Starting phenix.real_space_refine on Mon Aug 5 16:33:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zwc_14996/08_2024/7zwc_14996.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zwc_14996/08_2024/7zwc_14996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zwc_14996/08_2024/7zwc_14996.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zwc_14996/08_2024/7zwc_14996.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zwc_14996/08_2024/7zwc_14996.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zwc_14996/08_2024/7zwc_14996.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 83 5.49 5 S 68 5.16 5 C 8586 2.51 5 N 2459 2.21 5 O 2746 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "M ARG 127": "NH1" <-> "NH2" Residue "M ARG 132": "NH1" <-> "NH2" Residue "M PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 147": "OE1" <-> "OE2" Residue "M ASP 157": "OD1" <-> "OD2" Residue "M TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 207": "OD1" <-> "OD2" Residue "M PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 267": "OE1" <-> "OE2" Residue "M TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 307": "OD1" <-> "OD2" Residue "O GLU 191": "OE1" <-> "OE2" Residue "O TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 196": "NH1" <-> "NH2" Residue "O ARG 203": "NH1" <-> "NH2" Residue "O ARG 208": "NH1" <-> "NH2" Residue "O GLU 227": "OE1" <-> "OE2" Residue "O GLU 228": "OE1" <-> "OE2" Residue "O ARG 235": "NH1" <-> "NH2" Residue "O TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 269": "NH1" <-> "NH2" Residue "O PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 286": "OE1" <-> "OE2" Residue "O TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 294": "NH1" <-> "NH2" Residue "O ARG 299": "NH1" <-> "NH2" Residue "O ARG 318": "NH1" <-> "NH2" Residue "O GLU 323": "OE1" <-> "OE2" Residue "O GLU 326": "OE1" <-> "OE2" Residue "O ARG 336": "NH1" <-> "NH2" Residue "U TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 35": "OD1" <-> "OD2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U ARG 363": "NH1" <-> "NH2" Residue "U ASP 364": "OD1" <-> "OD2" Residue "U TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 373": "OD1" <-> "OD2" Residue "V PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 83": "OE1" <-> "OE2" Residue "V GLU 86": "OE1" <-> "OE2" Residue "V ASP 91": "OD1" <-> "OD2" Residue "a ASP 10": "OD1" <-> "OD2" Residue "a ASP 22": "OD1" <-> "OD2" Residue "a GLU 27": "OE1" <-> "OE2" Residue "a ASP 28": "OD1" <-> "OD2" Residue "a TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 105": "OD1" <-> "OD2" Residue "a GLU 106": "OE1" <-> "OE2" Residue "a PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 121": "OD1" <-> "OD2" Residue "a TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 133": "NH1" <-> "NH2" Residue "a PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 179": "OE1" <-> "OE2" Residue "a PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 33": "OE1" <-> "OE2" Residue "b GLU 65": "OE1" <-> "OE2" Residue "b ASP 78": "OD1" <-> "OD2" Residue "b ASP 80": "OD1" <-> "OD2" Residue "b ASP 89": "OD1" <-> "OD2" Residue "b ARG 140": "NH1" <-> "NH2" Residue "b GLU 141": "OE1" <-> "OE2" Residue "b TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 217": "OD1" <-> "OD2" Residue "b PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 276": "OE1" <-> "OE2" Residue "b GLU 279": "OE1" <-> "OE2" Residue "b GLU 318": "OE1" <-> "OE2" Residue "b ASP 325": "OD1" <-> "OD2" Residue "b ASP 369": "OD1" <-> "OD2" Residue "b GLU 374": "OE1" <-> "OE2" Residue "b GLU 392": "OE1" <-> "OE2" Residue "b TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 82": "OD1" <-> "OD2" Residue "c GLU 84": "OE1" <-> "OE2" Residue "c GLU 95": "OE1" <-> "OE2" Residue "c GLU 116": "OE1" <-> "OE2" Residue "c TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 178": "OE1" <-> "OE2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "c GLU 225": "OE1" <-> "OE2" Residue "c GLU 239": "OE1" <-> "OE2" Residue "c ARG 257": "NH1" <-> "NH2" Residue "c ASP 262": "OD1" <-> "OD2" Residue "c GLU 264": "OE1" <-> "OE2" Residue "c GLU 272": "OE1" <-> "OE2" Residue "c GLU 279": "OE1" <-> "OE2" Residue "c GLU 300": "OE1" <-> "OE2" Residue "c GLU 301": "OE1" <-> "OE2" Residue "c GLU 323": "OE1" <-> "OE2" Residue "c PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 352": "OE1" <-> "OE2" Residue "c GLU 363": "OE1" <-> "OE2" Residue "c TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 7": "OE1" <-> "OE2" Residue "d GLU 12": "OE1" <-> "OE2" Residue "d GLU 13": "OE1" <-> "OE2" Residue "d GLU 32": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 13944 Number of models: 1 Model: "" Number of chains: 11 Chain: "M" Number of atoms: 1567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1567 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 10, 'TRANS': 190} Chain: "O" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1422 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain: "U" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 734 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain breaks: 1 Chain: "V" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "a" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1807 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 207} Chain breaks: 1 Chain: "b" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2977 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 347} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "c" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2516 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 1 Chain: "d" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 424 Classifications: {'peptide': 52} Link IDs: {'TRANS': 51} Chain: "N" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 866 Classifications: {'DNA': 42} Link IDs: {'rna3p': 41} Chain: "T" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 836 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "b" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7713 SG CYS b 221 74.720 68.049 25.479 1.00 71.17 S ATOM 8510 SG CYS b 317 70.937 68.144 26.228 1.00 65.61 S ATOM 8832 SG CYS b 354 86.413 47.078 26.927 1.00 74.89 S ATOM 8856 SG CYS b 357 90.285 47.225 26.423 1.00 80.88 S ATOM 9047 SG CYS b 380 87.894 47.931 23.578 1.00 75.15 S ATOM 9068 SG CYS b 383 88.319 44.427 24.901 1.00 79.07 S Time building chain proxies: 8.03, per 1000 atoms: 0.58 Number of scatterers: 13944 At special positions: 0 Unit cell: (129.15, 164.85, 110.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 68 16.00 P 83 15.00 O 2746 8.00 N 2459 7.00 C 8586 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: 5.39 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN b 501 " pdb="ZN ZN b 501 " - pdb=" NE2 HIS b 313 " pdb="ZN ZN b 501 " - pdb=" NE2 HIS b 319 " pdb="ZN ZN b 501 " - pdb=" SG CYS b 317 " pdb="ZN ZN b 501 " - pdb=" SG CYS b 221 " pdb=" ZN b 502 " pdb="ZN ZN b 502 " - pdb=" SG CYS b 380 " pdb="ZN ZN b 502 " - pdb=" SG CYS b 383 " pdb="ZN ZN b 502 " - pdb=" SG CYS b 357 " pdb="ZN ZN b 502 " - pdb=" SG CYS b 354 " Number of angles added : 8 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2874 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 7 sheets defined 53.9% alpha, 12.7% beta 28 base pairs and 70 stacking pairs defined. Time for finding SS restraints: 4.66 Creating SS restraints... Processing helix chain 'M' and resid 117 through 129 Processing helix chain 'M' and resid 131 through 149 Processing helix chain 'M' and resid 155 through 172 removed outlier: 3.686A pdb=" N GLY M 172 " --> pdb=" O CYS M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 182 Processing helix chain 'M' and resid 187 through 203 Processing helix chain 'M' and resid 214 through 222 Processing helix chain 'M' and resid 225 through 242 Processing helix chain 'M' and resid 249 through 265 Processing helix chain 'M' and resid 270 through 279 removed outlier: 3.513A pdb=" N ILE M 274 " --> pdb=" O THR M 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 281 through 293 removed outlier: 3.671A pdb=" N LEU M 291 " --> pdb=" O GLN M 287 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE M 292 " --> pdb=" O SER M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 300 removed outlier: 3.711A pdb=" N LEU M 299 " --> pdb=" O ARG M 295 " (cutoff:3.500A) Processing helix chain 'O' and resid 179 through 187 Processing helix chain 'O' and resid 226 through 244 Processing helix chain 'O' and resid 269 through 277 Processing helix chain 'O' and resid 317 through 335 Proline residue: O 330 - end of helix Processing helix chain 'U' and resid 10 through 33 removed outlier: 4.647A pdb=" N ASP U 27 " --> pdb=" O ASN U 23 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE U 28 " --> pdb=" O ASP U 24 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY U 33 " --> pdb=" O PHE U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 35 through 51 removed outlier: 3.779A pdb=" N LEU U 39 " --> pdb=" O ASP U 35 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET U 51 " --> pdb=" O GLU U 47 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 25 Processing helix chain 'V' and resid 29 through 52 removed outlier: 3.859A pdb=" N VAL V 52 " --> pdb=" O LEU V 48 " (cutoff:3.500A) Processing helix chain 'a' and resid 6 through 20 Processing helix chain 'a' and resid 25 through 37 removed outlier: 3.853A pdb=" N PHE a 29 " --> pdb=" O ARG a 25 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 43 removed outlier: 4.142A pdb=" N PHE a 42 " --> pdb=" O GLY a 39 " (cutoff:3.500A) Processing helix chain 'a' and resid 47 through 67 Processing helix chain 'a' and resid 71 through 88 Processing helix chain 'a' and resid 103 through 117 Processing helix chain 'a' and resid 119 through 132 Processing helix chain 'a' and resid 166 through 172 removed outlier: 4.252A pdb=" N LYS a 170 " --> pdb=" O ASP a 166 " (cutoff:3.500A) Processing helix chain 'a' and resid 173 through 195 removed outlier: 3.691A pdb=" N SER a 195 " --> pdb=" O LYS a 191 " (cutoff:3.500A) Processing helix chain 'a' and resid 211 through 232 Processing helix chain 'b' and resid 44 through 55 Processing helix chain 'b' and resid 77 through 91 removed outlier: 3.644A pdb=" N ARG b 81 " --> pdb=" O ALA b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 93 through 104 Processing helix chain 'b' and resid 127 through 144 Processing helix chain 'b' and resid 150 through 161 Processing helix chain 'b' and resid 192 through 197 Processing helix chain 'b' and resid 221 through 226 removed outlier: 3.697A pdb=" N GLN b 226 " --> pdb=" O SER b 223 " (cutoff:3.500A) Processing helix chain 'b' and resid 242 through 247 Processing helix chain 'b' and resid 270 through 280 removed outlier: 4.150A pdb=" N ILE b 274 " --> pdb=" O LEU b 270 " (cutoff:3.500A) Processing helix chain 'b' and resid 297 through 300 Processing helix chain 'b' and resid 380 through 389 removed outlier: 3.558A pdb=" N TYR b 389 " --> pdb=" O ARG b 385 " (cutoff:3.500A) Processing helix chain 'c' and resid 82 through 123 removed outlier: 4.291A pdb=" N CYS c 86 " --> pdb=" O ASP c 82 " (cutoff:3.500A) Processing helix chain 'c' and resid 141 through 145 removed outlier: 3.576A pdb=" N HIS c 144 " --> pdb=" O TYR c 141 " (cutoff:3.500A) Processing helix chain 'c' and resid 162 through 171 Processing helix chain 'c' and resid 185 through 221 Proline residue: c 207 - end of helix Processing helix chain 'c' and resid 225 through 247 Processing helix chain 'c' and resid 249 through 255 removed outlier: 4.242A pdb=" N GLY c 255 " --> pdb=" O GLU c 251 " (cutoff:3.500A) Processing helix chain 'c' and resid 262 through 267 Processing helix chain 'c' and resid 276 through 287 Processing helix chain 'c' and resid 298 through 313 Processing helix chain 'c' and resid 316 through 324 Processing helix chain 'c' and resid 329 through 340 Processing helix chain 'c' and resid 350 through 365 Processing helix chain 'c' and resid 371 through 377 removed outlier: 3.969A pdb=" N TYR c 377 " --> pdb=" O ARG c 373 " (cutoff:3.500A) Processing helix chain 'c' and resid 383 through 394 Processing helix chain 'd' and resid 2 through 45 Processing sheet with id=AA1, first strand: chain 'O' and resid 190 through 192 removed outlier: 3.665A pdb=" N THR O 209 " --> pdb=" O ILE O 204 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LEU O 165 " --> pdb=" O VAL O 259 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL O 259 " --> pdb=" O LEU O 165 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN O 167 " --> pdb=" O ASN O 257 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN O 257 " --> pdb=" O ASN O 167 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL O 169 " --> pdb=" O ILE O 255 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE O 255 " --> pdb=" O VAL O 169 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N THR O 171 " --> pdb=" O PHE O 253 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE O 253 " --> pdb=" O THR O 171 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N MET O 258 " --> pdb=" O GLY O 314 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY O 314 " --> pdb=" O MET O 258 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE O 300 " --> pdb=" O MET O 295 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'U' and resid 363 through 367 removed outlier: 6.358A pdb=" N LYS U 348 " --> pdb=" O ARG U 344 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ARG U 344 " --> pdb=" O LYS U 348 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS U 350 " --> pdb=" O ILE U 342 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE U 342 " --> pdb=" O LYS U 350 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N HIS U 352 " --> pdb=" O ASP U 340 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLN U 338 " --> pdb=" O LYS U 354 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY U 356 " --> pdb=" O VAL U 336 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL U 336 " --> pdb=" O GLY U 356 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N MET U 358 " --> pdb=" O VAL U 334 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL U 334 " --> pdb=" O MET U 358 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL U 335 " --> pdb=" O VAL V 96 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LEU V 87 " --> pdb=" O ARG V 82 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ARG V 82 " --> pdb=" O LEU V 87 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS V 89 " --> pdb=" O GLU V 80 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLU V 80 " --> pdb=" O LYS V 89 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASP V 91 " --> pdb=" O ASP V 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'U' and resid 363 through 367 removed outlier: 3.908A pdb=" N PHE V 58 " --> pdb=" O ILE U 371 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE V 58 " --> pdb=" O PHE V 81 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE V 81 " --> pdb=" O PHE V 58 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLY V 60 " --> pdb=" O VAL V 79 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL V 79 " --> pdb=" O GLY V 60 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU V 62 " --> pdb=" O ASN V 77 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ASN V 77 " --> pdb=" O LEU V 62 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 97 through 99 Processing sheet with id=AA5, first strand: chain 'b' and resid 42 through 43 Processing sheet with id=AA6, first strand: chain 'b' and resid 289 through 291 removed outlier: 3.689A pdb=" N ASN b 260 " --> pdb=" O ALA b 291 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE b 321 " --> pdb=" O LEU b 187 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU b 187 " --> pdb=" O ILE b 321 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ILE b 323 " --> pdb=" O ASN b 185 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN b 185 " --> pdb=" O ILE b 323 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP b 325 " --> pdb=" O SER b 183 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N THR b 203 " --> pdb=" O ILE b 344 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU b 342 " --> pdb=" O LEU b 205 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 377 through 379 673 hydrogen bonds defined for protein. 1950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 64 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 70 stacking parallelities Total time for adding SS restraints: 4.35 Time building geometry restraints manager: 5.