Starting phenix.real_space_refine on Mon Aug 5 20:30:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a3b_15110/08_2024/8a3b_15110.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a3b_15110/08_2024/8a3b_15110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a3b_15110/08_2024/8a3b_15110.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a3b_15110/08_2024/8a3b_15110.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a3b_15110/08_2024/8a3b_15110.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a3b_15110/08_2024/8a3b_15110.cif" } resolution = 3.1 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= 0.002 sd= 0.029 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 84 5.16 5 C 9646 2.51 5 N 2219 2.21 5 O 2499 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 340": "OE1" <-> "OE2" Residue "B GLU 336": "OE1" <-> "OE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C GLU 336": "OE1" <-> "OE2" Residue "D GLU 31": "OE1" <-> "OE2" Residue "D GLU 335": "OE1" <-> "OE2" Residue "E GLU 31": "OE1" <-> "OE2" Residue "F GLU 335": "OE1" <-> "OE2" Residue "G GLU 335": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 14448 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2064 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain breaks: 2 Chain: "B" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2064 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain breaks: 2 Chain: "C" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2064 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain breaks: 2 Chain: "D" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2064 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain breaks: 2 Chain: "E" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2064 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain breaks: 2 Chain: "F" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2064 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain breaks: 2 Chain: "G" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2064 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain breaks: 2 Time building chain proxies: 8.54, per 1000 atoms: 0.59 Number of scatterers: 14448 At special positions: 0 Unit cell: (106.869, 105.778, 109.05, 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 84 16.00 O 2499 8.00 N 2219 7.00 C 9646 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=0, symmetry=0 Time building additional restraints: 6.15 Conformation dependent library (CDL) restraints added in 2.8 seconds 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3500 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 7 sheets defined 79.1% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 32 through 61 Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 73 through 87 Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 99 through 108 removed outlier: 4.059A pdb=" N LEU A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 108 " --> pdb=" O TRP A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 130 Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 146 Processing helix chain 'A' and resid 196 through 205 Processing helix chain 'A' and resid 207 through 236 Processing helix chain 'A' and resid 237 through 240 Processing helix chain 'A' and resid 249 through 253 removed outlier: 3.971A pdb=" N LEU A 252 " --> pdb=" O SER A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 295 Proline residue: A 288 - end of helix removed outlier: 3.616A pdb=" N PHE A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 338 removed outlier: 3.507A pdb=" N LEU A 329 " --> pdb=" O ASN A 325 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 332 " --> pdb=" O SER A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 349 Processing helix chain 'B' and resid 32 through 61 Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 73 through 87 Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 99 through 108 removed outlier: 4.030A pdb=" N LEU B 103 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE B 108 " --> pdb=" O TRP