Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 18 17:32:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trj_26098/08_2023/7trj_26098.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trj_26098/08_2023/7trj_26098.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trj_26098/08_2023/7trj_26098.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trj_26098/08_2023/7trj_26098.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trj_26098/08_2023/7trj_26098.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trj_26098/08_2023/7trj_26098.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.056 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 142 5.16 5 C 16062 2.51 5 N 4372 2.21 5 O 4614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A ARG 145": "NH1" <-> "NH2" Residue "A ASP 154": "OD1" <-> "OD2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A ARG 171": "NH1" <-> "NH2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 265": "OD1" <-> "OD2" Residue "A ASP 270": "OD1" <-> "OD2" Residue "A TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 418": "OE1" <-> "OE2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "D GLU 10": "OE1" <-> "OE2" Residue "D ARG 29": "NH1" <-> "NH2" Residue "D GLU 37": "OE1" <-> "OE2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 63": "NH1" <-> "NH2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D GLU 120": "OE1" <-> "OE2" Residue "D ASP 121": "OD1" <-> "OD2" Residue "D PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D GLU 143": "OE1" <-> "OE2" Residue "D GLU 145": "OE1" <-> "OE2" Residue "D GLU 149": "OE1" <-> "OE2" Residue "D ARG 183": "NH1" <-> "NH2" Residue "D PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 304": "OE1" <-> "OE2" Residue "D ARG 338": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E GLU 246": "OE1" <-> "OE2" Residue "E GLU 247": "OE1" <-> "OE2" Residue "E GLU 283": "OE1" <-> "OE2" Residue "E GLU 293": "OE1" <-> "OE2" Residue "E GLU 295": "OE1" <-> "OE2" Residue "E ARG 321": "NH1" <-> "NH2" Residue "E GLU 352": "OE1" <-> "OE2" Residue "E PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 374": "NH1" <-> "NH2" Residue "E GLU 397": "OE1" <-> "OE2" Residue "E ARG 417": "NH1" <-> "NH2" Residue "E GLU 439": "OE1" <-> "OE2" Residue "E ARG 467": "NH1" <-> "NH2" Residue "G GLU 5": "OE1" <-> "OE2" Residue "G GLU 8": "OE1" <-> "OE2" Residue "G GLU 16": "OE1" <-> "OE2" Residue "G ASP 17": "OD1" <-> "OD2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "G GLU 54": "OE1" <-> "OE2" Residue "G GLU 70": "OE1" <-> "OE2" Residue "G ARG 74": "NH1" <-> "NH2" Residue "G ASP 85": "OD1" <-> "OD2" Residue "G ARG 108": "NH1" <-> "NH2" Residue "G ARG 132": "NH1" <-> "NH2" Residue "G ARG 136": "NH1" <-> "NH2" Residue "G ASP 248": "OD1" <-> "OD2" Residue "I GLU 44": "OE1" <-> "OE2" Residue "I ASP 111": "OD1" <-> "OD2" Residue "I ASP 125": "OD1" <-> "OD2" Residue "I GLU 173": "OE1" <-> "OE2" Residue "I GLU 217": "OE1" <-> "OE2" Residue "I GLU 227": "OE1" <-> "OE2" Residue "I GLU 307": "OE1" <-> "OE2" Residue "I ARG 324": "NH1" <-> "NH2" Residue "B PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "B PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B ARG 145": "NH1" <-> "NH2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B ARG 171": "NH1" <-> "NH2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 265": "OD1" <-> "OD2" Residue "B ASP 270": "OD1" <-> "OD2" Residue "B TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 418": "OE1" <-> "OE2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "C GLU 10": "OE1" <-> "OE2" Residue "C ARG 29": "NH1" <-> "NH2" Residue "C GLU 37": "OE1" <-> "OE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 67": "NH1" <-> "NH2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C ASP 121": "OD1" <-> "OD2" Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C GLU 143": "OE1" <-> "OE2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 149": "OE1" <-> "OE2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 304": "OE1" <-> "OE2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "F ARG 170": "NH1" <-> "NH2" Residue "F GLU 246": "OE1" <-> "OE2" Residue "F GLU 247": "OE1" <-> "OE2" Residue "F GLU 283": "OE1" <-> "OE2" Residue "F GLU 293": "OE1" <-> "OE2" Residue "F GLU 295": "OE1" <-> "OE2" Residue "F ARG 321": "NH1" <-> "NH2" Residue "F GLU 352": "OE1" <-> "OE2" Residue "F PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 374": "NH1" <-> "NH2" Residue "F GLU 397": "OE1" <-> "OE2" Residue "F ARG 417": "NH1" <-> "NH2" Residue "F GLU 439": "OE1" <-> "OE2" Residue "F ARG 467": "NH1" <-> "NH2" Residue "H GLU 5": "OE1" <-> "OE2" Residue "H GLU 8": "OE1" <-> "OE2" Residue "H GLU 16": "OE1" <-> "OE2" Residue "H ASP 17": "OD1" <-> "OD2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H ARG 74": "NH1" <-> "NH2" Residue "H ASP 85": "OD1" <-> "OD2" Residue "H ARG 108": "NH1" <-> "NH2" Residue "H ARG 132": "NH1" <-> "NH2" Residue "H ARG 136": "NH1" <-> "NH2" Residue "H ASP 248": "OD1" <-> "OD2" Residue "J GLU 44": "OE1" <-> "OE2" Residue "J ASP 111": "OD1" <-> "OD2" Residue "J ASP 125": "OD1" <-> "OD2" Residue "J GLU 173": "OE1" <-> "OE2" Residue "J GLU 217": "OE1" <-> "OE2" Residue "J GLU 227": "OE1" <-> "OE2" Residue "J GLU 307": "OE1" <-> "OE2" Residue "J ARG 324": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 25190 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3210 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 395} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "D" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2571 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 314} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Chain: "G" Number of atoms: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2203 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1861 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 11, 'TRANS': 224} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 3210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3210 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 395} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "C" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2571 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 314} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Chain: "H" Number of atoms: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2203 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1861 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 