Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 10 18:47:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdm_31923/08_2023/7vdm_31923_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdm_31923/08_2023/7vdm_31923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdm_31923/08_2023/7vdm_31923.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdm_31923/08_2023/7vdm_31923.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdm_31923/08_2023/7vdm_31923_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdm_31923/08_2023/7vdm_31923_updated.pdb" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 63 5.16 5 C 5486 2.51 5 N 1438 2.21 5 O 1576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A GLU 25": "OE1" <-> "OE2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "G ASP 48": "OD1" <-> "OD2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "S PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 148": "NH1" <-> "NH2" Residue "S PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 222": "OE1" <-> "OE2" Residue "S PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 60": "NH1" <-> "NH2" Residue "R PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 138": "NH1" <-> "NH2" Residue "R ARG 140": "NH1" <-> "NH2" Residue "R PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 176": "OD1" <-> "OD2" Residue "R PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 208": "NH1" <-> "NH2" Residue "R ARG 214": "NH1" <-> "NH2" Residue "R ARG 220": "NH1" <-> "NH2" Residue "R TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 1": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 8563 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1744 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2590 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 415 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1749 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 2010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2010 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 8, 'TRANS': 244} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 27 Classifications: {'peptide': 3} Link IDs: {'PTRANS': 1, 'TRANS': 1} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.67, per 1000 atoms: 0.55 Number of scatterers: 8563 At special positions: 0 Unit cell: (118.56, 108.16, 109.2, 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 63 16.00 O 1576 8.00 N 1438 7.00 C 5486 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.06 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 1.2 seconds 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2038 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 12 sheets defined 31.5% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 7 through 27 removed outlier: 4.003A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 272 through 278 removed outlier: 3.784A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 310 removed outlier: 3.570A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.906A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 30 through 42 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'R' and resid 33 through 56 Processing helix chain 'R' and resid 65 through 94 removed outlier: 3.982A pdb=" N LEU R 77 " --> pdb=" O GLY R 73 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE R 78 " --> pdb=" O ALA R 74 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASN R 92 " --> pdb=" O VAL R 88 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE R 93 " --> pdb=" O TYR R 89 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 132 removed outlier: 4.056A pdb=" N LEU R 120 " --> pdb=" O GLY R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 139 Processing helix chain 'R' and resid 145 through 168 Processing helix chain 'R' and resid 180 through 211 Processing helix chain 'R' and resid 218 through 234 Processing helix chain 'R' and resid 239 through 242 No H-bonds generated for 'chain 'R' and resid 239 through 242' Processing helix chain 'R' and resid 246 through 249 No H-bonds generated for 'chain 'R' and resid 246 through 249' Processing helix chain 'R' and resid 260 through 280 Proline residue: R 276 - end of helix removed outlier: 3.530A pdb=" N TYR R 279 " --> pdb=" O ASN R 275 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.718A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.004A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.811A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.553A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 220 through 223 removed outlier: 4.167A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.745A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.561A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.790A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.505A pdb=" N THR S 78 " --> pdb=" O ASP S 73 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.732A pdb=" N GLY S 10 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 128 through 130 removed outlier: 3.532A pdb=" N THR S 201 " --> pdb=" O SER S 194 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.596A pdb=" N LYS S 232 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR S 216 " --> pdb=" O PHE S 165 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 373 hydrogen bonds defined for protein. 