211 " --> pdb=" O PRO A 194 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N TYR A 213 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL A 192 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE A 215 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 103 through 105 removed outlier: 7.386A pdb=" N VAL B 132 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 103 through 105 removed outlier: 7.386A pdb=" N VAL B 132 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TYR B 61 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ILE B 48 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N TRP B 63 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TYR B 46 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ARG B 65 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE B 44 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N TYR B 67 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ASP B 42 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N THR B 69 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 9.548A pdb=" N SER B 40 " --> pdb=" O THR B 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 100 removed outlier: 6.737A pdb=" N LYS B 211 " --> pdb=" O PRO B 194 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N TYR B 213 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL B 192 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE B 215 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 199 through 200 Processing sheet with id=AB1, first strand: chain 'C' and resid 85 through 88 removed outlier: 4.296A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TRP C 68 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL C 132 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 85 through 88 removed outlier: 4.296A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TRP C 68 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N TRP C 63 " --> pdb=" O MET C 45 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N MET C 45 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ARG C 65 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N VAL C 43 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N TYR C 67 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE C 41 " --> pdb=" O TYR C 67 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N THR C 69 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N VAL C 39 " --> pdb=" O THR C 69 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 98 through 99 Processing sheet with id=AB4, first strand: chain 'C' and resid 98 through 99 removed outlier: 6.234A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 40 through 41 removed outlier: 3.740A pdb=" N GLN D 66 " --> pdb=" O ASN D 125 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN D 125 " --> pdb=" O GLN D 66 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE D 88 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL D 117 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 86 " --> pdb=" O VAL D 117 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 44 through 51 removed outlier: 4.090A pdb=" N TYR D 61 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE D 48 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N THR D 59 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 98 through 100 Processing sheet with id=AB8, first strand: chain 'D' and resid 146 through 149 removed outlier: 3.652A pdb=" N GLN D 147 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LYS D 211 " --> pdb=" O PRO D 194 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TYR D 213 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL D 192 " --> pdb=" O TYR D 213 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE D 215 " --> pdb=" O LEU D 190 " (cutoff:3.500A) 569 hydrogen bonds defined for protein. 