Starting phenix.real_space_refine on Mon Feb 19 09:28:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzw_22582/02_2024/7jzw_22582.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzw_22582/02_2024/7jzw_22582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzw_22582/02_2024/7jzw_22582.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzw_22582/02_2024/7jzw_22582.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzw_22582/02_2024/7jzw_22582.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzw_22582/02_2024/7jzw_22582.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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: 5 Type Number sf(0) Gaussians P 60 5.49 5 S 29 5.16 5 C 15040 2.51 5 N 4422 2.21 5 O 4715 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 12": "OE1" <-> "OE2" Residue "A PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 55": "OD1" <-> "OD2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A ASP 76": "OD1" <-> "OD2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 259": "NH1" <-> "NH2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "A ARG 299": "NH1" <-> "NH2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A ASP 331": "OD1" <-> "OD2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A ARG 367": "NH1" <-> "NH2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "C ASP 6": "OD1" <-> "OD2" Residue "C ASP 12": "OD1" <-> "OD2" Residue "C ASP 38": "OD1" <-> "OD2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C ASP 65": "OD1" <-> "OD2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C ASP 140": "OD1" <-> "OD2" Residue "C PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B ASP 120": "OD1" <-> "OD2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ARG 151": "NH1" <-> "NH2" Residue "B PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B ARG 174": "NH1" <-> "NH2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B ARG 201": "NH1" <-> "NH2" Residue "B PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 268": "NH1" <-> "NH2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B ASP 272": "OD1" <-> "OD2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 53": "OD1" <-> "OD2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E ASP 82": "OD1" <-> "OD2" Residue "E PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "E ASP 204": "OD1" <-> "OD2" Residue "E ASP 208": "OD1" <-> "OD2" Residue "E PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 293": "OE1" <-> "OE2" Residue "E GLU 335": "OE1" <-> "OE2" Residue "D PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 53": "OD1" <-> "OD2" Residue "D ASP 130": "OD1" <-> "OD2" Residue "D ASP 135": "OD1" <-> "OD2" Residue "D PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D ASP 240": "OD1" <-> "OD2" Residue "D PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 270": "OD1" <-> "OD2" Residue "D TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 294": "OD1" <-> "OD2" Residue "D ASP 334": "OD1" <-> "OD2" Residue "F PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 34": "OE1" <-> "OE2" Residue "F ASP 53": "OD1" <-> "OD2" Residue "F ASP 82": "OD1" <-> "OD2" Residue "F ASP 147": "OD1" <-> "OD2" Residue "F ARG 169": "NH1" <-> "NH2" Residue "F ASP 208": "OD1" <-> "OD2" Residue "F GLU 216": "OE1" <-> "OE2" Residue "F PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 253": "OD1" <-> "OD2" Residue "F ASP 256": "OD1" <-> "OD2" Residue "F TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 322": "OD1" <-> "OD2" Residue "F GLU 335": "OE1" <-> "OE2" Residue "F GLU 357": "OE1" <-> "OE2" Residue "G PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 38": "OD1" <-> "OD2" Residue "G ASP 82": "OD1" <-> "OD2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "G ASP 208": "OD1" <-> "OD2" Residue "G GLU 216": "OE1" <-> "OE2" Residue "G PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 240": "OD1" <-> "OD2" Residue "G ASP 270": "OD1" <-> "OD2" Residue "G TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 292": "OD1" <-> "OD2" Residue "H GLU 34": "OE1" <-> "OE2" Residue "H ASP 38": "OD1" <-> "OD2" Residue "H ASP 82": "OD1" <-> "OD2" Residue "H ARG 169": "NH1" <-> "NH2" Residue "H ASP 292": "OD1" <-> "OD2" Residue "H GLU 293": "OE1" <-> "OE2" Residue "H GLU 302": "OE1" <-> "OE2" Residue "H ASP 322": "OD1" <-> "OD2" Residue "H GLU 335": "OE1" <-> "OE2" Residue "I PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 65": "OE1" <-> "OE2" Residue "I ASP 82": "OD1" <-> "OD2" Residue "I ASP 130": "OD1" <-> "OD2" Residue "I PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 169": "NH1" <-> "NH2" Residue "I GLU 188": "OE1" <-> "OE2" Residue "I GLU 216": "OE1" <-> "OE2" Residue "I GLU 249": "OE1" <-> "OE2" Residue "I GLU 302": "OE1" <-> "OE2" Residue "I ASP 322": "OD1" <-> "OD2" Residue "I GLU 335": "OE1" <-> "OE2" Residue "J ASP 10": "OD1" <-> "OD2" Residue "J ASP 31": "OD1" <-> "OD2" Residue "J GLU 32": "OE1" <-> "OE2" Residue "J GLU 50": "OE1" <-> "OE2" Residue "J TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 57": "NH1" <-> "NH2" Residue "J GLU 92": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24266 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3145 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 24, 'TRANS': 402} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 364 Unresolved non-hydrogen dihedrals: 232 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 192 Chain: "C" Number of atoms: 1448 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 1480 Chain: "B" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2411 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 24, 'TRANS': 281} Chain breaks: 1 Chain: "E" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "D" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2307 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 10, 'TRANS': 287} Chain breaks: 2 Chain: "F" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "G" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "H" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2554 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain breaks: 1 Chain: "I" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "J" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 760 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "M" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1273 Classifications: {'DNA': 1, 'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 28, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 13.52, per 1000 atoms: 0.56 Number of scatterers: 24266 At special positions: 0 Unit cell: (130.2, 157.5, 148.