B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 131 Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 146 Processing helix chain 'B' and resid 196 through 204 Processing helix chain 'B' and resid 206 through 236 Processing helix chain 'B' and resid 237 through 240 Processing helix chain 'B' and resid 249 through 255 removed outlier: 3.926A pdb=" N LEU B 252 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN B 254 " --> pdb=" O VAL B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 295 Proline residue: B 288 - end of helix removed outlier: 3.609A pdb=" N PHE B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE B 295 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'B' and resid 325 through 338 removed outlier: 3.698A pdb=" N LEU B 329 " --> pdb=" O ASN B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 349 removed outlier: 3.528A pdb=" N LYS B 345 " --> pdb=" O LEU B 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 61 Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 73 through 88 Processing helix chain 'C' and resid 99 through 108 removed outlier: 4.104A pdb=" N LEU C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS C 107 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE C 108 " --> pdb=" O TRP C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 131 Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 146 Processing helix chain 'C' and resid 196 through 205 removed outlier: 3.546A pdb=" N ASN C 204 " --> pdb=" O LYS C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 236 removed outlier: 3.534A pdb=" N LYS C 211 " --> pdb=" O HIS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 240 Processing helix chain 'C' and resid 249 through 255 removed outlier: 3.530A pdb=" N LEU C 252 " --> pdb=" O SER C 249 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN C 254 " --> pdb=" O VAL C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 295 removed outlier: 3.552A pdb=" N LEU C 274 " --> pdb=" O GLY C 270 " (cutoff:3.500A) Proline residue: C 288 - end of helix removed outlier: 3.573A pdb=" N PHE C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE C 295 " --> pdb=" O VAL C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 338 removed outlier: 3.660A pdb=" N LEU C 329 " --> pdb=" O ASN C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 349 removed outlier: 3.602A pdb=" N LYS C 345 " --> pdb=" O LEU C 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 61 Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 73 through 87 Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'D' and resid 99 through 108 removed outlier: 4.111A pdb=" N LEU D 103 " --> pdb=" O GLY D 99 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE D 108 " --> pdb=" O TRP D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 131 Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 147 Processing helix chain 'D' and resid 196 through 204 Processing helix chain 'D' and resid 206 through 236 removed outlier: 3.745A pdb=" N LYS D 211 " --> pdb=" O HIS D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 240 Processing helix chain 'D' and resid 249 through 255 removed outlier: 4.029A pdb=" N LEU D 252 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN D 254 " --> pdb=" O VAL D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 295 removed outlier: 3.666A pdb=" N LEU D 274 " --> pdb=" O GLY D 270 " (cutoff:3.500A) Proline residue: D 288 - end of helix removed outlier: 3.647A pdb=" N PHE D 294 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE D 295 " --> pdb=" O VAL D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 300 removed outlier: 3.829A pdb=" N GLN D 300 " --> pdb=" O ILE D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 338 removed outlier: 3.896A pdb=" N LEU D 329 " --> pdb=" O ASN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 349 Processing helix chain 'E' and resid 32 through 61 Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 73 through 87 Processing helix chain 'E' and resid 99 through 131 removed