11, 'TRANS': 224} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 11.64, per 1000 atoms: 0.46 Number of scatterers: 25190 At special positions: 0 Unit cell: (141.95, 132.765, 166.165, 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 142 16.00 O 4614 8.00 N 4372 7.00 C 16062 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: 9.05 Conformation dependent library (CDL) restraints added in 3.4 seconds 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6144 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 32 sheets defined 45.8% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'A' and resid 58 through 62 removed outlier: 3.726A pdb=" N ASP A 62 " --> pdb=" O ILE A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 68 removed outlier: 3.670A pdb=" N LEU A 67 " --> pdb=" O PRO A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 87 removed outlier: 3.523A pdb=" N TYR A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.534A pdb=" N ILE A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 130 through 142 Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.699A pdb=" N ALA A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 279 removed outlier: 3.751A pdb=" N PHE A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 315 removed outlier: 3.574A pdb=" N ALA A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'D' and resid 9 through 25 Processing helix chain 'D' and resid 30 through 48 Processing helix chain 'D' and resid 53 through 72 removed outlier: 3.518A pdb=" N GLN D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 98 removed outlier: 4.273A pdb=" N GLY D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 113 Processing helix chain 'D' and resid 128 through 153 removed outlier: 3.586A pdb=" N ASN D 132 " --> pdb=" O GLN D 128 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N MET D 148 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 180 Processing helix chain 'D' and resid 199 through 209 removed outlier: 3.722A pdb=" N MET D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 250 through 262 Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.564A pdb=" N LYS D 273 " --> pdb=" O PRO D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 305 removed outlier: 3.813A pdb=" N LEU D 303 " --> pdb=" O GLY D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 removed outlier: 3.680A pdb=" N LEU D 320 " --> pdb=" O PRO D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 334 No H-bonds generated for 'chain 'D' and resid 332 through 334' Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 345 through 349 removed outlier: 3.611A pdb=" N HIS D 349 " --> pdb=" O PRO D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 196 removed outlier: 3.827A pdb=" N GLN E 194 " --> pdb=" O SER E 191 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE E 195 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET E 196 " --> pdb=" O THR E 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 191 through 196' Processing helix chain 'E' and resid 204 through 216 Processing helix chain 'E' and resid 221 through 240 Processing helix chain 'E' and resid 247 through 267 removed outlier: 4.441A pdb=" N VAL E 253 " --> pdb=" O SER E 249 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 270 through 286 Processing helix chain 'E' and resid 292 through 312 Processing helix chain 'E' and resid 312 through 324 Processing helix chain 'E' and resid 339 through 352 Processing helix chain 'E' and resid 368 through 380 removed outlier: 4.085A pdb=" N THR E 372 " --> pdb=" O GLU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 395 Processing helix chain 'E' and resid 396 through 398 No H-bonds generated for 'chain 'E' and resid 396 through 398' Processing helix chain 'E' and resid 420 through 430 Processing helix chain 'E' and resid 439 through 443 Processing helix chain 'E' and resid 459 through 464 Processing helix chain 'E' and resid 493 through 497 Processing helix chain 'E' and resid 508 through 510 No H-bonds generated for 'chain 'E' and resid 508 through 510' Processing helix chain 'E' and resid 511 through 519 removed outlier: 3.556A pdb=" N VAL E 515 " --> pdb=" O SER E 511 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS E 519 " --> pdb=" O VAL E 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 17 removed outlier: 4.204A pdb=" N ASP G 17 " --> pdb=" O GLN G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.585A pdb=" N LYS G 35 " --> pdb=" O LEU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 60 Processing helix chain 'G' and resid 62 through 81 removed outlier: 3.868A pdb=" N SER G 66 " --> pdb=" O SER G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 106 removed outlier: 3.626A pdb=" N LEU G 106 " --> pdb=" O ARG G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 116 Processing helix chain 'G' and resid 117 through 119 No H-bonds generated for 'chain 'G' and resid 117 through 119' Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 160 through 170 Processing helix chain 'G' and resid 179 through 183 removed outlier: 4.047A pdb=" N VAL G 183 " --> pdb=" O ASP G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 222 Processing helix chain 'G' and resid 231 through 235 removed outlier: 3.850A pdb=" N LYS G 234 " --> pdb=" O GLU G 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 252 removed outlier: 3.516A pdb=" N LYS G 251 " --> pdb=" O PRO G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 277 through 281 Processing helix chain 'G' and resid 294 through 304 removed outlier: 3.588A pdb=" N ASP G 298 " --> pdb=" O SER G 294 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 33 Processing helix chain 'I' and resid 34 through 35 No H-bonds generated for 'chain 'I' and resid 34 through 35' Processing helix chain 'I' and resid 36 through 44 removed outlier: 3.539A pdb=" N LEU I 40 " --> pdb=" O ILE I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 93 Processing helix chain 'I' and resid 114 through 124 removed outlier: 4.169A pdb=" N LEU I 120 " --> pdb=" O GLU I 116 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR I 124 " --> pdb=" O LEU I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 190 Processing helix chain 'I' and resid 209 through 218 Processing helix chain 'I' and resid 223 through 236 removed outlier: 5.366A pdb=" N ILE I 229 " --> pdb=" O ARG I 225 " (cutoff:3.500A) Proline residue: I 230 - end of helix Processing helix chain 'I' and resid 262 through 266 Processing helix chain 