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 P 60 15.00 O 4715 8.00 N 4422 7.00 C 15040 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: 9.69 Conformation dependent library (CDL) restraints added in 4.5 seconds 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5548 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 56 sheets defined 32.4% alpha, 22.8% beta 6 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 8.56 Creating SS restraints... Processing helix chain 'A' and resid 9 through 31 Processing helix chain 'A' and resid 38 through 47 removed outlier: 4.417A pdb=" N THR A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 60 removed outlier: 3.663A pdb=" N ALA A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 114 Processing helix chain 'A' and resid 115 through 122 Processing helix chain 'A' and resid 129 through 136 removed outlier: 3.600A pdb=" N GLU A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 160 removed outlier: 3.500A pdb=" N ALA A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 196 through 212 Processing helix chain 'A' and resid 212 through 224 removed outlier: 3.785A pdb=" N ALA A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.658A pdb=" N ASN A 250 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 251 " --> pdb=" O PRO A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 251' Processing helix chain 'A' and resid 253 through 258 removed outlier: 3.819A pdb=" N GLU A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 removed outlier: 4.444A pdb=" N GLN A 273 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 309 removed outlier: 3.515A pdb=" N SER A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 340 Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 364 through 368 removed outlier: 4.044A pdb=" N ARG A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 368 " --> pdb=" O PRO A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 368' Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.590A pdb=" N ARG A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 376 through 381' Processing helix chain 'A' and resid 386 through 396 removed outlier: 3.667A pdb=" N ARG A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 408 removed outlier: 3.781A pdb=" N SER A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 431 removed outlier: 4.376A pdb=" N ALA A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 36 Processing helix chain 'C' and resid 63 through 71 Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.902A pdb=" N LEU C 76 " --> pdb=" O ARG C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 120 removed outlier: 3.889A pdb=" N LEU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 131 Processing helix chain 'B' and resid 33 through 49 removed outlier: 3.904A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 removed outlier: 3.648A pdb=" N ASP B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 165 through 178 Processing helix chain 'B' and resid 189 through 204 removed outlier: 3.581A pdb=" N LEU B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 218 Processing helix chain 'E' and resid 82 through 91 Processing helix chain 'E' and resid 130 through 148 Processing helix chain 'E' and resid 151 through 163 Processing helix chain 'E' and resid 208 through 223 Processing helix chain 'E' and resid 275 through 284 Processing helix chain 'E' and resid 322 through 331 Processing helix chain 'E' and resid 338 through 352 Processing helix chain 'D' and resid 130 through 148 Processing helix chain 'D' and resid 152 through 163 Processing helix chain 'D' and resid 209 through 224 Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 322 through 332 Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.633A pdb=" N SER F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 148 Processing helix chain 'F' and resid 151 through 163 Processing helix chain 'F' and resid 209 through 223 removed outlier: 3.588A pdb=" N ALA F 213 " --> pdb=" O ALA F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 284 Processing helix chain 'F' and resid 322 through 332 removed outlier: 3.504A pdb=" N LEU F 326 " --> pdb=" O ASP F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 352 Processing helix chain 'G' and resid 82 through 91 Processing helix chain 'G' and resid 130 through 148 Processing helix chain 'G' and resid 151 through 163 Processing helix chain 'G' and resid 209 through 223 removed outlier: 3.565A pdb=" N ALA G 213 " --> pdb=" O ALA G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 275 through 284 Processing helix chain 'G' and resid 293 through 297 Processing helix chain 'G' and resid 322 through 331 Processing helix chain 'G' and resid 338 through 352 Processing helix chain 'H' and resid 82 through 92 removed outlier: 3.739A pdb=" N SER H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 148 Processing helix chain 'H' and resid 151 through 163 Processing helix chain 'H' and resid 208 through 223 Processing helix chain 'H' and resid 275 through 284 Processing helix chain 'H' and resid 322 through 331 Processing helix chain 'H' and resid 338 through 352 Processing helix chain 'I' and resid 51 through 55 Processing helix chain 'I' and resid 82 through 90 Processing helix chain 'I' and resid 130 through 148 Processing helix chain 'I' and resid 152 through 163 Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 275 through 284 Processing helix chain 'I' and resid 322 through 332 Processing helix chain 'I' and resid 338 through 352 Processing helix chain 'J' and resid 5 through 14 removed outlier: 3.539A pdb=" N ILE J 9 " --> pdb=" O SER J 5 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR J 12 " --> pdb=" O ASP J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 78 Processing helix chain 'J' and resid 79 through 100 removed outlier: 3.690A pdb=" N VAL J 83 " --> pdb=" O ARG J 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 192 removed outlier: 6.211A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 191 through 192 removed outlier: 6.211A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY B 254 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLY B 285 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLY B 287 " --> pdb=" O PRO B 250 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 267 Processing sheet with id=AA7, first strand: chain 'C' and resid 41 through 43 