outlier: 4.082A pdb=" N LEU E 103 " --> pdb=" O GLY E 99 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS E 107 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE E 108 " --> pdb=" O TRP E 104 " (cutoff:3.500A) Proline residue: E 110 - end of helix Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 146 Processing helix chain 'E' and resid 196 through 204 Processing helix chain 'E' and resid 207 through 236 Processing helix chain 'E' and resid 237 through 240 Processing helix chain 'E' and resid 249 through 255 removed outlier: 3.924A pdb=" N LEU E 252 " --> pdb=" O SER E 249 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN E 254 " --> pdb=" O VAL E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 295 removed outlier: 3.654A pdb=" N LEU E 274 " --> pdb=" O GLY E 270 " (cutoff:3.500A) Proline residue: E 288 - end of helix removed outlier: 3.571A pdb=" N PHE E 294 " --> pdb=" O VAL E 290 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE E 295 " --> pdb=" O VAL E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 300 Processing helix chain 'E' and resid 325 through 338 removed outlier: 3.727A pdb=" N LEU E 329 " --> pdb=" O ASN E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 349 removed outlier: 3.543A pdb=" N LYS E 345 " --> pdb=" O LEU E 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 61 Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 73 through 87 Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'F' and resid 99 through 108 removed outlier: 4.310A pdb=" N LEU F 103 " --> pdb=" O GLY F 99 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE F 108 " --> pdb=" O TRP F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 146 Proline residue: F 123 - end of helix removed outlier: 4.234A pdb=" N ALA F 132 " --> pdb=" O ARG F 128 " (cutoff:3.500A) Proline residue: F 133 - end of helix Processing helix chain 'F' and resid 196 through 205 Processing helix chain 'F' and resid 206 through 236 removed outlier: 3.567A pdb=" N MET F 210 " --> pdb=" O SER F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 240 Processing helix chain 'F' and resid 249 through 255 removed outlier: 3.843A pdb=" N LEU F 252 " --> pdb=" O SER F 249 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASN F 254 " --> pdb=" O VAL F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 295 removed outlier: 3.635A pdb=" N LEU F 274 " --> pdb=" O GLY F 270 " (cutoff:3.500A) Proline residue: F 288 - end of helix removed outlier: 3.633A pdb=" N PHE F 294 " --> pdb=" O VAL F 290 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE F 295 " --> pdb=" O VAL F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 300 Processing helix chain 'F' and resid 325 through 338 removed outlier: 3.539A pdb=" N LEU F 329 " --> pdb=" O ASN F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 349 Processing helix chain 'G' and resid 32 through 61 Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 73 through 87 Processing helix chain 'G' and resid 99 through 108 removed outlier: 3.980A pdb=" N LEU G 103 " --> pdb=" O GLY G 99 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS G 107 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE G 108 " --> pdb=" O TRP G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 131 Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 146 Processing helix chain 'G' and resid 196 through 205 Processing helix chain 'G' and resid 206 through 236 removed outlier: 3.612A pdb=" N MET G 210 " --> pdb=" O SER G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 240 Processing helix chain 'G' and resid 249 through 253 removed outlier: 3.965A pdb=" N LEU G 252 " --> pdb=" O SER G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 295 removed outlier: 3.539A pdb=" N LEU G 274 " --> pdb=" O GLY G 270 " (cutoff:3.500A) Proline residue: G 288 - end of helix removed outlier: 3.520A pdb=" N PHE G 294 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE G 295 " --> pdb=" O VAL G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 300 removed outlier: 