'I' and resid 315 through 334 Proline residue: I 327 - end of helix removed outlier: 3.741A pdb=" N ALA I 332 " --> pdb=" O LYS I 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 62 removed outlier: 3.726A pdb=" N ASP B 62 " --> pdb=" O ILE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 68 removed outlier: 3.670A pdb=" N LEU B 67 " --> pdb=" O PRO B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 removed outlier: 3.523A pdb=" N TYR B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 109 removed outlier: 3.534A pdb=" N ILE B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 113 Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 161 through 175 Processing helix chain 'B' and resid 253 through 263 removed outlier: 3.699A pdb=" N ALA B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 279 removed outlier: 3.752A pdb=" N PHE B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 315 removed outlier: 3.574A pdb=" N ALA B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'C' and resid 9 through 25 Processing helix chain 'C' and resid 30 through 48 Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.518A pdb=" N GLN C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 98 removed outlier: 4.273A pdb=" N GLY C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 128 through 153 removed outlier: 3.586A pdb=" N ASN C 132 " --> pdb=" O GLN C 128 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N MET C 148 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 180 Processing helix chain 'C' and resid 199 through 209 removed outlier: 3.722A pdb=" N MET C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 270 through 274 removed outlier: 3.565A pdb=" N LYS C 273 " --> pdb=" O PRO C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 305 removed outlier: 3.813A pdb=" N LEU C 303 " --> pdb=" O GLY C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 321 removed outlier: 3.680A pdb=" N LEU C 320 " --> pdb=" O PRO C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 349 removed outlier: 3.611A pdb=" N HIS C 349 " --> pdb=" O PRO C 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 196 removed outlier: 3.827A pdb=" N GLN F 194 " --> pdb=" O SER F 191 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE F 195 " --> pdb=" O LEU F 192 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET F 196 " --> pdb=" O THR F 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 191 through 196' Processing helix chain 'F' and resid 204 through 216 Processing helix chain 'F' and resid 221 through 240 Processing helix chain 'F' and resid 247 through 267 removed outlier: 4.441A pdb=" N VAL F 253 " --> pdb=" O SER F 249 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 270 through 286 Processing helix chain 'F' and resid 292 through 312 Processing helix chain 'F' and resid 312 through 324 Processing helix chain 'F' and resid 339 through 352 Processing helix chain 'F' and resid 368 through 380 removed outlier: 4.086A pdb=" N THR F 372 " --> pdb=" O GLU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 395 Processing helix chain 'F' and resid 396 through 398 No H-bonds generated for 'chain 'F' and resid 396 through 398' Processing helix chain 'F' and resid 420 through 430 Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 459 through 464 Processing helix chain 'F' and resid 493 through 497 Processing helix chain 'F' and resid 508 through 510 No H-bonds generated for 'chain 'F' and resid 508 through 510' Processing helix chain 'F' and resid 511 through 519 removed outlier: 3.555A pdb=" N VAL F 515 " --> pdb=" O SER F 511 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS F 519 " --> pdb=" O VAL F 515 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 17 removed outlier: 4.205A pdb=" N ASP H 17 " --> pdb=" O GLN H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 35 removed outlier: 3.584A pdb=" N LYS H 35 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 60 Processing helix chain 'H' and resid 62 through 81 removed outlier: 3.867A pdb=" N SER H 66 " --> pdb=" O SER H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 106 removed outlier: 3.626A pdb=" N LEU H 106 " --> pdb=" O ARG H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 116 Processing helix chain 'H' and resid 117 through 119 No H-bonds generated for 'chain 'H' and resid 117 through 119' Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 160 through 170 Processing helix chain 'H' and resid 179 through 183 removed outlier: 4.047A pdb=" N VAL H 183 " --> pdb=" O ASP H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 222 Processing helix chain 'H' and resid 231 through 235 removed outlier: 3.849A pdb=" N LYS H 234 " --> pdb=" O GLU H 231 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 252 removed outlier: 3.515A pdb=" N LYS H 251 " --> pdb=" O PRO H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 277 through 281 Processing helix chain 'H' and resid 294 through 304 removed outlier: 3.588A pdb=" N ASP H 298 " --> pdb=" O SER H 294 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 33 Processing helix chain 'J' and resid 34 through 35 No H-bonds generated for 'chain 'J' and resid 34 through 35' Processing helix chain 'J' and resid 36 through 44 removed outlier: 3.539A pdb=" N LEU J 40 " --> pdb=" O ILE J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 93 Processing helix chain 'J' and resid 114 through 124 removed outlier: 4.169A pdb=" N LEU J 120 " --> pdb=" O GLU J 116 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR J 124 " --> pdb=" O LEU J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 190 Processing helix chain 'J' and resid 209 through 218 Processing helix chain 'J' and resid 223 through 236 removed outlier: 5.365A pdb=" N ILE J 229 " --> pdb=" O ARG J 225 " (cutoff:3.500A) Proline residue: J 230 - end of helix Processing helix chain 'J' and resid 262 through 266 Processing helix chain 'J' and resid 315 through 334 Proline residue: J 327 - end of helix removed outlier: 3.741A pdb=" N ALA J 332 " --> pdb=" O LYS J 328 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 124 removed outlier: 6.673A pdb=" N THR A 91 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE A 123 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL A 93 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TYR A 152 " --> pdb=" O HIS A 248 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N HIS A 248 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N CYS