removed outlier: 3.534A pdb=" N HIS C 3 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 41 through 43 removed outlier: 3.534A pdb=" N HIS C 3 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 97 through 98 removed outlier: 3.509A pdb=" N VAL C 184 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB2, first strand: chain 'B' and resid 54 through 60 removed outlier: 4.079A pdb=" N VAL B 59 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU B 110 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ALA B 103 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN B 19 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU B 109 " --> pdb=" O PRO B 13 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU B 111 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LEU B 11 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B 113 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU B 9 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER B 16 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 65 through 68 removed outlier: 5.198A pdb=" N ALA B 103 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN B 19 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU B 109 " --> pdb=" O PRO B 13 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU B 111 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LEU B 11 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B 113 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU B 9 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 157 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AB5, first strand: chain 'B' and resid 221 through 222 Processing sheet with id=AB6, first strand: chain 'B' and resid 304 through 306 Processing sheet with id=AB7, first strand: chain 'E' and resid 127 through 128 Processing sheet with id=AB8, first strand: chain 'E' and resid 38 through 39 removed outlier: 4.212A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU E 229 " --> pdb=" O ILE E 184 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 189 through 192 removed outlier: 6.553A pdb=" N HIS E 183 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA E 192 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE E 181 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU E 229 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 63 through 70 Processing sheet with id=AC2, first strand: chain 'E' and resid 285 through 287 Processing sheet with id=AC3, first strand: chain 'E' and resid 306 through 307 removed outlier: 3.519A pdb=" N VAL E 307 " --> pdb=" O LYS E 312 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS E 312 " --> pdb=" O VAL E 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AC5, first strand: chain 'D' and resid 38 through 39 removed outlier: 4.093A pdb=" N VAL D 228 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU D 229 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA D 176 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL D 177 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ASP D 196 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL D 179 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARG D 194 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE D 181 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA D 192 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N HIS D 183 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU D 188 " --> pdb=" O ARG D 185 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 38 through 39 Processing sheet with id=AC7, first strand: chain 'D' and resid 63 through 66 removed outlier: 4.598A pdb=" N ALA D 101 " --> pdb=" O VAL D 244 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 248 through 249 removed outlier: 4.603A pdb=" N THR D 264 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 285 through 287 Processing sheet with id=AD1, first strand: chain 'D' and resid 306 through 307 Processing sheet with id=AD2, first strand: chain 'F' and resid 127 through 128 Processing sheet with id=AD3, first strand: chain 'F' and resid 38 through 39 removed outlier: 4.181A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU F 229 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG F 191 " --> pdb=" O HIS F 183 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 38 through 39 Processing sheet with id=AD5, first strand: chain 'F' and resid 63 through 70 removed outlier: 3.671A pdb=" N GLY F 70 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN F 94 " --> pdb=" O GLY F 70 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 285 through 287 Processing sheet with id=AD7, first strand: chain 'F' and resid 306 through 307 removed outlier: 3.670A pdb=" N LYS F 312 " --> pdb=" O VAL F 307 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 127 through 128 Processing sheet with id=AD9, first strand: chain 'G' and resid 38 through 39 removed outlier: 4.040A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 189 through 192 removed outlier: 3.670A pdb=" N ARG G 191 " --> pdb=" O HIS G 183 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 63 through 70 removed outlier: 3.611A pdb=" N GLY G 70 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALA G 101 " --> pdb=" O VAL G 244 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 306 through 307 Processing sheet with id=AE4, first strand: chain 'H' and resid 127 through 128 removed outlier: 3.569A pdb=" N GLY H 353 " --> pdb=" O PHE H 33 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 38 through 39 removed outlier: 4.142A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 188 through 192 removed outlier: 6.731A pdb=" N HIS H 183 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ALA H 192 " --> pdb=" O ILE H 181 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE H 181 " --> pdb=" O ALA H 192 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 63 through 66 removed outlier: 4.576A pdb=" N ALA H 101 " --> pdb=" O VAL H 244 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 69 through 70 removed outlier: 3.697A pdb=" N GLY H 70 " --> pdb=" O ASN H 94 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'H' and resid 248 through 249 removed outlier: 4.702A pdb=" N THR H 264 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 285 through 287 Processing sheet with id=AF2, first strand: chain 'H' and resid 306 through 307 removed outlier: 3.653A pdb=" N LYS H 312 " --> pdb=" O VAL H 307 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 127 through 128 Processing