3.767A pdb=" N GLN G 300 " --> pdb=" O PRO G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 338 removed outlier: 3.531A pdb=" N LEU G 329 " --> pdb=" O ASN G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 341 through 349 removed outlier: 3.632A pdb=" N LYS G 345 " --> pdb=" O LEU G 341 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 67 removed outlier: 4.332A pdb=" N GLN A 263 " --> pdb=" O PHE A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 67 removed outlier: 4.320A pdb=" N GLN B 263 " --> pdb=" O PHE B 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 67 removed outlier: 4.343A pdb=" N GLN E 263 " --> pdb=" O PHE E 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 67 removed outlier: 4.476A pdb=" N GLN G 263 " --> pdb=" O PHE G 67 " (cutoff:3.500A) 991 hydrogen bonds defined for protein. 2892 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: 4.28 Time building geometry restraints manager: 6.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4221 1.34 - 1.46: 3513 1.46 - 1.58: 6952 1.58 - 1.69: 0 1.69 - 1.81: 105 Bond restraints: 14791 Sorted by residual: bond pdb=" N HIS G 134 " pdb=" CA HIS G 134 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.28e-02 6.10e+03 5.55e+00 bond pdb=" N LEU C 28 " pdb=" CA LEU C 28 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.34e+00 bond pdb=" N LEU A 28 " pdb=" CA LEU A 28 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" N LEU B 28 " pdb=" CA LEU B 28 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N LEU G 28 " pdb=" CA LEU G 28 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 ... (remaining 14786 not shown) Histogram of bond angle deviations from ideal: 100.45 - 107.18: 339 107.18 - 113.91: 8562 113.91 - 120.64: 6486 120.64 - 127.38: 4520 127.38 - 134.11: 141 Bond angle restraints: 20048 Sorted by residual: angle pdb=" C ILE E 287 " pdb=" CA ILE E 287 " pdb=" CB ILE E 287 " ideal model delta sigma weight residual 113.70 110.12 3.58 9.50e-01 1.11e+00 1.42e+01 angle pdb=" C PHE B 295 " pdb=" N ILE B 296 " pdb=" CA ILE B 296 " ideal model delta sigma weight residual 120.24 122.45 -2.21 6.30e-01 2.52e+00 1.23e+01 angle pdb=" C PHE D 295 " pdb=" N ILE D 296 " pdb=" CA ILE D 296 " ideal model delta sigma weight residual 120.24 122.36 -2.12 6.30e-01 2.52e+00 1.14e+01 angle pdb=" N LYS G 148 " pdb=" CA LYS G 148 " pdb=" C LYS G 148 " ideal model delta sigma weight residual 113.43 109.36 4.07 1.26e+00 6.30e-01 1.04e+01 angle pdb=" N ALA A 131 " pdb=" CA ALA A 131 " pdb=" CB ALA A 131 " ideal model delta sigma weight residual 114.17 110.52 3.65 1.14e+00 7.69e-01 1.03e+01 ... (remaining 20043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.40: 7899 16.40 - 32.79: 671 32.79 - 49.19: 154 49.19 - 65.59: 51 65.59 - 81.99: 24 Dihedral angle restraints: 8799 sinusoidal: 3437 harmonic: 5362 Sorted by residual: dihedral pdb=" CA GLU C 145 " pdb=" C GLU C 145 " pdb=" N LEU C 146 " pdb=" CA LEU C 146 " ideal model delta harmonic sigma weight residual 180.00 161.28 18.72 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA GLU E 145 " pdb=" C GLU E 145 " pdb=" N LEU E 146 " pdb=" CA LEU E 146 " ideal model delta harmonic sigma weight residual 180.00 161.49 18.51 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA GLU F 145 " pdb=" C GLU F 145 " pdb=" N LEU F 146 " pdb=" CA LEU F 146 " ideal model delta harmonic sigma weight residual 180.00 161.87 18.13 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 8796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1693 0.029 - 0.058: 427 0.058 - 0.087: 185 0.087 - 0.117: 58 0.117 - 0.146: 10 Chirality restraints: 2373 Sorted by residual: chirality pdb=" CA ILE C 258 " pdb=" N ILE C 258 " pdb=" C ILE C 258 " pdb=" CB ILE C 258 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA LEU F 28 " pdb=" N LEU F 28 " pdb=" C LEU F 28 " pdb=" CB LEU F 28 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA ILE A 258 " pdb=" N ILE A 258 " pdb=" C ILE A 258 " pdb=" CB ILE A 258 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 2370 not