Starting phenix.real_space_refine (version: dev) on Mon Mar 13 15:06:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk0_32554/03_2023/7wk0_32554.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk0_32554/03_2023/7wk0_32554.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk0_32554/03_2023/7wk0_32554.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk0_32554/03_2023/7wk0_32554.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk0_32554/03_2023/7wk0_32554.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk0_32554/03_2023/7wk0_32554.pdb" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.010 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 Process input model Symmetric amino acids flipped Residue "A ARG 16": "NH1" <-> "NH2" Residue "A ARG 19": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 87": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "D ARG 16": "NH1" <-> "NH2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D ARG 87": "NH1" <-> "NH2" Residue "E ARG 19": "NH1" <-> "NH2" Residue "E ARG 76": "NH1" <-> "NH2" Residue "E ARG 93": "NH1" <-> "NH2" Residue "E ARG 96": "NH1" <-> "NH2" Residue "E ARG 191": "NH1" <-> "NH2" Residue "F ARG 346": "NH1" <-> "NH2" Residue "F ARG 408": "NH1" <-> "NH2" Residue "F ARG 454": "NH1" <-> "NH2" Residue "F ARG 457": "NH1" <-> "NH2" Residue "F ARG 466": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 9724 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1699 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 214} Chain: "B" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1577 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 16, 'TRANS': 193} Chain: "C" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1572 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 183} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1699 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 214} Chain: "E" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1577 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 16, 'TRANS': 193} Chain: "F" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1572 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 183} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.68, per 1000 atoms: 0.58 Number of scatterers: 9724 At special positions: 0 Unit cell: (88.312, 155.344, 110.656, 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 34 16.00 O 1890 8.00 N 1646 7.00 C 6154 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 153 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 87 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 195 " distance=2.04 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.03 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " 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 Links applied NAG-ASN " NAG C 601 " - " ASN C 343 " " NAG F 601 " - " ASN F 343 " Time building additional restraints: 3.73 Conformation dependent library (CDL) restraints added in 1.7 seconds 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2328 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 25 sheets defined 2.2% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 87 through 91 removed outlier: 4.131A pdb=" N THR A 91 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.804A pdb=" N GLU B 126 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 127 " --> pdb=" O SER B 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 123 through 127' Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'E' and resid 78 through 82 removed outlier: 3.567A pdb=" N ASP E 81 " --> pdb=" O GLU E 78 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU E 82 " --> pdb=" O ALA E 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 78 through 82' Processing helix chain 'F' and resid 502 through 506 removed outlier: 3.798A pdb=" N GLN F 506 " --> pdb=" O VAL F 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 60 removed outlier: 5.936A pdb=" N GLY A 50 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR A 60 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL A 48 " --> pdb=" O TYR A 60 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 92 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A 94 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 120 " --> pdb=" O TYR A 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 removed outlier: 3.873A pdb=" N GLY A 152 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 163 through 166 removed outlier: 3.507A pdb=" N THR A 164 " --> pdb=" O ASN A 212 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS A 209 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS A 222 " --> pdb=" O CYS A 209 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 220 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS A 213 