sheet with id=AF4, first strand: chain 'I' and resid 38 through 39 removed outlier: 4.528A pdb=" N LEU I 229 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL I 177 " --> pdb=" O ASP I 196 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASP I 196 " --> pdb=" O VAL I 177 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL I 179 " --> pdb=" O ARG I 194 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG I 194 " --> pdb=" O VAL I 179 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE I 181 " --> pdb=" O ALA I 192 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA I 192 " --> pdb=" O ILE I 181 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N HIS I 183 " --> pdb=" O ALA I 190 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 38 through 39 Processing sheet with id=AF6, first strand: chain 'I' and resid 63 through 70 removed outlier: 3.729A pdb=" N ASN I 94 " --> pdb=" O GLY I 70 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA I 101 " --> pdb=" O VAL I 244 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 63 through 70 removed outlier: 3.729A pdb=" N ASN I 94 " --> pdb=" O GLY I 70 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LYS I 261 " --> pdb=" O LEU I 95 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR I 97 " --> pdb=" O LYS I 261 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS I 263 " --> pdb=" O THR I 97 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 285 through 287 Processing sheet with id=AF9, first strand: chain 'I' and resid 306 through 307 removed outlier: 3.665A pdb=" N LYS I 312 " --> pdb=" O VAL I 307 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 17 through 21 removed outlier: 12.893A pdb=" N TRP J 28 " --> pdb=" O VAL J 47 " (cutoff:3.500A) removed outlier: 9.401A pdb=" N VAL J 47 " --> pdb=" O TRP J 28 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ILE J 30 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY J 55 " --> pdb=" O VAL J 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 17 through 21 1050 hydrogen bonds defined for protein. 2925 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 8.58 Time building geometry restraints manager: 10.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5046 1.32 - 1.44: 5968 1.44 - 1.56: 13702 1.56 - 1.68: 120 1.68 - 1.80: 44 Bond restraints: 24880 Sorted by residual: bond pdb=" C LEU B 181 " pdb=" N PRO B 182 " ideal model delta sigma weight residual 1.337 1.382 -0.046 9.80e-03 1.04e+04 2.16e+01 bond pdb=" O3' A M 36 " pdb=" P C M 37 " ideal model delta sigma weight residual 1.607 1.660 -0.053 1.50e-02 4.44e+03 1.26e+01 bond pdb=" N LEU A 70 " pdb=" CA LEU A 70 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.32e-02 5.74e+03 8.10e+00 bond pdb=" N GLN H 186 " pdb=" CA GLN H 186 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.19e+00 bond pdb=" CG LEU D 229 " pdb=" CD1 LEU D 229 " ideal model delta sigma weight residual 1.521 1.441 0.080 3.30e-02 9.18e+02 5.90e+00 ... (remaining 24875 not shown) Histogram of bond angle deviations from ideal: 99.41 - 106.35: 993 106.35 - 113.29: 13482 113.29 - 120.23: 9214 120.23 - 127.17: 9946 127.17 - 134.11: 441 Bond angle restraints: 34076 Sorted by residual: angle pdb=" O ARG H 185 " pdb=" C ARG H 185 " pdb=" N GLN H 186 " ideal model delta sigma weight residual 122.23 129.29 -7.06 1.33e+00 5.65e-01 2.82e+01 angle pdb=" C ARG F 185 " pdb=" N GLN F 186 " pdb=" CA GLN F 186 " ideal model delta sigma weight residual 120.82 128.71 -7.89 1.50e+00 4.44e-01 2.77e+01 angle pdb=" C GLN A 124 " pdb=" N TYR A 125 " pdb=" CA TYR A 125 " ideal model delta sigma weight residual 120.79 127.65 -6.86 1.39e+00 5.18e-01 2.44e+01 angle pdb=" C ARG I 185 " pdb=" N GLN I 186 " pdb=" CA GLN I 186 " ideal model delta sigma weight residual 120.38 126.93 -6.55 1.37e+00 5.33e-01 2.28e+01 angle pdb=" C ARG H 185 " pdb=" N GLN H 186 " pdb=" CA GLN H 186 " ideal model delta sigma weight residual 121.54 130.61 -9.07 1.91e+00 2.74e-01 2.25e+01 ... (remaining 34071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 14498 35.59 - 71.19: 468 71.19 - 106.78: 39 106.78 - 142.37: 1 142.37 - 177.96: 5 Dihedral angle restraints: 15011 sinusoidal: 6419 harmonic: 8592 Sorted by residual: dihedral pdb=" O4' U M 33 " pdb=" C1' U M 33 " pdb=" N1 U M 33 " pdb=" C2 U M 33 " ideal model delta sinusoidal sigma weight residual 200.00 53.90 146.10 1 1.50e+01 4.44e-03 7.81e+01 dihedral pdb=" O4' U M 21 " pdb=" C1' U M 21 " pdb=" N1 U M 21 " pdb=" C2 U M 21 " ideal model delta sinusoidal sigma weight residual 200.00 65.69 134.31 1 1.50e+01 4.44e-03 7.25e+01 dihedral pdb=" O4' C M 38 " pdb=" C1' C M 38 " pdb=" N1 C M 38 " pdb=" C2 C M 38 " ideal model delta sinusoidal sigma weight residual -128.00 49.96 -177.96 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 15008 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3034 0.063 - 0.127: 682 0.127 - 0.190: 113 0.190 - 0.254: 6 0.254 - 0.317: 4 Chirality restraints: 3839 Sorted by residual: chirality pdb=" CB THR B 318 " pdb=" CA THR B 318 " pdb=" OG1 THR B 318 " pdb=" CG2 THR B 318 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CB ILE B 219 " pdb=" CA ILE B 219 " pdb=" CG1 ILE B 219 " pdb=" CG2 ILE B 219 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C1' U M 33 " pdb=" O4' U M 33 " pdb=" C2' U M 33 " pdb=" N1 U M 33 " both_signs ideal model delta sigma weight residual False 2.47 2.21 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 3836 not shown) Planarity restraints: 4272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 71 " 0.053 5.00e-02 4.00e+02 7.88e-02 9.95e+00 pdb=" N PRO A 72 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 73 " -0.047 5.00e-02 4.00e+02 7.08e-02 8.03e+00 pdb=" N PRO C 74 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 74 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 74 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 103 " 0.046 5.00e-02 4.00e+02 6.93e-02 7.68e+00 pdb=" N PRO D 104 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO D 104 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 104 " 0.038 5.00e-02 4.00e+02 ... (remaining 4269 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4954 2.77 - 3.30: 21528 3.30 - 3.83: 42348 3.83 - 4.37: 51903 4.37 - 4.90: 87079 Nonbonded interactions: 207812 Sorted by model distance: nonbonded pdb=" OH TYR F 324 " pdb=" O SER G 73 " model vdw 2.237 2.440 nonbonded pdb=" OH TYR E 324 " pdb=" O SER F 73 " model vdw 2.237 2.440 nonbonded pdb=" OH TYR G 324 " pdb=" O SER H 73 " model