Starting phenix.real_space_refine on Wed Jun 26 08:13:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7r_27231/06_2024/8d7r_27231.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7r_27231/06_2024/8d7r_27231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7r_27231/06_2024/8d7r_27231.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7r_27231/06_2024/8d7r_27231.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7r_27231/06_2024/8d7r_27231.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d7r_27231/06_2024/8d7r_27231.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 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 36 5.16 5 C 6158 2.51 5 N 1608 2.21 5 O 1825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 78": "NH1" <-> "NH2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D ARG 95": "NH1" <-> "NH2" Residue "D ARG 102": "NH1" <-> "NH2" Residue "D GLU 108": "OE1" <-> "OE2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "D ARG 131": "NH1" <-> "NH2" Residue "D PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 204": "NH1" <-> "NH2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "C TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 157": "OD1" <-> "OD2" Residue "C PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 208": "OE1" <-> "OE2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "C ASP 252": "OD1" <-> "OD2" Residue "C TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 304": "OE1" <-> "OE2" Residue "B ASP 147": "OD1" <-> "OD2" Residue "B TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 160": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 249": "OD1" <-> "OD2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 275": "OE1" <-> "OE2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 384": "NH1" <-> "NH2" Residue "B TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 443": "OD1" <-> "OD2" Residue "B PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 497": "OD1" <-> "OD2" Residue "B PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 276": "OD1" <-> "OD2" Residue "A PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "A PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "A ASP 429": "OD1" <-> "OD2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 474": "OD1" <-> "OD2" Residue "A TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 9627 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1432 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 16, 'TRANS': 161} Chain: "C" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1607 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 20, 'TRANS': 178} Chain: "B" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3197 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 378} Chain breaks: 1 Chain: "A" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3167 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 25, 'TRANS': 366} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.70, per 1000 atoms: 0.70 Number of scatterers: 9627 At special positions: 0 Unit cell: (102.34, 144.48, 151.36, 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 36 16.00 O 1825 8.00 N 1608 7.00 C 6158 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 341 " - pdb=" SG CYS B 351 " distance=2.03 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 144 " distance=2.04 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 458 " - pdb=" SG CYS A 466 " 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 BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 701 " - " ASN A 131 " " NAG A 702 " - " ASN A 157 " " NAG A 703 " - " ASN A 383 " " NAG A 704 " - " ASN A 379 " " NAG B 901 " - " ASN B 426 " " NAG C 401 " - " ASN C 142 " " NAG E 1 " - " ASN C 190 " " NAG F 1 " - " ASN B 407 " " NAG G 1 " - " ASN B 303 " " NAG H 1 " - " ASN B 243 " " NAG I 1 " - " ASN A 227 " Time building additional restraints: 4.13 Conformation dependent library (CDL) restraints added in 1.8 seconds 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2240 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 21 sheets defined 12.4% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'D' and resid 35 through 65 removed outlier: 3.987A pdb=" N SER D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 40 " --> pdb=" O PRO D 36 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 71 removed outlier: 3.699A pdb=" N ASN D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU D 71 " --> pdb=" O PRO D 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 66 through 71' Processing helix chain 'D' and resid 90 through 97 removed outlier: 3.969A pdb=" N LEU D 97 " --> pdb=" O VAL D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 124 Processing helix chain 'D' and resid 126 through 154 Processing helix chain 'D' and resid 176 through 210 Processing helix chain 'A' and resid 273 through 277 Processing helix chain 'A' and resid 355 through 360 Processing sheet with id=AA1, first strand: chain 'C' and resid 144 through 145 Processing