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 218 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 9 through 12 removed outlier: 3.868A pdb=" N VAL B 10 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR B 106 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 18 through 22 removed outlier: 3.747A pdb=" N ILE B 74 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 20 " --> pdb=" O LEU B 72 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 117 through 120 removed outlier: 3.503A pdb=" N ILE B 138 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 176 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP B 140 " --> pdb=" O TYR B 174 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TYR B 174 " --> pdb=" O ASP B 140 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 155 through 156 removed outlier: 3.752A pdb=" N THR B 147 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS B 195 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS B 206 " --> pdb=" O CYS B 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.726A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.726A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.534A pdb=" N LEU D 18 " --> pdb=" O MET D 83 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.628A pdb=" N TYR D 94 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL D 48 " --> pdb=" O TYR D 60 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N TYR D 60 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLY D 50 " --> pdb=" O ILE D 58 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 151 through 153 removed outlier: 3.533A pdb=" N LEU D 151 " --> pdb=" O VAL D 195 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER D 193 " --> pdb=" O CYS D 153 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER D 192 " --> pdb=" O PHE D 179 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 208 through 211 Processing sheet with id=AB8, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.887A pdb=" N VAL E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AC1, first strand: chain 'E' and resid 44 through 47 removed outlier: 5.626A pdb=" N LEU E 45 " --> pdb=" O GLN E 36 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLN E 36 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL E 47 " --> pdb=" O TRP E 34 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 117 through 120 removed outlier: 3.899A pdb=" N VAL E 135 " --> pdb=" O PHE E 120 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE E 138 " --> pdb=" O ALA E 176 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASP E 140 " --> pdb=" O TYR E 174 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR E 174 " --> pdb=" O ASP E 140 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 194 through 196 removed outlier: 3.674A pdb=" N CYS E 195 " --> pdb=" O LYS E 206 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS E 206 " --> pdb=" O CYS E 195 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 357 through 358 removed outlier: 4.190A pdb=" N ASN F 394 " --> pdb=" O GLU F 516 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU F 516 " --> pdb=" O ASN F 394 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA F 435 " --> pdb=" O THR F 376 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 357 through 358 removed outlier: 4.190A pdb=" N ASN F 394 " --> pdb=" O GLU F 516 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU F 516 " --> pdb=" O ASN F 394 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'F' and resid 473 through 474 183 hydrogen bonds defined for protein. 447 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: 2.59 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1593 1.31 - 1.44: 2884 1.44 - 1.56: 5469 1.56 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 9982 Sorted by residual: bond pdb=" CA LYS D 65 " pdb=" C LYS D 65 " ideal model delta sigma weight residual 1.524 1.445 0.079 1.31e-02 5.83e+03 3.62e+01 bond pdb=" N ASN C 448 " pdb=" CA ASN C 448 " ideal model delta sigma weight residual 1.455 1.397 0.059 1.25e-02 6.40e+03 2.19e+01 bond pdb=" N GLU F 406 " pdb=" CA GLU F 406 " ideal model delta sigma weight residual 1.457 1.405 0.052 1.16e-02 7.43e+03 2.02e+01 bond pdb=" C ILE C 358 " pdb=" O ILE C 358 " ideal model delta sigma weight residual 1.237 1.188 0.050 1.13e-02 7.83e+03 1.93e+01 bond pdb=" CA ASN C 354 " pdb=" C ASN C 354 " ideal model delta sigma weight residual 1.523 1.469 0.053 1.23e-02 6.61e+03 1.89e+01 ... (remaining 9977 not shown) Histogram of bond angle deviations from ideal: 100.76 - 107.41: 450 107.41 - 114.06: 5473 114.06 - 120.71: 3689 120.71 - 127.36: 3881 127.36 - 134.01: 121 Bond angle restraints: 13614 Sorted by residual: angle pdb=" N ASN C 370 " pdb=" CA ASN C 370 " pdb=" C ASN C 370 " ideal model delta sigma