A 247 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N LYS A 186 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ILE A 249 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N MET A 181 " --> pdb=" O HIS A 288 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N HIS A 290 " --> pdb=" O MET A 181 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N MET A 183 " --> pdb=" O HIS A 290 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N THR A 292 " --> pdb=" O MET A 183 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE A 185 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 157 Processing sheet with id=AA3, first strand: chain 'A' and resid 212 through 217 removed outlier: 6.623A pdb=" N VAL A 212 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASP A 206 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL A 238 " --> pdb=" O PHE I 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 227 Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 338 removed outlier: 3.544A pdb=" N ILE A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 355 through 356 removed outlier: 6.423A pdb=" N ILE A 355 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE A 373 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL A 390 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLN A 407 " --> pdb=" O LEU A 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 378 through 379 removed outlier: 6.339A pdb=" N VAL A 378 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N TYR A 395 " --> pdb=" O LEU A 413 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 401 through 402 removed outlier: 6.785A pdb=" N ARG A 401 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N GLU A 418 " --> pdb=" O VAL A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 430 through 431 removed outlier: 6.797A pdb=" N VAL A 430 " --> pdb=" O ILE A 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 329 through 331 removed outlier: 3.732A pdb=" N SER D 326 " --> pdb=" O GLY D 329 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU D 265 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE D 325 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL D 267 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL D 232 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N CYS D 268 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE D 234 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL D 164 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ILE D 233 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N MET D 166 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLU D 163 " --> pdb=" O HIS D 188 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE D 190 " --> pdb=" O GLU D 163 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE D 165 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ALA D 192 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR D 167 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR D 214 " --> pdb=" O ARG E 483 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 238 through 239 removed outlier: 3.761A pdb=" N THR D 238 " --> pdb=" O ARG D 246 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 307 through 308 removed outlier: 6.279A pdb=" N SER D 307 " --> pdb=" O TYR E 385 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N LEU E 387 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE E 333 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL E 361 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL E 335 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR E 336 " --> pdb=" O LEU E 402 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLY E 404 " --> pdb=" O TYR E 336 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL E 401 " --> pdb=" O LEU E 435 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N CYS E 437 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU E 403 " --> pdb=" O CYS E 437 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL E 434 " --> pdb=" O LEU E 499 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ILE E 501 " --> pdb=" O VAL E 434 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL E 436 " --> pdb=" O ILE E 501 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 407 through 408 Processing sheet with id=AB5, first strand: chain 'G' and resid 175 through 178 removed outlier: 6.459A pdb=" N VAL G 150 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL G 178 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL G 152 " --> pdb=" O VAL G 178 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL G 193 " --> pdb=" O TYR G 227 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL G 229 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL G 195 " --> pdb=" O VAL G 229 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE G 226 " --> pdb=" O LEU G 283 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N PHE G 285 " --> pdb=" O PHE G 226 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL G 228 " --> pdb=" O PHE G 285 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 199 through 200 Processing sheet with id=AB7, first strand: chain 'I' and resid 73 through 77 removed outlier: 6.546A pdb=" N GLN I 4 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N LEU I 104 " --> pdb=" O GLN I 4 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL I 6 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER I 105 " --> pdb=" O HIS I 203 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N HIS I 203 " --> pdb=" O SER I 105 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA I 202 " --> pdb=" O LEU I 131 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU I 131 " --> pdb=" O ALA I 202 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU I 204 " --> pdb=" O ALA I 129 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA I 129 " --> pdb=" O LEU I 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 119 through 124 removed outlier: 6.673A pdb=" N THR B 91 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE B 123 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL B 93 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TYR B 152 " --> pdb=" O HIS B 248 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N HIS B 248 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N CYS B 247 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N LYS B 186 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ILE B 249 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N