sheet with id=AA2, first strand: chain 'C' and resid 211 through 214 Processing sheet with id=AA3, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AA4, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA5, first strand: chain 'B' and resid 143 through 147 removed outlier: 3.875A pdb=" N ASN B 143 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 156 " --> pdb=" O ASN B 143 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 152 " --> pdb=" O ASP B 147 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TRP B 157 " --> pdb=" O HIS B 201 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N HIS B 201 " --> pdb=" O TRP B 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 186 through 192 removed outlier: 3.565A pdb=" N ASN B 191 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG B 221 " --> pdb=" O GLU B 173 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS B 175 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU B 219 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 177 " --> pdb=" O PHE B 217 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N HIS B 216 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE B 244 " --> pdb=" O HIS B 216 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS B 242 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 254 through 255 removed outlier: 3.720A pdb=" N ILE B 267 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE B 301 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE B 269 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL B 297 " --> pdb=" O CYS B 271 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 260 through 262 removed outlier: 3.652A pdb=" N ILE B 261 " --> pdb=" O PHE B 328 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY B 330 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE B 323 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL B 315 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ALA B 280 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR B 317 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 337 through 342 removed outlier: 5.712A pdb=" N GLN B 338 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASN B 354 " --> pdb=" O GLN B 338 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN B 340 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 352 " --> pdb=" O ASN B 340 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 379 through 381 removed outlier: 3.844A pdb=" N VAL B 380 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 371 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR B 409 " --> pdb=" O VAL B 372 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR B 406 " --> pdb=" O VAL B 425 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 425 " --> pdb=" O TYR B 406 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 421 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER B 419 " --> pdb=" O ALA B 412 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 477 through 481 removed outlier: 3.688A pdb=" N ARG B 510 " --> pdb=" O GLU B 467 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU B 469 " --> pdb=" O ARG B 508 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG B 508 " --> pdb=" O GLU B 469 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS B 471 " --> pdb=" O THR B 506 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 136 through 137 removed outlier: 7.684A pdb=" N VAL A 136 " --> pdb=" O LYS A 221 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 159 through 161 removed outlier: 3.613A pdb=" N LYS A 161 " --> pdb=" O TRP A 197 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP A 197 " --> pdb=" O LYS A 161 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 159 through 161 removed outlier: 3.613A pdb=" N LYS A 161 " --> pdb=" O TRP A 197 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP A 197 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE A 194 " --> pdb=" O PHE A 214 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE A 214 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL A 196 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE A 212 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 226 through 231 removed outlier: 6.527A pdb=" N ASN A 227 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N THR A 245 " --> pdb=" O ASN A 227 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A 229 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 243 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE A 231 " --> pdb=" O LYS A 241 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS A 241 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 270 through 271 removed outlier: 3.781A pdb=" N MET A 302 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN A 258 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG A 300 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN A 260 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG A 298 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG A 262 