weight residual 114.31 104.48 9.83 1.29e+00 6.01e-01 5.81e+01 angle pdb=" N VAL F 407 " pdb=" CA VAL F 407 " pdb=" C VAL F 407 " ideal model delta sigma weight residual 111.58 104.58 7.00 1.06e+00 8.90e-01 4.36e+01 angle pdb=" N GLY D 66 " pdb=" CA GLY D 66 " pdb=" C GLY D 66 " ideal model delta sigma weight residual 115.27 107.54 7.73 1.41e+00 5.03e-01 3.00e+01 angle pdb=" N ASN C 448 " pdb=" CA ASN C 448 " pdb=" C ASN C 448 " ideal model delta sigma weight residual 109.24 101.13 8.11 1.67e+00 3.59e-01 2.36e+01 angle pdb=" N SER C 359 " pdb=" CA SER C 359 " pdb=" C SER C 359 " ideal model delta sigma weight residual 108.74 114.66 -5.92 1.38e+00 5.25e-01 1.84e+01 ... (remaining 13609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 5536 17.71 - 35.42: 304 35.42 - 53.14: 45 53.14 - 70.85: 16 70.85 - 88.56: 1 Dihedral angle restraints: 5902 sinusoidal: 2246 harmonic: 3656 Sorted by residual: dihedral pdb=" CA ARG B 191 " pdb=" C ARG B 191 " pdb=" N SER B 192 " pdb=" CA SER B 192 " ideal model delta harmonic sigma weight residual 180.00 155.96 24.04 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" N ASN C 448 " pdb=" C ASN C 448 " pdb=" CA ASN C 448 " pdb=" CB ASN C 448 " ideal model delta harmonic sigma weight residual 122.80 111.49 11.31 0 2.50e+00 1.60e-01 2.05e+01 dihedral pdb=" CA GLU A 161 " pdb=" C GLU A 161 " pdb=" N PRO A 162 " pdb=" CA PRO A 162 " ideal model delta harmonic sigma weight residual 180.00 159.66 20.34 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 5899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1322 0.071 - 0.142: 169 0.142 - 0.212: 4 0.212 - 0.283: 2 0.283 - 0.354: 1 Chirality restraints: 1498 Sorted by residual: chirality pdb=" CA LYS D 65 " pdb=" N LYS D 65 " pdb=" C LYS D 65 " pdb=" CB LYS D 65 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA ASN F 448 " pdb=" N ASN F 448 " pdb=" C ASN F 448 " pdb=" CB ASN F 448 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ALA C 372 " pdb=" N ALA C 372 " pdb=" C ALA C 372 " pdb=" CB ALA C 372 " both_signs ideal model delta sigma weight residual False 2.48 2.27 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1495 not shown) Planarity restraints: 1766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 601 " 0.257 2.00e-02 2.50e+03 2.18e-01 5.92e+02 pdb=" C7 NAG F 601 " -0.066 2.00e-02 2.50e+03 pdb=" C8 NAG F 601 " 0.169 2.00e-02 2.50e+03 pdb=" N2 NAG F 601 " -0.371 2.00e-02 2.50e+03 pdb=" O7 NAG F 601 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 400 " -0.021 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C PHE C 400 " 0.075 2.00e-02 2.50e+03 pdb=" O PHE C 400 " -0.029 2.00e-02 2.50e+03 pdb=" N VAL C 401 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP C 353 " 0.017 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C TRP C 353 " -0.058 2.00e-02 2.50e+03 pdb=" O TRP C 353 " 0.022 2.00e-02 2.50e+03 pdb=" N ASN C 354 " 0.020 2.00e-02 2.50e+03 ... (remaining 1763 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1603 2.77 - 3.30: 9290 3.30 - 3.83: 15901 3.83 - 4.37: 18585 4.37 - 4.90: 31950 Nonbonded interactions: 77329 Sorted by model distance: nonbonded pdb=" OG SER E 62 " pdb=" OG1 THR E 73 " model vdw 2.233 2.440 nonbonded pdb=" OG SER B 64 " pdb=" OG1 THR B 71 " model vdw 2.263 2.440 nonbonded pdb=" OD2 ASP C 398 " pdb=" OH TYR C 423 " model vdw 2.272 2.440 nonbonded pdb=" OD2 ASP E 91 " pdb=" OG SER E 94 " model vdw 2.278 2.440 nonbonded pdb=" OE1 GLU E 126 " pdb=" OG1 THR E 133 " model vdw 2.286 2.440 ... (remaining 77324 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 6154 2.51 5 N 1646 2.21 5 O 1890 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 7.520 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: 25.580 Check model and map are aligned: 0.000 Process input model: 27.230 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 9982 Z= 0.273 Angle : 0.655 9.922 13614 Z= 0.387 Chirality : 0.045 0.354 1498 Planarity : 0.007 0.218 1764 Dihedral : 11.039 88.559 3526 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.22 % Favored : 87.54 % Rotamer Outliers : 7.71 % 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: -4.96 (0.20), residues: 1252 helix: -5.35 (0.10), residues: 70 sheet: -2.88 (0.22), residues: 452 loop : -3.46 (0.19), residues: 730 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 237 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 35 residues processed: 296 average time/residue: 0.2330 time to fit residues: 93.6697 Evaluate side-chains 232 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 197 time to evaluate : 1.090 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.1912 time to fit residues: 10.6707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 0.0980 chunk 97 optimal weight: 0.9990 chunk 37 optimal weight: 0.0770 chunk 59 