MET B 181 " --> pdb=" O HIS B 288 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N HIS B 290 " --> pdb=" O MET B 181 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N MET B 183 " --> pdb=" O HIS B 290 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR B 292 " --> pdb=" O MET B 183 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE B 185 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 155 through 157 Processing sheet with id=AC1, first strand: chain 'B' and resid 212 through 217 removed outlier: 6.624A pdb=" N VAL B 212 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASP B 206 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL B 238 " --> pdb=" O PHE J 195 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 223 through 226 Processing sheet with id=AC3, first strand: chain 'B' and resid 336 through 338 removed outlier: 3.544A pdb=" N ILE B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 355 through 356 removed outlier: 6.423A pdb=" N ILE B 355 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE B 373 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL B 390 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLN B 407 " --> pdb=" O LEU B 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 378 through 379 removed outlier: 6.339A pdb=" N VAL B 378 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N TYR B 395 " --> pdb=" O LEU B 413 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 401 through 402 removed outlier: 6.786A pdb=" N ARG B 401 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N GLU B 418 " --> pdb=" O VAL B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 430 through 431 removed outlier: 6.797A pdb=" N VAL B 430 " --> pdb=" O ILE B 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 329 through 331 removed outlier: 3.732A pdb=" N SER C 326 " --> pdb=" O GLY C 329 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU C 265 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ILE C 325 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL C 267 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL C 232 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N CYS C 268 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE C 234 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL C 164 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ILE C 233 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N MET C 166 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU C 163 " --> pdb=" O HIS C 188 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ILE C 190 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE C 165 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ALA C 192 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR C 167 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR C 214 " --> pdb=" O ARG F 483 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 238 through 239 removed outlier: 3.762A pdb=" N THR C 238 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 307 through 308 removed outlier: 6.321A pdb=" N SER C 307 " --> pdb=" O TYR F 385 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N LEU F 387 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE F 333 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL F 361 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL F 335 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR F 336 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N GLY F 404 " --> pdb=" O TYR F 336 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL F 401 " --> pdb=" O LEU F 435 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N CYS F 437 " --> pdb=" O VAL F 401 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU F 403 " --> pdb=" O CYS F 437 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL F 434 " --> pdb=" O LEU F 499 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ILE F 501 " --> pdb=" O VAL F 434 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL F 436 " --> pdb=" O ILE F 501 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 407 through 408 Processing sheet with id=AD3, first strand: chain 'H' and resid 175 through 178 removed outlier: 6.458A pdb=" N VAL H 150 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL H 178 " --> pdb=" O VAL H 150 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL H 152 " --> pdb=" O VAL H 178 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL H 193 " --> pdb=" O TYR H 227 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL H 229 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL H 195 " --> pdb=" O VAL H 229 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE H 226 " --> pdb=" O LEU H 283 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N PHE H 285 " --> pdb=" O PHE H 226 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL H 228 " --> pdb=" O PHE H 285 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 199 through 200 Processing sheet with id=AD5, first strand: chain 'J' and resid 73 through 77 removed outlier: 6.546A pdb=" N GLN J 4 " --> pdb=" O LEU J 102 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LEU J 104 " --> pdb=" O GLN J 4 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL J 6 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER J 105 " --> pdb=" O HIS J 203 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N HIS J 203 " --> pdb=" O SER J 105 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA J 202 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU J 131 " --> pdb=" O ALA J 202 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU J 204 " --> pdb=" O ALA J 129 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA J 129 " --> pdb=" O LEU J 204 " (cutoff:3.500A) 1086 hydrogen bonds defined for protein. 3039 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: 8.41 Time building geometry restraints manager: 9.