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 296 " --> pdb=" O ARG A 262 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 347 through 349 removed outlier: 3.905A pdb=" N VAL A 347 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL A 389 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 349 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 387 " --> pdb=" O LEU A 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 377 through 378 removed outlier: 3.748A pdb=" N GLN A 378 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ASP A 365 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG A 403 " --> pdb=" O ASP A 365 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 397 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR A 396 " --> pdb=" O ILE A 416 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 431 through 432 Processing sheet with id=AC2, first strand: chain 'A' and resid 459 through 460 removed outlier: 4.019A pdb=" N CYS A 491 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY A 503 " --> pdb=" O TYR A 500 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 469 through 474 removed outlier: 3.568A pdb=" N ASP A 469 " --> pdb=" O TRP A 457 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 471 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU A 455 " --> pdb=" O GLN A 471 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS A 452 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 499 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A 454 " --> pdb=" O THR A 497 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR A 492 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 512 " --> pdb=" O TYR A 492 " (cutoff:3.500A) 213 hydrogen bonds defined for protein. 585 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: 2.37 Time building geometry restraints manager: 4.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3010 1.34 - 1.46: 2438 1.46 - 1.58: 4403 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 9899 Sorted by residual: bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.02e+00 bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.11e+00 bond pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.09e+00 ... (remaining 9894 not shown) Histogram of bond angle deviations from ideal: 100.78 - 107.42: 496 107.42 - 114.06: 5733 114.06 - 120.69: 3471 120.69 - 127.33: 3642 127.33 - 133.97: 166 Bond angle restraints: 13508 Sorted by residual: angle pdb=" C PRO A 434 " pdb=" N LYS A 435 " pdb=" CA LYS A 435 " ideal model delta sigma weight residual 121.54 128.05 -6.51 1.91e+00 2.74e-01 1.16e+01 angle pdb=" C ALA B 448 " pdb=" N VAL B 449 " pdb=" CA VAL B 449 " ideal model delta sigma weight residual 120.49 125.19 -4.70 1.38e+00 5.25e-01 1.16e+01 angle pdb=" N ASN A 131 " pdb=" CA ASN A 131 " pdb=" CB ASN A 131 " ideal model delta sigma weight residual 114.17 110.31 3.86 1.14e+00 7.69e-01 1.15e+01 angle pdb=" CA GLY A 361 " pdb=" C GLY A 361 " pdb=" N LYS A 362 " ideal model delta sigma weight residual 114.23 116.74 -2.51 8.80e-01 1.29e+00 8.14e+00 angle pdb=" C LEU B 194 " pdb=" N ASN B 195 " pdb=" CA ASN B 195 " ideal model delta sigma weight residual 121.54 126.97 -5.43 1.91e+00 2.74e-01 8.08e+00 ... (remaining 13503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.88: 5767 21.88 - 43.76: 270 43.76 - 65.64: 57 65.64 - 87.52: 9 87.52 - 109.39: 26 Dihedral angle restraints: 6129 sinusoidal: 2682 harmonic: 3447 Sorted by residual: dihedral pdb=" CB CYS A 172 " pdb=" SG CYS A 172 " pdb=" SG CYS A 182 " pdb=" CB CYS A 182 " ideal model delta sinusoidal sigma weight residual 93.00 173.22 -80.22 1 1.00e+01 1.00e-02 7.97e+01 dihedral pdb=" CB CYS A 458 " pdb=" SG CYS A 458 " pdb=" SG CYS A 466 " pdb=" CB CYS A 466 " ideal model delta sinusoidal sigma weight residual -86.00 -34.89 -51.11 1 1.00e+01 1.00e-02 3.57e+01 dihedral pdb=" CB CYS C 116 " pdb=" SG CYS C 116 " pdb=" SG CYS C 127 " pdb=" CB CYS C 127 " ideal model delta sinusoidal sigma weight residual 93.00 60.67 32.33 1 1.00e+01 1.00e-02 1.49e+01 ... (remaining 6126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1270 0.049 - 0.098: 198 0.098 - 0.147: 76 0.147 - 0.196: 2 0.196 - 0.245: 1 Chirality restraints: 1547 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN C 190 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 131 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 383 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.59e-01 ... (remaining 1544 not shown) Planarity restraints: 1696 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 66 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO D 67 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 500 " 0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO B 501 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 501 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 501 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 272 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO A 273 