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4084 1.34 - 1.45: 2473 1.45 - 1.57: 7561 1.57 - 1.69: 165 1.69 - 1.81: 105 Bond restraints: 14388 Sorted by residual: bond pdb=" N MET d 1 " pdb=" CA MET d 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" CB PRO M 131 " pdb=" CG PRO M 131 " ideal model delta sigma weight residual 1.492 1.577 -0.085 5.00e-02 4.00e+02 2.86e+00 bond pdb=" CG MET c 91 " pdb=" SD MET c 91 " ideal model delta sigma weight residual 1.803 1.767 0.036 2.50e-02 1.60e+03 2.10e+00 bond pdb=" N HIS b 281 " pdb=" CA HIS b 281 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.17e-02 7.31e+03 1.80e+00 bond pdb=" CG PRO M 131 " pdb=" CD PRO M 131 " ideal model delta sigma weight residual 1.503 1.540 -0.037 3.40e-02 8.65e+02 1.22e+00 ... (remaining 14383 not shown) Histogram of bond angle deviations from ideal: 99.09 - 106.07: 687 106.07 - 113.04: 7688 113.04 - 120.02: 5150 120.02 - 126.99: 5882 126.99 - 133.96: 348 Bond angle restraints: 19755 Sorted by residual: angle pdb=" CA PRO M 131 " pdb=" N PRO M 131 " pdb=" CD PRO M 131 " ideal model delta sigma weight residual 112.00 106.51 5.49 1.40e+00 5.10e-01 1.54e+01 angle pdb=" N GLY U 356 " pdb=" CA GLY U 356 " pdb=" C GLY U 356 " ideal model delta sigma weight residual 110.38 116.06 -5.68 1.48e+00 4.57e-01 1.47e+01 angle pdb=" N PHE c 145 " pdb=" CA PHE c 145 " pdb=" C PHE c 145 " ideal model delta sigma weight residual 114.31 109.69 4.62 1.29e+00 6.01e-01 1.28e+01 angle pdb=" CA MET c 91 " pdb=" CB MET c 91 " pdb=" CG MET c 91 " ideal model delta sigma weight residual 114.10 120.50 -6.40 2.00e+00 2.50e-01 1.03e+01 angle pdb=" N MET c 91 " pdb=" CA MET c 91 " pdb=" CB MET c 91 " ideal model delta sigma weight residual 110.40 115.44 -5.04 1.63e+00 3.76e-01 9.56e+00 ... (remaining 19750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.40: 7943 30.40 - 60.80: 577 60.80 - 91.21: 37 91.21 - 121.61: 0 121.61 - 152.01: 1 Dihedral angle restraints: 8558 sinusoidal: 4148 harmonic: 4410 Sorted by residual: dihedral pdb=" CA PHE c 145 " pdb=" C PHE c 145 " pdb=" N MET c 146 " pdb=" CA MET c 146 " ideal model delta harmonic sigma weight residual -180.00 -152.12 -27.88 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA PRO b 341 " pdb=" C PRO b 341 " pdb=" N LEU b 342 " pdb=" CA LEU b 342 " ideal model delta harmonic sigma weight residual -180.00 -158.45 -21.55 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA LYS O 297 " pdb=" C LYS O 297 " pdb=" N PRO O 298 " pdb=" CA PRO O 298 " ideal model delta harmonic sigma weight residual 180.00 159.10 20.90 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 8555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1588 0.034 - 0.068: 412 0.068 - 0.102: 116 0.102 - 0.137: 46 0.137 - 0.171: 4 Chirality restraints: 2166 Sorted by residual: chirality pdb=" CA ILE b 321 " pdb=" N ILE b 321 " pdb=" C ILE b 321 " pdb=" CB ILE b 321 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.29e-01 chirality pdb=" CA ILE b 186 " pdb=" N ILE b 186 " pdb=" C ILE b 186 " pdb=" CB ILE b 186 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" CA ILE V 28 " pdb=" N ILE V 28 " pdb=" C ILE V 28 " pdb=" CB ILE V 28 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 2163 not shown) Planarity restraints: 2253 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU M 130 " -0.061 5.00e-02 4.00e+02 9.01e-02 1.30e+01 pdb=" N PRO M 131 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO M 131 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO M 131 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR b 340 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO b 341 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO b 341 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO b 341 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR a 80 " 0.013 2.00e-02 2.50e+03 1.13e-02 2.56e+00 pdb=" CG TYR a 80 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR a 80 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR a 80 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR a 80 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR a 80 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR a 80 