1650 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: 3.88 Time building geometry restraints manager: 4.86 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: 3623 1.34 - 1.46: 2113 1.46 - 1.57: 6511 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 12295 Sorted by residual: bond pdb=" CG SRO C 501 " pdb=" CD2 SRO C 501 " ideal model delta sigma weight residual 1.438 1.362 0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" CG SRO B 501 " pdb=" CD2 SRO B 501 " ideal model delta sigma weight residual 1.438 1.364 0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" N ASP D 312 " pdb=" CA ASP D 312 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.89e+00 bond pdb=" CD2 SRO B 501 " pdb=" CE2 SRO B 501 " ideal model delta sigma weight residual 1.419 1.368 0.051 2.00e-02 2.50e+03 6.61e+00 bond pdb=" CD2 SRO C 501 " pdb=" CE2 SRO C 501 " ideal model delta sigma weight residual 1.419 1.368 0.051 2.00e-02 2.50e+03 6.53e+00 ... (remaining 12290 not shown) Histogram of bond angle deviations from ideal: 99.86 - 106.70: 400 106.70 - 113.54: 6890 113.54 - 120.38: 4492 120.38 - 127.22: 4838 127.22 - 134.06: 199 Bond angle restraints: 16819 Sorted by residual: angle pdb=" N VAL A 104 " pdb=" CA VAL A 104 " pdb=" C VAL A 104 " ideal model delta sigma weight residual 111.62 108.53 3.09 7.90e-01 1.60e+00 1.53e+01 angle pdb=" C THR A 159 " pdb=" N ILE A 160 " pdb=" CA ILE A 160 " ideal model delta sigma weight residual 121.97 128.66 -6.69 1.80e+00 3.09e-01 1.38e+01 angle pdb=" CA GLN A 161 " pdb=" CB GLN A 161 " pdb=" CG GLN A 161 " ideal model delta sigma weight residual 114.10 121.21 -7.11 2.00e+00 2.50e-01 1.26e+01 angle pdb=" N LEU D 313 " pdb=" CA LEU D 313 " pdb=" C LEU D 313 " ideal model delta sigma weight residual 112.58 108.27 4.31 1.22e+00 6.72e-01 1.25e+01 angle pdb=" CB SRO B 501 " pdb=" CG SRO B 501 " pdb=" CD1 SRO B 501 " ideal model delta sigma weight residual 128.15 118.25 9.90 3.00e+00 1.11e-01 1.09e+01 ... (remaining 16814 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 6444 17.46 - 34.92: 596 34.92 - 52.38: 125 52.38 - 69.83: 18 69.83 - 87.29: 17 Dihedral angle restraints: 7200 sinusoidal: 2898 harmonic: 4302 Sorted by residual: dihedral pdb=" CB CYS B 135 " pdb=" SG CYS B 135 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 141.13 -48.13 1 1.00e+01 1.00e-02 3.19e+01 dihedral pdb=" CB CYS A 135 " pdb=" SG CYS A 135 " pdb=" SG CYS A 149 " pdb=" CB CYS A 149 " ideal model delta sinusoidal sigma weight residual 93.00 49.15 43.85 1 1.00e+01 1.00e-02 2.68e+01 dihedral pdb=" CB CYS C 135 " pdb=" SG CYS C 135 " pdb=" SG CYS C 149 " pdb=" CB CYS C 149 " ideal model delta sinusoidal sigma weight residual 93.00 58.32 34.68 1 1.00e+01 1.00e-02 1.71e+01 ... (remaining 7197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1299 0.036 - 0.073: 469 0.073 - 0.109: 127 0.109 - 0.145: 61 0.145 - 0.182: 2 Chirality restraints: 1958 Sorted by residual: chirality pdb=" CB ILE D 160 " pdb=" CA ILE D 160 " pdb=" CG1 ILE D 160 " pdb=" CG2 ILE D 160 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.24e-01 chirality pdb=" CA VAL C 305 " pdb=" N VAL C 305 " pdb=" C VAL C 305 " pdb=" CB VAL C 305 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA VAL D 104 " pdb=" N VAL D 104 " pdb=" C VAL D 104 " pdb=" CB VAL D 104 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 1955 not shown) Planarity restraints: 2047 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 170 " -0.036 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO A 171 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 171 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 171 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 317 " 0.032 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO C 318 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 318 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 318 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 160 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.42e+00 pdb=" C ILE A 160 " 0.032 2.00e-02 2.50e+03 pdb=" O ILE A 160 " -0.012 2.00e-02 2.50e+03 pdb=" N GLN A 161 " -0.011 2.00e-02 2.50e+03 ... (remaining 2044 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1740 2.76 - 3.29: 11666 3.29 - 3.83: 20126 3.83 - 4.36: 22856 4.36 - 4.90: 40360 Nonbonded interactions: 96748 Sorted by model distance: nonbonded pdb=" OH TYR C 114 " pdb=" O LYS D 25 " model vdw 2.223 3.040 nonbonded pdb=" OG1 THR B 154 " pdb=" O ALA B 208 " model vdw 2.226 3.040 nonbonded pdb=" OE1 GLN C 124 " pdb=" OH TYR C 126 " model vdw 2.256 3.040 nonbonded pdb=" OD2 ASP D 434 " pdb=" NH2 ARG D 435 " model vdw 2.266 3.120 nonbonded pdb=" OE2 GLU B 122 " pdb=" NE2 GLN B 124 " model vdw 2.289 3.120 ... (remaining 96743 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 75 or resid 85 through 105 or resid 113 through \ 181 or resid 186 through 332 or resid 422 through 462)) selection = (chain 'B' and (resid 13 through 75 or resid 85 through 105 or resid 113 through \ 181 or resid 186 through 311 or resid 313 or resid 316 through 332 or resid 422 \ through 462)) selection = (chain 'C' and (resid 13 through 75 or resid 85 through 105 or resid 113 through \ 181 or resid 186 through 311 or resid 313 or resid 316 through 332 or resid 422 \ through 462)) selection = (chain 'D' and (resid 13 through 311 or resid 313 or resid 316 through 332 or re \ sid 422 through 462)) } 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=0.00 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: 2.430 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 35.200 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 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 : 0.003 0.076 12295 Z= 0.193 Angle : 0.576 9.900 16819 Z= 0.296 Chirality : 0.043 0.182 1958 Planarity : 0.004 0.055 2047 Dihedral : 14.613 87.293 4382 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.23 % Favored : 94.35 % Rotamer: Outliers : 0.07 % Allowed : 0.74 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % 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: -0.00 (0.23), residues: 1416 helix: 2.06 (0.22), residues: 529 sheet: -1.13 (0.30), residues: 312 loop : -1.30 (0.27), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 459 HIS 0.008 0.001 HIS D 323 PHE 0.013 0.001 PHE B 254 TYR 0.019 0.001 TYR A 116 ARG 0.007 0.000 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 385 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 THR cc_start: 0.7451 (p) cc_final: 0.7194 (p) REVERT: C 162 ASP cc_start: 0.5449 (m-30) cc_final: 0.5204 (m-30) outliers start: 1 outliers final: 0 residues processed: 386 average time/residue: 0.2108 time to fit residues: 118.6270 Evaluate side-chains 262 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- 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: 70.0544 > 50: distance: 2 - 19: 13.490 distance: 6 - 26: 27.808 distance: 10 - 34: 28.353 distance: 14 - 19: 12.883 distance: 15 - 42: 22.949 distance: 19 - 20: 33.933 distance: 20 - 21: 40.708 distance: 20 - 23: 8.263 distance: 21 - 22: 33.639 distance: 21 - 26: 48.345 distance: 22 - 49: 21.084 distance: 23 - 24: 26.972 distance: 23 - 25: 15.259 distance: 26 - 27: 32.010 distance: 27 - 28: 17.944 distance: 27 - 30: 27.184 distance: 28 - 29: 21.075 distance: 28 - 34: 17.946 distance: 30 - 31: 15.608 distance: 31 - 32: 21.821 distance: 34 - 35: 36.400 distance: 35 - 36: 12.046 distance: 35 - 38: 5.270 distance: 36 - 37: 9.523 distance: 36 - 42: 16.477 distance: 38 - 39: 39.873 distance: 42 - 43: 29.040 distance: 43 - 44: 25.898 distance: 43 - 46: 45.756 distance: 44 - 45: 44.661 distance: 44 - 49: 21.181 distance: 46 - 47: 39.678 distance: 49 - 50: 30.333 distance: 50 - 51: 47.878 distance: 51 - 52: 20.937 distance: 53 - 54: 25.512 distance: 54 - 55: 55.427 distance: 54 - 57: 20.604 distance: 55 - 56: 16.977 distance: 55 - 64: 13.138 distance: 57 - 58: 8.178 distance: 58 - 59: 40.626 distance: 58 - 60: 35.551 distance: 60 - 62: 7.015 distance: 62 - 63: 51.002 distance: 64 - 65: 13.310 distance: 65 - 66: 31.626 distance: 65 - 68: 51.822 distance: 66 - 70: 40.349 distance: 68 - 69: 26.405 distance: 70 - 71: 40.476 distance: 71 - 72: 32.487 distance: 71 - 74: 14.885 distance: 72 - 73: 19.205 distance: 72 - 78: 28.416 distance: 74 - 75: 41.612 distance: 75 - 76: 34.261 distance: 75 - 77: 39.272 distance: 78 - 79: 26.514 distance: 78 - 84: 28.989 distance: 79 - 80: 36.764 distance: 79 - 82: 11.403 distance: 80 - 81: 32.626 distance: 80 - 85: 40.140 distance: 82 - 83: 18.663 distance: 83 - 84: 18.215 distance: 85 - 86: 5.676 distance: 85 - 91: 48.149 distance: 86 - 87: 3.267 distance: 86 - 89: 40.163 distance: 87 - 92: 34.819 distance: 89 - 90: 27.445 distance: 90 - 91: 12.576