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 273 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 273 " 0.022 5.00e-02 4.00e+02 ... (remaining 1693 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 3184 2.86 - 3.37: 8390 3.37 - 3.88: 14623 3.88 - 4.39: 15262 4.39 - 4.90: 26904 Nonbonded interactions: 68363 Sorted by model distance: nonbonded pdb=" NH1 ARG A 262 " pdb=" O THR A 263 " model vdw 2.345 2.520 nonbonded pdb=" O GLU D 92 " pdb=" OG SER D 96 " model vdw 2.348 2.440 nonbonded pdb=" O TYR A 257 " pdb=" OG1 THR A 277 " model vdw 2.370 2.440 nonbonded pdb=" OG SER B 374 " pdb=" O5 NAG F 1 " model vdw 2.375 2.440 nonbonded pdb=" OE1 GLU B 373 " pdb=" N SER B 376 " model vdw 2.380 2.520 ... (remaining 68358 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 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.420 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: 13.110 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 30.760 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5432 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 0.039 9899 Z= 0.173 Angle : 0.536 7.043 13508 Z= 0.271 Chirality : 0.042 0.245 1547 Planarity : 0.004 0.056 1685 Dihedral : 15.026 109.395 3865 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -3.25 (0.21), residues: 1157 helix: 1.59 (0.42), residues: 129 sheet: -1.70 (0.28), residues: 305 loop : -3.30 (0.17), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 146 HIS 0.001 0.000 HIS A 340 PHE 0.013 0.000 PHE A 332 TYR 0.011 0.001 TYR B 502 ARG 0.001 0.000 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 MET cc_start: 0.5426 (ptp) cc_final: 0.4966 (mpp) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2652 time to fit residues: 64.5806 Evaluate side-chains 99 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.0370 chunk 86 optimal weight: 0.0010 chunk 47 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 overall best weight: 1.4070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 105 GLN D 112 HIS D 123 GLN D 135 HIS D 192 GLN C 162 ASN C 253 GLN C 256 HIS B 166 HIS B 190 HIS B 201 HIS B 226 ASN B 286 ASN B 402 ASN B 411 ASN B 420 GLN B 434 HIS A 287 GLN A 348 GLN A 478 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6002 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 9899 Z= 0.275 Angle : 0.732 12.148 13508 Z= 0.352 Chirality : 0.049 0.384 1547 Planarity : 0.005 0.049 1685 Dihedral : 11.979 88.214 1592 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 1.80 % Allowed : 14.74 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.23), residues: 1157 helix: 2.15 (0.46), residues: 135 sheet: -1.56 (0.26), residues: 363 loop : -2.89 (0.20), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 269 HIS 0.007 0.001 HIS C 147 PHE 0.025 0.002 PHE C 141 TYR 0.026 0.002 TYR B 502 ARG 0.006 0.001 ARG D 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 103 LEU cc_start: 0.4967 (mm) cc_final: 0.4755 (mt) REVERT: D 182 MET cc_start: 0.7088 (mmm) cc_final: 0.6861 (mmp) REVERT: B 251 GLN cc_start: 0.6131 (tp-100) cc_final: 0.5903 (mm-40) REVERT: A 351 TRP cc_start: 0.5846 (p90) cc_final: 0.5305 (p90) REVERT: A 438 MET cc_start: 0.5309 (ptp) cc_final: 0.4917 (mpp) outliers start: 19 outliers final: 13 residues processed: 132 average time/residue: 0.2616 time to fit residues: 46.0135 Evaluate side-chains 116 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 ASN Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 478 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 0.2980 chunk 70 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6022 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9899 Z= 0.178 Angle : 0.622 10.240 13508 Z= 0.296 Chirality : 0.047 0.733 1547 Planarity : 0.004 0.042 1685 Dihedral : 10.015 82.090 1592 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 2.55 % Allowed : 16.35 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.23), residues: 1157 helix: 2.74 (0.47), residues: 135 sheet: -1.32 (0.28), residues: 331 loop : -2.65 (0.20), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 246 HIS 0.009 0.001 HIS A 478 PHE 0.012 0.001 PHE B 217 TYR 0.012 0.001 TYR A 322 ARG 0.010 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 111 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 182 MET cc_start: 0.6970 (mmm) cc_final: 0.6725 (mmp) REVERT: C 142 ASN cc_start: 0.4948 (m110) cc_final: 0.3666 (m-40) REVERT: C 245 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7120 (ptm160) REVERT: C 252 ASP cc_start: 0.5963 (OUTLIER) cc_final: 0.5683 (t0) REVERT: A 351 TRP cc_start: 0.5798 (p90) cc_final: 0.5348 (p90) REVERT: A 438 MET cc_start: 0.5259 (ptp) cc_final: 0.4890 (mpp) outliers start: 27 outliers final: 16 residues processed: 130 average time/residue: 0.2279 time to fit residues: 40.9809 Evaluate side-chains 118 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 75 ASN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 167 HIS Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 389 