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8288 1.35 - 1.47: 5617 1.47 - 1.59: 11533 1.59 - 1.71: 0 1.71 - 1.84: 216 Bond restraints: 25654 Sorted by residual: bond pdb=" CA ILE J 229 " pdb=" CB ILE J 229 " ideal model delta sigma weight residual 1.539 1.497 0.042 5.40e-03 3.43e+04 5.94e+01 bond pdb=" CA ILE I 229 " pdb=" CB ILE I 229 " ideal model delta sigma weight residual 1.539 1.498 0.041 5.40e-03 3.43e+04 5.80e+01 bond pdb=" CA SER F 510 " pdb=" C SER F 510 " ideal model delta sigma weight residual 1.525 1.505 0.020 1.38e-02 5.25e+03 2.15e+00 bond pdb=" CA SER E 510 " pdb=" C SER E 510 " ideal model delta sigma weight residual 1.525 1.505 0.020 1.38e-02 5.25e+03 2.07e+00 bond pdb=" C VAL I 326 " pdb=" N PRO I 327 " ideal model delta sigma weight residual 1.334 1.355 -0.021 1.51e-02 4.39e+03 1.88e+00 ... (remaining 25649 not shown) Histogram of bond angle deviations from ideal: 98.75 - 105.80: 517 105.80 - 112.85: 14176 112.85 - 119.90: 8538 119.90 - 126.96: 11274 126.96 - 134.01: 267 Bond angle restraints: 34772 Sorted by residual: angle pdb=" CA LYS J 328 " pdb=" CB LYS J 328 " pdb=" CG LYS J 328 " ideal model delta sigma weight residual 114.10 125.16 -11.06 2.00e+00 2.50e-01 3.06e+01 angle pdb=" CA LYS I 328 " pdb=" CB LYS I 328 " pdb=" CG LYS I 328 " ideal model delta sigma weight residual 114.10 125.15 -11.05 2.00e+00 2.50e-01 3.05e+01 angle pdb=" N PHE B 56 " pdb=" CA PHE B 56 " pdb=" C PHE B 56 " ideal model delta sigma weight residual 110.70 102.65 8.05 1.55e+00 4.16e-01 2.69e+01 angle pdb=" N PHE A 56 " pdb=" CA PHE A 56 " pdb=" C PHE A 56 " ideal model delta sigma weight residual 110.70 102.71 7.99 1.55e+00 4.16e-01 2.66e+01 angle pdb=" C LYS H 15 " pdb=" N GLU H 16 " pdb=" CA GLU H 16 " ideal model delta sigma weight residual 120.44 114.04 6.40 1.30e+00 5.92e-01 2.42e+01 ... (remaining 34767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 14009 17.41 - 34.83: 1033 34.83 - 52.24: 340 52.24 - 69.66: 170 69.66 - 87.07: 44 Dihedral angle restraints: 15596 sinusoidal: 6152 harmonic: 9444 Sorted by residual: dihedral pdb=" CA ASP A 139 " pdb=" CB ASP A 139 " pdb=" CG ASP A 139 " pdb=" OD1 ASP A 139 " ideal model delta sinusoidal sigma weight residual -30.00 -86.26 56.26 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA ASP B 139 " pdb=" CB ASP B 139 " pdb=" CG ASP B 139 " pdb=" OD1 ASP B 139 " ideal model delta sinusoidal sigma weight residual -30.00 -86.22 56.22 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA ASP B 265 " pdb=" C ASP B 265 " pdb=" N TYR B 266 " pdb=" CA TYR B 266 " ideal model delta harmonic sigma weight residual 180.00 163.85 16.15 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 15593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3179 0.056 - 0.111: 751 0.111 - 0.167: 163 0.167 - 0.222: 5 0.222 - 0.278: 6 Chirality restraints: 4104 Sorted by residual: chirality pdb=" CA GLN J 325 " pdb=" N GLN J 325 " pdb=" C GLN J 325 " pdb=" CB GLN J 325 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA GLN I 325 " pdb=" N GLN I 325 " pdb=" C GLN I 325 " pdb=" CB GLN I 325 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA LYS H 15 " pdb=" N LYS H 15 " pdb=" C LYS H 15 " pdb=" CB LYS H 15 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 4101 not shown) Planarity restraints: 4414 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS E 509 " -0.028 2.00e-02 2.50e+03 5.47e-02 2.99e+01 pdb=" C CYS E 509 " 0.095 2.00e-02 2.50e+03 pdb=" O CYS E 509 " -0.035 2.00e-02 2.50e+03 pdb=" N SER E 510 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS F 509 " 0.028 2.00e-02 2.50e+03 5.46e-02 2.98e+01 pdb=" C CYS F 509 " -0.094 2.00e-02 2.50e+03 pdb=" O CYS F 509 " 0.035 2.00e-02 2.50e+03 pdb=" N SER F 510 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 104 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C GLU B 104 " 0.064 2.00e-02 2.50e+03 pdb=" O GLU B 104 " -0.024 2.00e-02 2.50e+03 pdb=" N HIS B 105 " -0.022 2.00e-02 2.50e+03 ... (remaining 4411 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 398 2.64 - 3.21: 22662 3.21 - 3.77: 38435 3.77 - 4.34: 53319 4.34 - 4.90: 89533 Nonbonded interactions: 204347 Sorted by model distance: nonbonded pdb=" OD1 ASP A 271 " pdb=" NH2 ARG A 274 " model vdw 2.080 2.520 nonbonded pdb=" OD1 ASP B 271 " pdb=" NH2 ARG B 274 " model vdw 2.082 2.520 nonbonded pdb=" OG SER C 30 " pdb=" OE1 GLU C 33 " model vdw 2.142 2.440 nonbonded pdb=" OG SER D 30 " pdb=" OE1 GLU D 33 " model vdw 2.142 2.440 nonbonded pdb=" O TYR J 124 " pdb=" NH1 ARG J 299 " model vdw 2.180 2.520 ... (remaining 204342 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.140 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: 0.020 Extract box with map and model: 15.560 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 59.020 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.140 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:11.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 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 0.044 25654 Z= 0.216 Angle : 0.843 11.287 34772 Z= 0.477 Chirality : 0.050 0.278 4104 Planarity : 0.005 0.055 4414 Dihedral : 16.162 87.072 9452 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.62 % Favored : 96.25 % Rotamer Outliers : 6.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: -1.80 (0.14), residues: 3174 helix: 0.03 (0.14), residues: 1282 sheet: -1.82 (0.21), residues: 452 loop : -2.12 (0.14), residues: 1440 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 517 time to evaluate : 2.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 192 outliers final: 44 residues processed: 658 average time/residue: 1.4026 time to fit residues: 1057.9348 Evaluate side-chains 301 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 257 time to evaluate : 3.012 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 43 residues processed: 2 average time/residue: 1.0428 time to fit residues: 6.3800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 9.9990 chunk 241 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 249 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 288 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 177 ASN A 214 HIS A 219 GLN A 255 GLN A 286 GLN A 333 GLN A 337 HIS A 341 ASN A 359 ASN A 371 ASN A 376 ASN D 49 HIS D 80 ASN D 132 ASN D 188 HIS E 194 GLN E 213 GLN E 448 GLN E 455 ASN E 464 GLN G 48 ASN G 128 HIS G 243 GLN I 323 ASN B 72 ASN B 197 HIS B 219 GLN B 286 GLN B 359 ASN B 371 ASN B 376 ASN B 384 HIS C 49 HIS C 80 ASN C 132 ASN C 162 ASN C 230 ASN F 189 GLN F 213 GLN F 265 GLN F 347 GLN F 448 GLN F 455 ASN F 464 GLN H 48 ASN H 128 HIS H 222 GLN H 243 GLN J 323 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 25654 Z= 0.296 Angle : 0.629 11.583 34772 Z= 0.318 Chirality : 0.046 0.287 4104 Planarity : 0.004 0.041 4414 Dihedral : 4.135 19.751 3488 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 6.