optimal weight: 0.4980 chunk 72 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN B 33 HIS B 88 GLN B 190 HIS C 409 GLN C 437 ASN C 481 ASN D 3 GLN D 118 GLN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 HIS ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN E 172 ASN F 409 GLN ** F 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 474 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 9982 Z= 0.360 Angle : 0.674 7.530 13614 Z= 0.345 Chirality : 0.047 0.224 1498 Planarity : 0.005 0.055 1764 Dihedral : 5.093 29.675 1378 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.58 % Favored : 86.42 % Rotamer Outliers : 4.04 % 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: -4.19 (0.21), residues: 1252 helix: -5.00 (0.31), residues: 56 sheet: -2.25 (0.24), residues: 414 loop : -3.05 (0.19), residues: 782 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 229 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 21 residues processed: 259 average time/residue: 0.2424 time to fit residues: 84.6529 Evaluate side-chains 231 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 210 time to evaluate : 1.093 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.0877 time to fit residues: 5.0510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 121 optimal weight: 0.2980 chunk 100 optimal weight: 0.0000 chunk 111 optimal weight: 0.3980 chunk 38 optimal weight: 0.0570 chunk 90 optimal weight: 0.4980 overall best weight: 0.2502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN A 168 ASN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 448 ASN F 450 ASN F 481 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 9982 Z= 0.228 Angle : 0.617 7.513 13614 Z= 0.313 Chirality : 0.044 0.199 1498 Planarity : 0.005 0.050 1764 Dihedral : 4.943 30.782 1378 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.76 (0.22), residues: 1252 helix: -5.00 (0.26), residues: 56 sheet: -1.86 (0.26), residues: 398 loop : -2.79 (0.20), residues: 798 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 213 time to evaluate : 1.157 Fit side-chains outliers start: 28 outliers final: 9 residues processed: 230 average time/residue: 0.2299 time to fit residues: 73.2008 Evaluate side-chains 219 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 210 time to evaluate : 1.100 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1158 time to fit residues: 3.2470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-4893/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-4893/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-4893/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-4893/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-4893/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-4893/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-4893/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-4893/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-4893/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-4893/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-4893/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: 67.4949 > 50: distance: 0 - 1: 17.631 distance: 1 - 2: 14.588 distance: 1 - 4: 7.654 distance: 2 - 12: 9.426 distance: 4 - 5: 4.542 distance: 5 - 6: 17.702 distance: 5 - 7: 21.042 distance: 6 - 8: 22.028 distance: 7 - 9: 18.265 distance: 8 - 10: 15.176 distance: 9 - 10: 25.489 distance: 10 - 11: 5.457 distance: 12 - 13: 25.741 distance: 13 - 14: 12.567 distance: 13 - 16: 40.976 distance: 14 - 15: 16.811 distance: 14 - 21: 9.566 distance: 16 - 17: 26.369 distance: 17 - 18: 6.758 distance: 18 - 19: 18.195 distance: 18 - 20: 40.307 distance: 21 - 22: 26.601 distance: 22 - 23: 21.613 distance: 22 - 25: 22.788 distance: 23 - 29: 34.010 distance: 25 - 26: 40.106 distance: 26 - 27: 51.511 distance: 26 - 28: 20.018 distance: 29 - 30: 40.834 distance: 30 - 31: 19.702 distance: 30 - 33: 30.597 distance: 31 - 32: 19.619 distance: 31 - 36: 23.363 distance: 33 - 34: 24.521 distance: 33 - 35: 26.521 distance: 36 - 37: 11.101 distance: 37 - 38: 18.915 distance: 37 - 40: 15.512 distance: 38 - 39: 4.448 distance: 38 - 45: 25.084 distance: 40 - 41: 3.080 distance: 41 - 42: 7.653 distance: 42 - 43: 9.490 distance: 42 - 44: 47.131 distance: 45 - 46: 6.660 distance: 45 - 51: 40.554 distance: 47 - 52: 19.505 distance: 49 - 50: 39.785 distance: 52 - 53: 18.320 distance: 52 - 58: 4.655 distance: 53 - 54: 55.614 distance: 53 - 56: 39.772 distance: 56 - 57: 40.000 distance: 57 - 58: 23.016 distance: 59 - 60: 9.732 distance: 60 - 61: 20.937 distance: 60 - 63: 21.527 distance: 61 - 62: 60.984 distance: 61 - 65: 8.493 distance: 63 - 64: 10.112 distance: 65 - 66: 16.394 distance: 66 - 67: 20.094 distance: 66 - 69: 39.514 distance: 67 - 72: 34.725 distance: 69 - 70: 26.056 distance: 69 - 71: 30.163