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 53 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 110 optimal weight: 0.5980 chunk 54 optimal weight: 0.2980 chunk 98 optimal weight: 0.2980 chunk 29 optimal weight: 0.0970 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5997 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 9899 Z= 0.157 Angle : 0.597 8.274 13508 Z= 0.283 Chirality : 0.045 0.506 1547 Planarity : 0.004 0.044 1685 Dihedral : 8.605 72.710 1592 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 2.74 % Allowed : 16.92 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.24), residues: 1157 helix: 2.94 (0.47), residues: 135 sheet: -1.18 (0.28), residues: 337 loop : -2.47 (0.21), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 246 HIS 0.015 0.001 HIS A 478 PHE 0.008 0.001 PHE C 243 TYR 0.022 0.001 TYR B 502 ARG 0.006 0.000 ARG D 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 105 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LEU cc_start: 0.8715 (tt) cc_final: 0.8479 (tp) REVERT: C 245 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.7127 (ptm160) REVERT: C 252 ASP cc_start: 0.5868 (OUTLIER) cc_final: 0.5608 (t0) REVERT: A 351 TRP cc_start: 0.5748 (p90) cc_final: 0.5328 (p90) outliers start: 29 outliers final: 15 residues processed: 126 average time/residue: 0.2254 time to fit residues: 39.3394 Evaluate side-chains 120 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 467 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 1.9990 chunk 62 optimal weight: 0.0010 chunk 1 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 76 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 98 optimal weight: 0.7980 chunk 27 optimal weight: 0.3980 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 434 HIS B 527 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9899 Z= 0.180 Angle : 0.610 9.766 13508 Z= 0.289 Chirality : 0.044 0.445 1547 Planarity : 0.004 0.041 1685 Dihedral : 7.826 64.038 1592 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 2.93 % Allowed : 18.43 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -1.89 (0.24), residues: 1157 helix: 2.88 (0.46), residues: 135 sheet: -1.05 (0.27), residues: 356 loop : -2.39 (0.21), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 246 HIS 0.013 0.001 HIS A 478 PHE 0.013 0.001 PHE A 169 TYR 0.010 0.001 TYR D 49 ARG 0.008 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 103 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 245 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7232 (ptm160) REVERT: A 305 ASP cc_start: 0.7277 (p0) cc_final: 0.7012 (p0) REVERT: A 351 TRP cc_start: 0.6052 (p90) cc_final: 0.5495 (p90) outliers start: 31 outliers final: 24 residues processed: 124 average time/residue: 0.2423 time to fit residues: 41.4612 Evaluate side-chains 121 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 ASN Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 467 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.903 > 50: distance: 41 - 128: 34.548 distance: 44 - 125: 33.352 distance: 54 - 110: 28.228 distance: 57 - 107: 32.060 distance: 97 - 101: 33.380 distance: 101 - 102: 56.827 distance: 102 - 103: 39.286 distance: 102 - 105: 36.199 distance: 105 - 106: 34.850 distance: 107 - 108: 6.015 distance: 108 - 109: 42.278 distance: 108 - 111: 8.569 distance: 109 - 110: 26.454 distance: 109 - 118: 51.007 distance: 111 - 112: 53.801 distance: 112 - 114: 33.209 distance: 113 - 115: 32.645 distance: 114 - 116: 56.049 distance: 115 - 117: 44.933 distance: 116 - 117: 20.870 distance: 118 - 119: 21.922 distance: 119 - 120: 40.297 distance: 119 - 122: 56.550 distance: 120 - 121: 40.184 distance: 120 - 125: 40.810 distance: 122 - 123: 39.833 distance: 122 - 124: 41.441 distance: 126 - 127: 40.537 distance: 127 - 132: 39.384 distance: 129 - 131: 40.331 distance: 132 - 133: 39.485 distance: 133 - 134: 39.915 distance: 133 - 136: 22.794 distance: 134 - 135: 22.125 distance: 134 - 141: 56.542 distance: 136 - 137: 10.708 distance: 137 - 138: 39.988 distance: 138 - 139: 20.069 distance: 138 - 140: 40.996 distance: 141 - 142: 40.533 distance: 142 - 145: 5.595 distance: 143 - 149: 57.170 distance: 145 - 146: 24.577 distance: 146 - 147: 31.380 distance: 146 - 148: 13.469 distance: 149 - 150: 39.255 distance: 150 - 151: 39.031 distance: 150 - 153: 68.992 distance: 151 - 152: 55.738 distance: 153 - 154: 27.301 distance: 154 - 155: 16.383 distance: 154 - 156: 48.158 distance: 157 - 158: 41.210 distance: 158 - 159: 40.304 distance: 158 - 161: 51.468 distance: 159 - 160: 40.714 distance: 159 - 166: 30.114 distance: 161 - 162: 32.604 distance: 163 - 164: 12.056 distance: 164 - 165: 43.235 distance: 166 - 167: 9.192 distance: 166 - 172: 7.890 distance: 167 - 168: 36.806 distance: 167 - 170: 40.361 distance: 168 - 169: 4.099 distance: 168 - 173: 5.144 distance: 170 - 171: 57.799 distance: 171 - 172: 40.803 distance: 174 - 175: 58.036 distance: 174 - 177: 54.068 distance: 175 - 176: 19.667 distance: 175 - 184: 28.753 distance: 177 - 178: 39.750