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: -0.47 (0.15), residues: 3174 helix: 1.00 (0.15), residues: 1306 sheet: -1.00 (0.24), residues: 446 loop : -1.32 (0.15), residues: 1422 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 254 time to evaluate : 2.983 Fit side-chains outliers start: 171 outliers final: 84 residues processed: 397 average time/residue: 1.1457 time to fit residues: 538.3398 Evaluate side-chains 295 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 211 time to evaluate : 2.903 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 77 residues processed: 7 average time/residue: 0.5631 time to fit residues: 9.0792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 240 optimal weight: 9.9990 chunk 196 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 chunk 289 optimal weight: 6.9990 chunk 312 optimal weight: 8.9990 chunk 257 optimal weight: 0.7980 chunk 286 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 232 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN D 230 ASN E 189 GLN E 479 HIS B 197 HIS B 337 HIS B 359 ASN H 170 HIS J 172 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.050 25654 Z= 0.380 Angle : 0.621 12.016 34772 Z= 0.316 Chirality : 0.046 0.220 4104 Planarity : 0.004 0.046 4414 Dihedral : 4.304 20.984 3488 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 6.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: -0.02 (0.15), residues: 3174 helix: 1.27 (0.15), residues: 1302 sheet: -0.72 (0.24), residues: 462 loop : -0.96 (0.16), residues: 1410 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 229 time to evaluate : 3.213 Fit side-chains revert: symmetry clash outliers start: 180 outliers final: 101 residues processed: 376 average time/residue: 1.1589 time to fit residues: 513.5769 Evaluate side-chains 297 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 196 time to evaluate : 2.911 Switching outliers to nearest non-outliers outliers start: 101 outliers final: 91 residues processed: 10 average time/residue: 0.4485 time to fit residues: 10.3926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 0.9990 chunk 217 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 290 optimal weight: 0.7980 chunk 307 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 275 optimal weight: 20.0000 chunk 82 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN E 189 GLN B 333 GLN F 371 HIS F 455 ASN ** H 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 25654 Z= 0.188 Angle : 0.526 10.537 34772 Z= 0.269 Chirality : 0.043 0.191 4104 Planarity : 0.004 0.046 4414 Dihedral : 4.051 20.267 3488 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 5.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.45 (0.15), residues: 3174 helix: 1.63 (0.15), residues: 1290 sheet: -0.57 (0.24), residues: 456 loop : -0.60 (0.16), residues: 1428 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 227 time to evaluate : 2.963 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 155 outliers final: 101 residues processed: 363 average time/residue: 1.1492 time to fit residues: 494.9483 Evaluate side-chains 303 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 202 time to evaluate : 2.897 Switching outliers to nearest non-outliers outliers start: 101 outliers final: 96 residues processed: 5 average time/residue: 0.8465 time to fit residues: 9.2071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 0.9990 chunk 174 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 228 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 chunk 262 optimal weight: 0.0970 chunk 212 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 275 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN E 189 GLN E 371 HIS E 464 GLN ** B 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 455 ASN H 48 ASN J 172 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 25654 Z= 0.256 Angle : 0.549 13.743 34772 Z= 0.279 Chirality : 0.044 0.172 4104 Planarity : 0.004 0.054 4414 Dihedral : 4.094 19.973 3488 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 5.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.52 (0.15), residues: 3174 helix: 1.66 (0.15), residues: 1300 sheet: -0.50 (0.24), residues: 468 loop : -0.55 (0.17), residues: 1406 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 218 time to evaluate : 3.419 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 152 outliers final: 98 residues processed: 358 average time/residue: 1.1699 time to fit residues: 497.6169 Evaluate side-chains 297 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 199 time to evaluate : 3.223 Switching outliers to nearest non-outliers outliers start: 98 outliers final: 94 residues processed: 4 average time/residue: 0.8111 time to fit residues: 8.3800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 0.4980 chunk 276 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 75 optimal weight: 0.0870 chunk 307 optimal weight: 5.9990 chunk 255 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 101 optimal weight: 0.1980 chunk 161 optimal weight: 1.9990 overall best weight: 0.5360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 HIS A 359 ASN E 189 GLN E 281 ASN E 347 GLN E 371 HIS E 455 ASN E 464 GLN B 333 GLN F 455 ASN F 470 HIS ** H 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 ASN J 303 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 25654 Z= 0.158 Angle : 0.511 12.519 34772 Z= 0.261 Chirality : 0.042 0.163 4104 Planarity : 0.004 0.054 4414 Dihedral : 3.910 21.922 3488 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 5.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.81 (0.15), residues: 3174 helix: 1.87 (0.15), residues: 1286 sheet: -0.31 (0.25), residues: 456 loop : -0.36 (0.17), residues: 1432 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 220 time to evaluate : 3.207 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 145 outliers final: 90 residues processed: 354 average time/residue: 1.2018 time to fit residues: 504.8545 Evaluate side-chains 283 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 193 time to evaluate : 2.941 Switching outliers to nearest non-outliers outliers start: 90 outliers final: 89 residues processed: 1 average time/residue: 0.2255 time to fit residues: 4.3978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 0.0980 chunk 34 optimal weight: 4.9990 chunk 175 optimal weight: 5.9990 chunk 224 optimal weight: 0.2980 chunk 174 optimal weight: 4.9990 chunk 259 optimal weight: 0.9990 chunk 171 optimal weight: 8.9990 chunk 306 optimal weight: 7.9990 chunk 191 optimal weight: 9.9990 chunk 186 optimal weight: 0.1980 chunk 141 optimal weight: 0.9980 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN E 347 GLN E 371 HIS I 323 ASN ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 GLN F 455 ASN J 172 ASN J 323 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 25654 Z= 0.157 Angle : 0.509 14.864 34772 Z= 0.260 Chirality : 0.042 0.151 4104 Planarity : 0.004 0.053 4414 Dihedral : 3.821 21.845 3488 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 4.