vdw 2.255 2.440 nonbonded pdb=" OH TYR H 324 " pdb=" O SER I 73 " model vdw 2.256 2.440 nonbonded pdb=" O SER E 73 " pdb=" OH TYR D 324 " model vdw 2.266 2.440 ... (remaining 207807 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 'D' selection = (chain 'E' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'F' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'G' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'H' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'I' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) } 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=0.37 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 5.060 Check model and map are aligned: 0.400 Set scattering table: 0.250 Process input model: 70.760 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.100 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 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 : 0.010 0.080 24880 Z= 0.635 Angle : 0.973 10.119 34076 Z= 0.541 Chirality : 0.055 0.317 3839 Planarity : 0.007 0.079 4272 Dihedral : 17.319 177.963 9463 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.93 % Favored : 93.04 % Rotamer: Outliers : 0.13 % Allowed : 8.21 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -3.86 (0.12), residues: 2959 helix: -2.82 (0.11), residues: 933 sheet: -1.31 (0.22), residues: 482 loop : -2.85 (0.12), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP I 49 HIS 0.010 0.002 HIS E 275 PHE 0.027 0.003 PHE B 40 TYR 0.021 0.003 TYR F 290 ARG 0.014 0.001 ARG H 237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 285 time to evaluate : 2.880 Fit side-chains revert: symmetry clash REVERT: A 290 ASP cc_start: 0.7798 (m-30) cc_final: 0.7553 (m-30) REVERT: A 420 LYS cc_start: 0.7768 (ttpp) cc_final: 0.7522 (ttpp) REVERT: C 84 GLN cc_start: 0.8369 (pt0) cc_final: 0.8137 (pt0) REVERT: B 76 LYS cc_start: 0.8895 (mttp) cc_final: 0.8517 (mttt) REVERT: B 152 PHE cc_start: 0.6389 (p90) cc_final: 0.6107 (p90) REVERT: B 268 ARG cc_start: 0.6784 (tpt170) cc_final: 0.6581 (ttt90) REVERT: D 66 LYS cc_start: 0.7757 (ptmt) cc_final: 0.7439 (ptmt) REVERT: D 138 LEU cc_start: 0.8765 (mt) cc_final: 0.8448 (mp) REVERT: I 307 VAL cc_start: 0.8933 (t) cc_final: 0.8709 (t) REVERT: J 26 TRP cc_start: 0.8634 (m100) cc_final: 0.8087 (m100) outliers start: 3 outliers final: 2 residues processed: 288 average time/residue: 0.5064 time to fit residues: 204.3515 Evaluate side-chains 204 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 202 time to evaluate : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain H residue 78 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 252 optimal weight: 1.9990 chunk 226 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 234 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 142 optimal weight: 0.8980 chunk 174 optimal weight: 0.5980 chunk 271 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN C 29 HIS ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 24880 Z= 0.187 Angle : 0.554 10.778 34076 Z= 0.293 Chirality : 0.040 0.204 3839 Planarity : 0.004 0.057 4272 Dihedral : 15.405 179.490 4206 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.85 % Favored : 94.12 % Rotamer: Outliers : 1.47 % Allowed : 11.88 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -2.43 (0.13), residues: 2959 helix: -0.93 (0.15), residues: 950 sheet: -0.54 (0.23), residues: 460 loop : -2.46 (0.13), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 49 HIS 0.005 0.001 HIS C 29 PHE 0.012 0.001 PHE A 425 TYR 0.011 0.002 TYR G 290 ARG 0.006 0.000 ARG F 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 229 time to evaluate : 2.612 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.7916 (pt0) REVERT: A 422 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8282 (mt) REVERT: C 84 GLN cc_start: 0.8369 (pt0) cc_final: 0.8049 (pt0) REVERT: B 76 LYS cc_start: 0.8796 (mttp) cc_final: 0.8458 (mttt) REVERT: B 152 PHE cc_start: 0.6327 (p90) cc_final: 0.6117 (p90) REVERT: B 170 ARG cc_start: 0.7447 (ttp80) cc_final: 0.7074 (mtp-110) REVERT: B 200 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8127 (tp) REVERT: D 138 LEU cc_start: 0.8717 (mt) cc_final: 0.8384 (mt) REVERT: J 26 TRP cc_start: 0.8432 (m100) cc_final: 0.7955 (m100) outliers start: 34 outliers final: 16 residues processed: 251 average time/residue: 0.4964 time to fit residues: 178.5639 Evaluate side-chains 224 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 205 time to evaluate : 2.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 333 ARG Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 319 GLN Chi-restraints excluded: chain I residue 203 ARG Chi-restraints excluded: chain I residue 296 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 150 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 225 optimal weight: 0.9980 chunk 184 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 272 optimal weight: 4.9990 chunk 293 optimal weight: 5.9990 chunk 242 optimal weight: 0.9980 chunk 269 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 218 optimal weight: 0.0870 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 ASN C 84 GLN C 154 HIS ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 342 GLN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24880 Z= 0.179 Angle : 0.521 11.573 34076 Z= 0.270 Chirality : 0.039 0.188 3839 Planarity : 0.004 0.052 4272 Dihedral : 15.210 179.460 4206 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.05 % Favored : 93.91 % Rotamer: Outliers : 1.94 % Allowed : 13.00 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -1.67 (0.14), residues: 2959 helix: 0.12 (0.16), residues: 954 sheet: -0.45 (0.23), residues: 492 loop : -2.23 (0.14), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 49 HIS 0.004 0.001 HIS C 29 PHE 0.011 0.001 PHE B 40 TYR 0.021 0.001 TYR C 176 ARG 0.013 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 210 time to evaluate : 2.743 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.7876 (pt0) REVERT: A 422 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8378 (mt) REVERT: C 84 GLN cc_start: 0.8329 (pt0) cc_final: 0.8085 (pt0) REVERT: B 76 LYS cc_start: 0.8769 (mttp) cc_final: 0.8445 (mttt) REVERT: B 268 ARG cc_start: 0.6762 (tpt170) cc_final: 0.6491 (ttt90) REVERT: D 138 LEU cc_start: 0.8679 (mt) cc_final: 0.8329 (mt) REVERT: D 212 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7265 (t0) REVERT: F 185 ARG cc_start: 0.7797 (mmt-90) cc_final: 0.7519 (mmp80) REVERT: H 307 