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR a 80 " 0.001 2.00e-02 2.50e+03 ... (remaining 2250 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 188 2.63 - 3.20: 12656 3.20 - 3.77: 22851 3.77 - 4.33: 31749 4.33 - 4.90: 49975 Nonbonded interactions: 117419 Sorted by model distance: nonbonded pdb=" O VAL a 24 " pdb=" OH TYR a 80 " model vdw 2.067 3.040 nonbonded pdb=" OD2 ASP M 311 " pdb=" OG SER d 3 " model vdw 2.074 3.040 nonbonded pdb=" OD1 ASP a 105 " pdb=" NH2 ARG b 54 " model vdw 2.096 3.120 nonbonded pdb=" NH1 ARG V 51 " pdb=" OD2 ASP c 262 " model vdw 2.097 3.120 nonbonded pdb=" O GLN c 217 " pdb=" OG SER c 220 " model vdw 2.112 3.040 ... (remaining 117414 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 42.890 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 0.085 14388 Z= 0.159 Angle : 0.527 6.405 19755 Z= 0.313 Chirality : 0.037 0.171 2166 Planarity : 0.003 0.090 2253 Dihedral : 18.423 152.008 5684 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.23), residues: 1474 helix: 2.16 (0.20), residues: 762 sheet: -0.15 (0.42), residues: 142 loop : -1.09 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 277 HIS 0.003 0.000 HIS b 195 PHE 0.011 0.001 PHE b 47 TYR 0.028 0.001 TYR a 80 ARG 0.003 0.000 ARG a 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 140 ASN cc_start: 0.8324 (t0) cc_final: 0.8086 (t0) REVERT: M 213 ASP cc_start: 0.8583 (m-30) cc_final: 0.8092 (m-30) REVERT: M 230 MET cc_start: 0.8385 (mtm) cc_final: 0.8062 (mpp) REVERT: U 19 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7900 (mt-10) REVERT: U 36 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7046 (tm-30) REVERT: U 41 GLU cc_start: 0.8630 (pp20) cc_final: 0.8426 (pp20) REVERT: U 44 THR cc_start: 0.9209 (p) cc_final: 0.8991 (p) REVERT: U 375 GLU cc_start: 0.6604 (tm-30) cc_final: 0.6386 (tm-30) REVERT: V 17 GLU cc_start: 0.8406 (mp0) cc_final: 0.8094 (mp0) REVERT: a 27 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8063 (mm-30) REVERT: b 104 CYS cc_start: 0.7638 (m) cc_final: 0.7359 (m) REVERT: b 276 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8179 (mt-10) REVERT: b 316 ASP cc_start: 0.8014 (p0) cc_final: 0.7801 (t0) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.2677 time to fit residues: 97.6831 Evaluate side-chains 194 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.470 ------------------------------------------------------------------------------- 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: 52.559 > 50: distance: 47 - 71: 3.284 distance: 51 - 75: 5.877 distance: 58 - 83: 5.799 distance: 62 - 95: 5.444 distance: 74 - 103: 4.372 distance: 75 - 76: 3.767 distance: 76 - 77: 3.387 distance: 76 - 79: 3.010 distance: 79 - 80: 5.001 distance: 80 - 81: 6.497 distance: 80 - 82: 4.221 distance: 84 - 87: 5.412 distance: 85 - 86: 4.160 distance: 88 - 90: 3.923 distance: 89 - 91: 3.057 distance: 92 - 93: 3.459 distance: 93 - 94: 3.037 distance: 95 - 96: 3.366 distance: 97 - 98: 3.977 distance: 97 - 103: 3.884 distance: 99 - 100: 4.512 distance: 100 - 101: 7.057 distance: 100 - 102: 15.935 distance: 103 - 104: 5.267 distance: 104 - 105: 5.537 distance: 104 - 107: 5.972 distance: 107 - 109: 4.780 distance: 110 - 111: 3.998 distance: 111 - 112: 7.299 distance: 111 - 114: 4.739 distance: 112 - 113: 8.053 distance: 112 - 119: 5.336 distance: 114 - 115: 5.748 distance: 115 - 116: 4.482 distance: 116 - 118: 3.255 distance: 119 - 120: 3.499 distance: 120 - 123: 4.647 distance: 121 - 122: 5.142 distance: 121 - 127: 7.011 distance: 123 - 124: 3.742 distance: 124 - 125: 5.354 distance: 124 - 126: 6.049 distance: 127 - 128: 12.787 distance: 128 - 129: 7.692 distance: 128 - 131: 16.106 distance: 129 - 130: 5.425 distance: 129 - 133: 4.820 distance: 131 - 132: 52.559 distance: 133 - 134: 3.962 distance: 134 - 135: 4.391 distance: 134 - 137: 3.081 distance: 135 - 136: 6.691 distance: 135 - 142: 6.959 distance: 137 - 138: 3.153 distance: 138 - 139: 9.028 distance: 139 - 140: 3.334 distance: 139 - 141: 7.572 distance: 142 - 143: 6.717 distance: 143 - 144: 6.793 distance: 143 - 146: 6.328 distance: 144 - 145: 3.982 distance: 146 - 147: 3.567 distance: 147 - 148: 3.723