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.93 (0.16), residues: 3174 helix: 1.96 (0.15), residues: 1282 sheet: -0.22 (0.25), residues: 446 loop : -0.27 (0.17), residues: 1446 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 217 time to evaluate : 3.030 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 130 outliers final: 93 residues processed: 334 average time/residue: 1.1591 time to fit residues: 463.7186 Evaluate side-chains 309 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 216 time to evaluate : 2.929 Switching outliers to nearest non-outliers outliers start: 93 outliers final: 88 residues processed: 6 average time/residue: 0.8762 time to fit residues: 10.3403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 chunk 151 optimal weight: 0.1980 chunk 28 optimal weight: 4.9990 chunk 240 optimal weight: 8.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN D 130 GLN E 371 HIS ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 GLN F 455 ASN F 470 HIS ** H 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 25654 Z= 0.219 Angle : 0.538 14.083 34772 Z= 0.274 Chirality : 0.043 0.174 4104 Planarity : 0.004 0.051 4414 Dihedral : 3.918 21.715 3488 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer Outliers : 4.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.93 (0.16), residues: 3174 helix: 1.93 (0.15), residues: 1286 sheet: -0.13 (0.24), residues: 482 loop : -0.29 (0.17), residues: 1406 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 217 time to evaluate : 2.956 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 117 outliers final: 93 residues processed: 329 average time/residue: 1.1858 time to fit residues: 462.6750 Evaluate side-chains 293 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 200 time to evaluate : 2.991 Switching outliers to nearest non-outliers outliers start: 93 outliers final: 93 residues processed: 0 time to fit residues: 4.1332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 6.9990 chunk 293 optimal weight: 0.9980 chunk 267 optimal weight: 6.9990 chunk 285 optimal weight: 0.2980 chunk 171 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 224 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 258 optimal weight: 0.4980 chunk 270 optimal weight: 7.9990 chunk 284 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN E 371 HIS E 464 GLN ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 GLN F 455 ASN ** H 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 25654 Z= 0.215 Angle : 0.542 13.705 34772 Z= 0.278 Chirality : 0.043 0.165 4104 Planarity : 0.004 0.050 4414 Dihedral : 3.940 21.998 3488 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 4.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.95 (0.16), residues: 3174 helix: 1.93 (0.15), residues: 1284 sheet: -0.08 (0.25), residues: 472 loop : -0.27 (0.17), residues: 1418 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 209 time to evaluate : 3.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 123 outliers final: 96 residues processed: 324 average time/residue: 1.1960 time to fit residues: 460.8704 Evaluate side-chains 300 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 204 time to evaluate : 3.039 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 91 residues processed: 6 average time/residue: 0.8682 time to fit residues: 10.5484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 0.0070 chunk 302 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 chunk 143 optimal weight: 0.8980 chunk 209 optimal weight: 4.9990 chunk 316 optimal weight: 9.9990 chunk 291 optimal weight: 0.0040 chunk 252 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 194 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 overall best weight: 0.7412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN E 347 GLN E 371 HIS E 464 GLN ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 GLN F 455 ASN F 470 HIS ** H 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 25654 Z= 0.180 Angle : 0.539 13.655 34772 Z= 0.276 Chirality : 0.043 0.143 4104 Planarity : 0.004 0.058 4414 Dihedral : 3.892 22.132 3488 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer Outliers : 3.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 1.03 (0.16), residues: 3174 helix: 1.98 (0.15), residues: 1284 sheet: -0.04 (0.25), residues: 462 loop : -0.20 (0.17), residues: 1428 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 206 time to evaluate : 2.911 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 108 outliers final: 89 residues processed: 308 average time/residue: 1.1792 time to fit residues: 431.8077 Evaluate side-chains 288 residues out of total 2834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 199 time to evaluate : 2.917 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 88 residues processed: 1 average time/residue: 0.4038 time to fit residues: 4.5889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 9.9990 chunk 268 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 232 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 252 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 259 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN E 347 GLN E 371 HIS ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 GLN F 455 ASN ** H 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 ASN J 172 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.110356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.079663 restraints weight = 43948.459| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.51 r_work: 0.3046 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 25654 Z= 0.237 Angle : 0.558 13.639 34772 Z= 0.286 Chirality : 0.043 0.172 4104 Planarity : 0.004 0.060 4414 Dihedral : 3.992 21.032 3488 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 3.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 1.01 (0.16), residues: 3174 helix: 1.94 (0.15), residues: 1286 sheet: -0.02 (0.25), residues: 482 loop : -0.21 (0.17), residues: 1406 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9396.76 seconds wall clock time: 167 minutes 22.05 seconds (10042.05 seconds total)