shown) Planarity restraints: 2394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 74 " 0.003 2.00e-02 2.50e+03 8.20e-03 1.68e+00 pdb=" CG TRP A 74 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP A 74 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 74 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 74 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 74 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP A 74 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 74 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 74 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 74 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 128 " -0.104 9.50e-02 1.11e+02 4.70e-02 1.58e+00 pdb=" NE ARG A 128 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 128 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 128 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 128 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 333 " 0.009 2.00e-02 2.50e+03 9.07e-03 1.44e+00 pdb=" CG PHE B 333 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE B 333 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 333 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 333 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 333 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 333 " 0.001 2.00e-02 2.50e+03 ... (remaining 2391 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 120 2.65 - 3.21: 13993 3.21 - 3.78: 22510 3.78 - 4.34: 30452 4.34 - 4.90: 51494 Nonbonded interactions: 118569 Sorted by model distance: nonbonded pdb=" OD1 ASP G 147 " pdb=" OG SER G 343 " model vdw 2.091 3.040 nonbonded pdb=" OD1 ASP B 147 " pdb=" OG SER B 343 " model vdw 2.129 3.040 nonbonded pdb=" O TYR F 232 " pdb=" OG SER F 235 " model vdw 2.195 3.040 nonbonded pdb=" O TYR G 232 " pdb=" OG SER G 235 " model vdw 2.258 3.040 nonbonded pdb=" O TYR E 232 " pdb=" OG SER E 235 " model vdw 2.259 3.040 ... (remaining 118564 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 1.190 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: 0.600 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 41.720 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 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 0.035 14791 Z= 0.166 Angle : 0.546 6.661 20048 Z= 0.333 Chirality : 0.034 0.146 2373 Planarity : 0.003 0.047 2394 Dihedral : 14.171 81.986 5299 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: 2.21 (0.20), residues: 1750 helix: 2.26 (0.14), residues: 1288 sheet: None (None), residues: 0 loop : -0.87 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 74 HIS 0.004 0.001 HIS G 134 PHE 0.020 0.001 PHE B 333 TYR 0.011 0.001 TYR B 111 ARG 0.008 0.001 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 449 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8616 (tp) cc_final: 0.8160 (tp) REVERT: A 50 ILE cc_start: 0.8141 (mt) cc_final: 0.7926 (tt) REVERT: A 51 SER cc_start: 0.7780 (m) cc_final: 0.7529 (p) REVERT: A 65 SER cc_start: 0.8337 (p) cc_final: 0.8082 (m) REVERT: A 83 TYR cc_start: 0.7661 (t80) cc_final: 0.7449 (t80) REVERT: A 118 ILE cc_start: 0.8312 (mm) cc_final: 0.8095 (mm) REVERT: A 233 TYR cc_start: 0.8254 (t80) cc_final: 0.7817 (t80) REVERT: B 36 LYS cc_start: 0.8330 (tppt) cc_final: 0.7907 (tppt) REVERT: B 48 LEU cc_start: 0.8583 (tp) cc_final: 0.8216 (tp) REVERT: B 203 LYS cc_start: 0.7902 (ttpt) cc_final: 0.7525 (ttpt) REVERT: B 224 LEU cc_start: 0.8201 (tp) cc_final: 0.7893 (tp) REVERT: B 234 PHE cc_start: 0.8579 (t80) cc_final: 0.8290 (t80) REVERT: B 349 VAL cc_start: 0.6444 (t) cc_final: 0.6108 (m) REVERT: C 36 LYS cc_start: 0.8430 (tmtt) cc_final: 0.7844 (tmtt) REVERT: C 48 LEU cc_start: 0.8599 (tp) cc_final: 0.8226 (tp) REVERT: C 51 SER cc_start: 0.8097 (m) cc_final: 0.7852 (p) REVERT: C 198 TYR cc_start: 0.7460 (t80) cc_final: 0.7227 (t80) REVERT: C 221 VAL cc_start: 0.8457 (t) cc_final: 0.8121 (p) REVERT: C 234 PHE cc_start: 0.8524 (t80) cc_final: 0.8213 (t80) REVERT: D 36 LYS cc_start: 0.8370 (tmtt) cc_final: 0.7783 (tmtt) REVERT: D 37 MET cc_start: 