1080 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: 2.56 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 2712 1.35 - 1.48: 2341 1.48 - 1.61: 3611 1.61 - 1.75: 1 1.75 - 1.88: 87 Bond restraints: 8752 Sorted by residual: bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.668 -0.133 2.00e-02 2.50e+03 4.44e+01 bond pdb=" C HIS R 261 " pdb=" N PRO R 262 " ideal model delta sigma weight residual 1.336 1.393 -0.057 1.20e-02 6.94e+03 2.28e+01 bond pdb=" CG LEU B 79 " pdb=" CD2 LEU B 79 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.54e+00 bond pdb=" CG LEU B 146 " pdb=" CD1 LEU B 146 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 5.96e+00 bond pdb=" C13 CLR R 401 " pdb=" C17 CLR R 401 " ideal model delta sigma weight residual 1.550 1.598 -0.048 2.00e-02 2.50e+03 5.79e+00 ... (remaining 8747 not shown) Histogram of bond angle deviations from ideal: 93.90 - 102.77: 47 102.77 - 111.63: 3688 111.63 - 120.50: 4791 120.50 - 129.37: 3260 129.37 - 138.23: 79 Bond angle restraints: 11865 Sorted by residual: angle pdb=" CA LEU R 237 " pdb=" CB LEU R 237 " pdb=" CG LEU R 237 " ideal model delta sigma weight residual 116.30 138.23 -21.93 3.50e+00 8.16e-02 3.93e+01 angle pdb=" C ARG L 1 " pdb=" N PRO L 2 " pdb=" CA PRO L 2 " ideal model delta sigma weight residual 119.84 127.32 -7.48 1.25e+00 6.40e-01 3.58e+01 angle pdb=" CA LEU R 45 " pdb=" CB LEU R 45 " pdb=" CG LEU R 45 " ideal model delta sigma weight residual 116.30 135.77 -19.47 3.50e+00 8.16e-02 3.09e+01 angle pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta sigma weight residual 121.54 132.11 -10.57 1.91e+00 2.74e-01 3.06e+01 angle pdb=" N THR B 143 " pdb=" CA THR B 143 " pdb=" C THR B 143 " ideal model delta sigma weight residual 112.47 118.75 -6.28 1.24e+00 6.50e-01 2.56e+01 ... (remaining 11860 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 4683 17.86 - 35.72: 387 35.72 - 53.57: 49 53.57 - 71.43: 15 71.43 - 89.29: 5 Dihedral angle restraints: 5139 sinusoidal: 1979 harmonic: 3160 Sorted by residual: dihedral pdb=" CA LEU R 237 " pdb=" C LEU R 237 " pdb=" N PRO R 238 " pdb=" CA PRO R 238 " ideal model delta harmonic sigma weight residual 180.00 140.63 39.37 0 5.00e+00 4.00e-02 6.20e+01 dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 162.18 -69.18 1 1.00e+01 1.00e-02 6.19e+01 dihedral pdb=" CA LEU A 268 " pdb=" C LEU A 268 " pdb=" N ASN A 269 " pdb=" CA ASN A 269 " ideal model delta harmonic sigma weight residual -180.00 -144.58 -35.42 0 5.00e+00 4.00e-02 5.02e+01 ... (remaining 5136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1051 0.074 - 0.148: 250 0.148 - 0.222: 37 0.222 - 0.295: 10 0.295 - 0.369: 3 Chirality restraints: 1351 Sorted by residual: chirality pdb=" CG LEU S 162 " pdb=" CB LEU S 162 " pdb=" CD1 LEU S 162 " pdb=" CD2 LEU S 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" C9 CLR R 401 " pdb=" C10 CLR R 401 " pdb=" C11 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.45 -2.75 0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 1348 not shown) Planarity restraints: 1486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 237 " 0.064 5.00e-02 4.00e+02 9.73e-02 1.52e+01 pdb=" N PRO R 238 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO R 238 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO R 238 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE R 32 " -0.055 5.00e-02 4.00e+02 8.27e-02 1.09e+01 pdb=" N PRO R 33 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO R 33 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO R 33 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 275 " 0.046 5.00e-02 4.00e+02 6.87e-02 7.54e+00 pdb=" N PRO R 276 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO R 276 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 276 " 0.039 5.00e-02 4.00e+02 ... (remaining 1483 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1926 2.79 - 3.32: 7101 3.32 - 3.84: 14499 3.84 - 4.37: 16981 4.37 - 4.90: 29314 Nonbonded interactions: 69821 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.261 2.440 nonbonded pdb=" O THR R 107 " pdb=" OG SER R 161 " model vdw 2.306 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.317 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.319 2.440 nonbonded pdb=" OG1 THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.336 2.440 ... (remaining 69816 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.310 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: 2.030 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.370 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 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 : 0.008 0.133 8752 Z= 0.511 Angle : 1.291 21.931 11865 Z= 0.678 Chirality : 0.066 0.369 1351 Planarity : 0.008 0.097 1486 Dihedral : 13.537 89.286 3092 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.19 % 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: -2.74 (0.22), residues: 1078 helix: -2.29 (0.20), residues: 363 sheet: -0.82 (0.29), residues: 299 loop : -1.91 (0.27), residues: 416 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 142 time to evaluate : 1.033 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 143 average time/residue: 1.3943 time to fit residues: 211.0036 Evaluate side-chains 104 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 102 time to evaluate : 1.009 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 1.1311 time to fit residues: 2.5627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 83 optimal weight: 0.2980 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 340 ASN G 18 GLN R 48 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 8752 Z= 0.278 Angle : 0.666 12.484 11865 Z= 0.336 Chirality : 0.044 0.217 1351 Planarity : 0.005 0.074 1486 Dihedral : 6.072 68.809 1187 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 3.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.24), residues: 1078 helix: -0.09 (0.26), residues: 364 sheet: -0.71 (0.29), residues: 294 loop : -1.55 (0.28), residues: 420 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 113 time to evaluate : 0.894 Fit side-chains outliers start: 29 outliers final: 14 residues processed: 127 average time/residue: 1.4050 time to fit residues: 188.9086 Evaluate side-chains 119 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 0.884 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 9 residues processed: 6 average time/residue: 0.4308 time to fit residues: 4.3248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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-1.21rc1-5044/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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: 50.8825 > 50: distance: 31 - 116: 13.998 distance: 38 - 42: 20.831 distance: 42 - 43: 4.062 distance: 43 - 44: 20.363 distance: 43 - 46: 4.952 distance: 44 - 45: 7.181 distance: 44 - 50: 20.804 distance: 46 - 47: 13.705 distance: 47 - 48: 14.998 distance: 47 - 49: 22.827 distance: 50 - 51: 6.567 distance: 51 - 52: 21.892 distance: 51 - 54: 3.935 distance: 52 - 53: 34.479 distance: 52 - 61: 22.300 distance: 54 - 55: 23.690 distance: 55 - 56: 27.689 distance: 55 - 57: 18.397 distance: 56 - 58: 13.971 distance: 57 - 59: 14.535 distance: 58 - 60: 10.841 distance: 59 - 60: 32.691 distance: 61 - 62: 26.630 distance: 62 - 63: 6.968 distance: 63 - 64: 25.741 distance: 63 - 67: 26.559 distance: 65 - 66: 34.732 distance: 67 - 68: 15.559 distance: 68 - 69: 21.151 distance: 68 - 71: 7.314 distance: 69 - 70: 20.595 distance: 69 - 75: 25.450 distance: 71 - 72: 12.028 distance: 72 - 73: 18.814 distance: 72 - 74: 28.330 distance: 75 - 76: 15.380 distance: 76 - 77: 19.596 distance: 77 - 78: 21.187 distance: 77 - 79: 16.952 distance: 79 - 80: 3.474 distance: 80 - 81: 23.526 distance: 80 - 83: 15.838 distance: 81 - 82: 24.813 distance: 81 - 87: 24.708 distance: 83 - 84: 24.379 distance: 84 - 85: 5.869 distance: 84 - 86: 16.103 distance: 87 - 88: 14.701 distance: 88 - 89: 21.506 distance: 88 - 91: 17.517 distance: 89 - 90: 19.845 distance: 89 - 93: 4.657 distance: 91 - 92: 12.067 distance: 93 - 94: 25.615 distance: 94 - 95: 39.800 distance: 95 - 96: 12.034 distance: 95 - 97: 13.776 distance: 97 - 98: 11.416 distance: 98 - 99: 5.272 distance: 98 - 101: 27.137 distance: 99 - 100: 14.491 distance: 99 - 111: 24.257 distance: 101 - 102: 31.241 distance: 102 - 103: 23.890 distance: 102 - 104: 14.463 distance: 103 - 105: 19.767 distance: 104 - 106: 9.421 distance: 104 - 107: 6.129 distance: 106 - 108: 10.695 distance: 107 - 109: 9.118 distance: 108 - 110: 3.860 distance: 109 - 110: 7.279 distance: 111 - 112: 18.209 distance: 112 - 113: 23.569 distance: 112 - 115: 19.501 distance: 113 - 114: 24.804 distance: 113 - 117: 13.686 distance: 114 - 141: 14.021 distance: 115 - 116: 15.685