0.6877 (tpt) cc_final: 0.6580 (tpt) REVERT: D 89 GLN cc_start: 0.7760 (mt0) cc_final: 0.7126 (mt0) REVERT: D 104 TRP cc_start: 0.6781 (t-100) cc_final: 0.6504 (t-100) REVERT: D 203 LYS cc_start: 0.8235 (tmmt) cc_final: 0.7732 (tmmt) REVERT: D 221 VAL cc_start: 0.8207 (t) cc_final: 0.7975 (t) REVERT: E 51 SER cc_start: 0.7832 (m) cc_final: 0.7621 (p) REVERT: E 108 PHE cc_start: 0.8324 (m-80) cc_final: 0.7947 (m-80) REVERT: E 148 LYS cc_start: 0.6983 (mtpt) cc_final: 0.6747 (mtmt) REVERT: E 203 LYS cc_start: 0.8023 (tmmt) cc_final: 0.7809 (tmmt) REVERT: E 232 TYR cc_start: 0.7707 (t80) cc_final: 0.7357 (t80) REVERT: F 36 LYS cc_start: 0.8411 (tmtt) cc_final: 0.8076 (tmtt) REVERT: G 47 LEU cc_start: 0.8431 (mt) cc_final: 0.8159 (mp) REVERT: G 48 LEU cc_start: 0.8575 (tp) cc_final: 0.8055 (tp) REVERT: G 50 ILE cc_start: 0.8137 (mt) cc_final: 0.7876 (tt) REVERT: G 202 LYS cc_start: 0.7365 (mmtt) cc_final: 0.7109 (mmtt) REVERT: G 203 LYS cc_start: 0.7711 (tttt) cc_final: 0.7490 (tttt) outliers start: 0 outliers final: 0 residues processed: 449 average time/residue: 0.2684 time to fit residues: 173.2883 Evaluate side-chains 377 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 377 time to evaluate : 1.776 ------------------------------------------------------------------------------- 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: 51.5912 > 50: distance: 102 - 121: 9.888 distance: 107 - 132: 10.769 distance: 115 - 121: 10.152 distance: 116 - 149: 21.792 distance: 121 - 122: 15.244 distance: 122 - 123: 15.520 distance: 122 - 125: 15.975 distance: 123 - 124: 14.932 distance: 123 - 132: 11.544 distance: 124 - 157: 22.853 distance: 125 - 126: 3.668 distance: 126 - 127: 5.686 distance: 126 - 128: 3.925 distance: 127 - 129: 6.867 distance: 128 - 130: 9.673 distance: 129 - 131: 6.407 distance: 130 - 131: 4.542 distance: 132 - 133: 19.698 distance: 133 - 134: 13.456 distance: 133 - 136: 19.367 distance: 134 - 135: 17.536 distance: 134 - 141: 28.441 distance: 135 - 163: 25.957 distance: 136 - 137: 10.261 distance: 137 - 138: 6.840 distance: 138 - 139: 13.211 distance: 138 - 140: 10.631 distance: 141 - 142: 40.448 distance: 142 - 143: 18.875 distance: 142 - 145: 16.632 distance: 143 - 144: 6.332 distance: 143 - 149: 7.454 distance: 144 - 171: 16.634 distance: 145 - 146: 21.221 distance: 146 - 147: 17.020 distance: 146 - 148: 19.042 distance: 149 - 150: 13.756 distance: 150 - 151: 11.163 distance: 150 - 153: 3.056 distance: 151 - 152: 14.566 distance: 151 - 157: 20.038 distance: 152 - 179: 13.658 distance: 153 - 154: 7.354 distance: 154 - 155: 11.583 distance: 154 - 156: 18.756 distance: 157 - 158: 18.599 distance: 158 - 159: 11.697 distance: 158 - 161: 10.027 distance: 159 - 160: 3.740 distance: 159 - 163: 10.814 distance: 160 - 187: 13.461 distance: 161 - 162: 12.728 distance: 163 - 164: 5.568 distance: 164 - 165: 6.924 distance: 164 - 167: 19.412 distance: 165 - 166: 5.974 distance: 165 - 171: 8.178 distance: 166 - 195: 10.910 distance: 167 - 168: 20.110 distance: 168 - 169: 23.067 distance: 168 - 170: 17.587 distance: 171 - 172: 9.369 distance: 172 - 173: 6.960 distance: 172 - 175: 8.415 distance: 173 - 174: 7.207 distance: 173 - 179: 5.251 distance: 174 - 203: 11.753 distance: 175 - 176: 9.147 distance: 175 - 177: 5.513 distance: 176 - 178: 11.831 distance: 179 - 180: 6.641 distance: 180 - 181: 13.028 distance: 180 - 183: 7.734 distance: 181 - 182: 11.170 distance: 181 - 187: 8.215 distance: 182 - 210: 18.161 distance: 183 - 184: 5.471 distance: 184 - 185: 7.225 distance: 184 - 186: 15.201 distance: 187 - 188: 9.046 distance: 188 - 189: 7.656 distance: 188 - 191: 8.382 distance: 189 - 190: 12.251 distance: 189 - 195: 12.223 distance: 190 - 222: 16.911 distance: 191 - 192: 21.627 distance: 192 - 193: 15.436 distance: 192 - 194: 23.260 distance: 195 - 196: 21.016 distance: 196 - 197: 10.159 distance: 196 - 199: 18.288 distance: 197 - 198: 11.291 distance: 197 - 203: 6.114 distance: 198 - 227: 13.171 distance: 199 - 200: 11.475 distance: 199 - 201: 10.223 distance: 200 - 202: 17.890