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8368 (m) REVERT: J 26 TRP cc_start: 0.8431 (m100) cc_final: 0.8013 (m100) outliers start: 45 outliers final: 27 residues processed: 240 average time/residue: 0.4573 time to fit residues: 159.3597 Evaluate side-chains 226 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 195 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 333 ARG Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain H residue 319 GLN Chi-restraints excluded: chain I residue 203 ARG Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 18 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 268 optimal weight: 0.8980 chunk 204 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 129 optimal weight: 0.7980 chunk 182 optimal weight: 4.9990 chunk 272 optimal weight: 4.9990 chunk 289 optimal weight: 4.9990 chunk 142 optimal weight: 0.2980 chunk 258 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 HIS E 94 ASN E 186 GLN E 242 GLN D 102 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 348 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24880 Z= 0.173 Angle : 0.504 12.090 34076 Z= 0.261 Chirality : 0.039 0.183 3839 Planarity : 0.003 0.052 4272 Dihedral : 15.077 179.562 4206 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.88 % Favored : 94.08 % Rotamer: Outliers : 2.07 % Allowed : 14.08 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -1.17 (0.15), residues: 2959 helix: 0.72 (0.17), residues: 959 sheet: -0.19 (0.23), residues: 486 loop : -2.06 (0.14), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 49 HIS 0.004 0.001 HIS A 283 PHE 0.010 0.001 PHE C 155 TYR 0.010 0.001 TYR G 304 ARG 0.008 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 212 time to evaluate : 2.546 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.7908 (pt0) REVERT: A 422 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8268 (mt) REVERT: C 84 GLN cc_start: 0.8266 (pt0) cc_final: 0.8024 (pt0) REVERT: B 76 LYS cc_start: 0.8787 (mttp) cc_final: 0.8445 (mttt) REVERT: B 268 ARG cc_start: 0.6778 (tpt170) cc_final: 0.6513 (ttt90) REVERT: E 43 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8708 (mp) REVERT: E 186 GLN cc_start: 0.7550 (mm-40) cc_final: 0.7250 (mp10) REVERT: D 138 LEU cc_start: 0.8654 (mt) cc_final: 0.8215 (mp) REVERT: D 212 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.7247 (t0) REVERT: F 185 ARG cc_start: 0.7789 (mmt-90) cc_final: 0.7513 (mmp80) REVERT: H 307 VAL cc_start: 0.8640 (OUTLIER) cc_final: 0.8354 (m) REVERT: J 26 TRP cc_start: 0.8396 (m100) cc_final: 0.8023 (m100) outliers start: 48 outliers final: 33 residues processed: 243 average time/residue: 0.4651 time to fit residues: 164.7510 Evaluate side-chains 235 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 197 time to evaluate : 2.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 247 SER Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 304 TYR Chi-restraints excluded: chain G residue 333 ARG Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain H residue 319 GLN Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 203 ARG Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain J residue 17 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 240 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 246 optimal weight: 0.0270 chunk 199 optimal weight: 0.0000 chunk 0 optimal weight: 40.0000 chunk 147 optimal weight: 0.4980 chunk 259 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.5046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 HIS ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 GLN ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 342 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 24880 Z= 0.139 Angle : 0.485 11.926 34076 Z= 0.252 Chirality : 0.038 0.181 3839 Planarity : 0.003 0.051 4272 Dihedral : 14.966 179.984 4203 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.65 % Favored : 94.32 % Rotamer: Outliers : 2.12 % Allowed : 15.12 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.85 (0.15), residues: 2959 helix: 1.08 (0.17), residues: 959 sheet: 0.00 (0.23), residues: 486 loop : -1.94 (0.14), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 49 HIS 0.005 0.001 HIS A 283 PHE 0.009 0.001 PHE B 40 TYR 0.010 0.001 TYR A 235 ARG 0.008 0.000 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 210 time to evaluate : 2.656 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.7826 (pt0) REVERT: A 422 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8276 (mt) REVERT: B 76 LYS cc_start: 0.8791 (mttp) cc_final: 0.8466 (mttt) REVERT: B 268 ARG cc_start: 0.6804 (tpt170) cc_final: 0.6557 (ttt90) REVERT: E 186 GLN cc_start: 0.7457 (mm-40) cc_final: 0.7066 (mp10) REVERT: E 308 THR cc_start: 0.8496 (t) cc_final: 0.8204 (p) REVERT: D 212 ASP cc_start: 0.7489 (OUTLIER) cc_final: 0.7235 (t0) REVERT: F 185 ARG cc_start: 0.7756 (mmt-90) cc_final: 0.7511 (mmt90) REVERT: G 155 ARG cc_start: 0.7647 (ttp80) cc_final: 0.7438 (ttp-110) REVERT: H 147 ASP cc_start: 0.7060 (m-30) cc_final: 0.6840 (m-30) REVERT: H 307 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8289 (m) REVERT: I 94 ASN cc_start: 0.8186 (p0) cc_final: 0.7549 (t0) REVERT: J 26 TRP cc_start: 0.8363 (m100) cc_final: 0.7990 (m100) outliers start: 49 outliers final: 33 residues processed: 245 average time/residue: 0.4554 time to fit residues: 162.9672 Evaluate side-chains 226 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 189 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 247 SER Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 304 TYR Chi-restraints excluded: chain G residue 333 ARG Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 203 ARG Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain J residue 17 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 97 optimal weight: 7.9990 chunk 260 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 169 optimal weight: 0.5980 chunk 71 optimal weight: 9.9990 chunk 289 optimal weight: 8.9990 chunk 240 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 151 optimal weight: 0.6980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 HIS E 94 ASN D 148 GLN F 148 GLN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24880 Z= 0.251 Angle : 0.528 12.529 34076 Z= 0.272 Chirality : 0.040 0.182 3839 Planarity : 0.004 0.053 4272 Dihedral : 14.984 178.549 4203 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.36 % Favored : 93.61 % Rotamer: Outliers : 2.07 % Allowed : 15.68 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.83 (0.15), residues: 2959 helix: 1.14 (0.17), residues: 956 sheet: -0.08 (0.23), residues: 496 loop : -1.92 (0.15), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 49 HIS 0.006 0.001 HIS C 29 PHE 0.012 0.001 PHE C 44 TYR 0.015 0.002 TYR A 336 ARG 0.008 0.000 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 199 time to evaluate : 2.827 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.7876 (pt0) REVERT: A 289 HIS cc_start: 0.6985 (m-70) cc_final: 0.6535 (m-70) REVERT: A 290 ASP cc_start: 0.7933 (m-30) cc_final: 0.7683 (m-30) REVERT: A 422 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8374 (mt) REVERT: B 76 LYS cc_start: 0.8799 (mttp) cc_final: 0.8438 (mttt) REVERT: B 268 ARG cc_start: 0.6807 (tpt170) cc_final: 0.6523 (ttt90) REVERT: E 186 GLN cc_start: 0.7512 (mm-40) cc_final: 0.7220 (mp10) REVERT: E 308 THR cc_start: 0.8571 (t) cc_final: 0.8243 (p) REVERT: D 212 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7204 (t0) REVERT: F 185 ARG cc_start: 0.7785 (mmt-90) cc_final: 0.7553 (mmt90) REVERT: G 290 TYR cc_start: 0.8953 (p90) cc_final: 0.8554 (p90) REVERT: H 147 ASP cc_start: 0.7073 (m-30) cc_final: 0.6794 (m-30) REVERT: H 307 VAL cc_start: 0.8662 (OUTLIER) cc_final: 0.8356 (m) REVERT: J 26 TRP cc_start: 0.8421 (m100) cc_final: 0.7993 (m100) outliers start: 48 outliers final: 35 residues processed: 231 average time/residue: 0.4682 time to fit residues: 157.3800 Evaluate side-chains 227 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 188 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 247 SER Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 304 TYR Chi-restraints excluded: chain G residue 333 ARG Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 203 ARG Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain J residue 17 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 278 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 164 optimal weight: 0.8980 chunk 211 optimal weight: 0.5980 chunk 163 optimal weight: 0.9990 chunk 243 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 288 optimal weight: 5.9990 chunk 180 optimal weight: 0.7980 chunk 175 optimal weight: 0.1980 chunk 133 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 HIS E 94 ASN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24880 Z= 0.158 Angle : 0.486 12.150 34076 Z= 0.251 Chirality : 0.038 0.181 3839 Planarity : 0.003 0.051 4272 Dihedral : 14.906 179.743 4203 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.71 % Favored : 94.25 % Rotamer: Outliers : 2.20 % Allowed : 16.29 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.59 (0.15), residues: 2959 helix: 1.39 (0.17), residues: 958 sheet: 0.16 (0.24), residues: 474 loop : -1.84 (0.15), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 49 HIS 0.011 0.001 HIS C 29 PHE 0.010 0.001 PHE B 40 TYR 0.015 0.001 TYR A 336 ARG 0.008 0.000 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 204 time to evaluate : 2.670 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.7901 (pt0) REVERT: A 289 HIS cc_start: 0.6927 (m-70) cc_final: 0.6496 (m-70) REVERT: A 290 ASP cc_start: 0.7940 (m-30) cc_final: 0.7709 (m-30) REVERT: A 422 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8335 (mt) REVERT: B 76 LYS cc_start: 0.8757 (mttp) cc_final: 0.8418 (mttt) REVERT: B 268 ARG cc_start: 0.6869 (tpt170) cc_final: 0.6623 (ttt90) REVERT: B 288 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7486 (tt0) REVERT: E 186 GLN cc_start: 0.7439 (mm-40) cc_final: 0.7074 (mp10) REVERT: E 308 THR cc_start: 0.8450 (t) cc_final: 0.8219 (p) REVERT: E 314 TYR cc_start: 0.8054 (m-80) cc_final: 0.7612 (m-80) REVERT: D 212 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.7196 (t0) REVERT: F 185 ARG cc_start: 0.7726 (mmt-90) cc_final: 0.7491 (mmt90) REVERT: G 155 ARG cc_start: 0.7686 (ttp80) cc_final: 0.7474 (ttp-110) REVERT: G 290 TYR cc_start: 0.8934 (p90) cc_final: 0.8591 (p90) REVERT: H 147 ASP cc_start: 0.7051 (m-30) cc_final: 0.6769 (m-30) REVERT: H 307 VAL cc_start: 0.8597 (OUTLIER) cc_final: 0.8300 (m) REVERT: I 94 ASN cc_start: 0.8057 (p0) cc_final: 0.7675 (t0) REVERT: J 26 TRP cc_start: 0.8357 (m100) cc_final: 0.7933 (m100) outliers start: 51 outliers final: 37 residues processed: 238 average time/residue: 0.4649 time to fit residues: 161.2289 Evaluate side-chains 237 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 195 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 247 SER Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 304 TYR Chi-restraints excluded: chain G residue 333 ARG Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 203 ARG Chi-restraints excluded: chain I residue 296 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 178 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 172 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 55 optimal weight: 0.0670 chunk 183 optimal weight: 0.4980 chunk 196 optimal weight: 0.6980 chunk 142 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 226 optimal weight: 3.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24880 Z= 0.146 Angle : 0.481 11.975 34076 Z= 0.249 Chirality : 0.038 0.180 3839 Planarity : 0.003 0.051 4272 Dihedral : 14.844 179.542 4203 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.58 % Favored : 94.39 % Rotamer: Outliers : 1.86 % Allowed : 16.63 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.49 (0.15), residues: 2959 helix: 1.51 (0.17), residues: 958 sheet: 0.19 (0.23), residues: 474 loop : -1.80 (0.15), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 49 HIS 0.014 0.001 HIS C 29 PHE 0.011 0.001 PHE C 44 TYR 0.015 0.001 TYR A 179 ARG 0.009 0.000 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 203 time to evaluate : 2.858 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8012 (pt0) REVERT: A 289 HIS cc_start: 0.6997 (m-70) cc_final: 0.6592 (m-70) REVERT: A 422 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8329 (mt) REVERT: B 76 LYS cc_start: 0.8748 (mttp) cc_final: 0.8409 (mttt) REVERT: B 268 ARG cc_start: 0.6857 (tpt170) cc_final: 0.6630 (ttt90) REVERT: E 186 GLN cc_start: 0.7356 (mm-40) cc_final: 0.7058 (mp10) REVERT: E 308 THR cc_start: 0.8420 (t) cc_final: 0.8194 (p) REVERT: D 212 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.7190 (t0) REVERT: F 185 ARG cc_start: 0.7713 (mmt-90) cc_final: 0.7477 (mmt90) REVERT: G 65 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7791 (mt-10) REVERT: G 155 ARG cc_start: 0.7686 (ttp80) cc_final: 0.7478 (ttp-110) REVERT: G 290 TYR cc_start: 0.8927 (p90) cc_final: 0.8601 (p90) REVERT: H 147 ASP cc_start: 0.7060 (m-30) cc_final: 0.6772 (m-30) REVERT: H 307 VAL cc_start: 0.8552 (OUTLIER) cc_final: 0.8252 (m) REVERT: I 94 ASN cc_start: 0.8017 (p0) cc_final: 0.7695 (t0) REVERT: I 307 VAL cc_start: 0.8668 (t) cc_final: 0.8349 (t) REVERT: J 26 TRP cc_start: 0.8346 (m100) cc_final: 0.7936 (m100) outliers start: 43 outliers final: 32 residues processed: 234 average time/residue: 0.4886 time to fit residues: 166.1585 Evaluate side-chains 230 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 194 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 247 SER Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 304 TYR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 203 ARG Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain J residue 17 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 262 optimal weight: 7.9990 chunk 276 optimal weight: 3.9990 chunk 251 optimal weight: 5.9990 chunk 268 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 242 optimal weight: 3.9990 chunk 253 optimal weight: 0.9990 chunk 267 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 HIS E 94 ASN D 102 ASN F 342 GLN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 24880 Z= 0.428 Angle : 0.615 13.008 34076 Z= 0.314 Chirality : 0.044 0.189 3839 Planarity : 0.004 0.053 4272 Dihedral : 15.040 179.008 4203 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.27 % Favored : 92.70 % Rotamer: Outliers : 2.03 % Allowed : 16.80 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.83 (0.15), residues: 2959 helix: 1.14 (0.17), residues: 957 sheet: -0.19 (0.22), residues: 514 loop : -1.90 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 49 HIS 0.020 0.001 HIS C 29 PHE 0.015 0.002 PHE H 114 TYR 0.028 0.002 TYR A 179 ARG 0.009 0.001 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 198 time to evaluate : 2.757 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8204 (pt0) REVERT: A 289 HIS cc_start: 0.7086 (m-70) cc_final: 0.6682 (m-70) REVERT: A 290 ASP cc_start: 0.7939 (m-30) cc_final: 0.7704 (m-30) REVERT: A 422 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8384 (mt) REVERT: B 76 LYS cc_start: 0.8900 (mttp) cc_final: 0.8518 (mttt) REVERT: B 288 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7514 (tt0) REVERT: H 51 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7441 (pt0) REVERT: H 147 ASP cc_start: 0.7099 (m-30) cc_final: 0.6834 (m-30) REVERT: H 307 VAL cc_start: 0.8748 (OUTLIER) cc_final: 0.8437 (m) REVERT: I 94 ASN cc_start: 0.8117 (p0) cc_final: 0.7709 (t0) REVERT: J 26 TRP cc_start: 0.8431 (m100) cc_final: 0.7925 (m100) outliers start: 47 outliers final: 32 residues processed: 232 average time/residue: 0.4580 time to fit residues: 154.9882 Evaluate side-chains 225 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 188 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 247 SER Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 304 TYR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 51 GLN Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 203 ARG Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 18 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 176 optimal weight: 0.0980 chunk 283 optimal weight: 0.8980 chunk 173 optimal weight: 0.8980 chunk 134 optimal weight: 0.0010 chunk 197 optimal weight: 0.0570 chunk 297 optimal weight: 10.0000 chunk 274 optimal weight: 0.6980 chunk 237 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 145 optimal weight: 0.6980 overall best weight: 0.3104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN E 316 GLN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 24880 Z= 0.138 Angle : 0.498 12.234 34076 Z= 0.258 Chirality : 0.039 0.182 3839 Planarity : 0.003 0.051 4272 Dihedral : 14.931 179.207 4203 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.44 % Favored : 94.52 % Rotamer: Outliers : 1.73 % Allowed : 17.24 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: 2959 helix: 1.53 (0.17), residues: 957 sheet: 0.16 (0.23), residues: 474 loop : -1.76 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 193 HIS 0.014 0.001 HIS C 29 PHE 0.015 0.001 PHE C 44 TYR 0.014 0.001 TYR A 179 ARG 0.010 0.000 ARG B 170 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 194 time to evaluate : 3.084 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.7950 (pt0) REVERT: A 290 ASP cc_start: 0.7950 (m-30) cc_final: 0.7719 (m-30) REVERT: A 422 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8331 (mt) REVERT: B 76 LYS cc_start: 0.8753 (mttp) cc_final: 0.8403 (mttt) REVERT: B 288 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7483 (tt0) REVERT: E 186 GLN cc_start: 0.7484 (mm-40) cc_final: 0.7187 (mp10) REVERT: E 314 TYR cc_start: 0.8047 (m-80) cc_final: 0.7622 (m-80) REVERT: F 185 ARG cc_start: 0.7788 (mmt-90) cc_final: 0.7534 (mmp80) REVERT: G 65 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7852 (mt-10) REVERT: G 155 ARG cc_start: 0.7673 (ttp80) cc_final: 0.7459 (ttp-110) REVERT: G 290 TYR cc_start: 0.8977 (p90) cc_final: 0.8589 (p90) REVERT: H 147 ASP cc_start: 0.7066 (m-30) cc_final: 0.6855 (m-30) REVERT: H 307 VAL cc_start: 0.8563 (OUTLIER) cc_final: 0.8264 (m) REVERT: I 94 ASN cc_start: 0.7999 (p0) cc_final: 0.7747 (t0) REVERT: I 307 VAL cc_start: 0.8703 (t) cc_final: 0.8396 (t) REVERT: J 26 TRP cc_start: 0.8321 (m100) cc_final: 0.7936 (m100) outliers start: 40 outliers final: 29 residues processed: 222 average time/residue: 0.5083 time to fit residues: 164.5503 Evaluate side-chains 219 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 186 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 247 SER Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 304 TYR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain J residue 17 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 188 optimal weight: 0.0470 chunk 252 optimal weight: 0.4980 chunk 72 optimal weight: 6.9990 chunk 218 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 237 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 243 optimal weight: 1.9990 chunk 30 optimal weight: 20.0000 chunk 43 optimal weight: 0.0000 overall best weight: 0.5082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 GLN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.123240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.093653 restraints weight = 48850.978| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.72 r_work: 0.2914 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.147 24880 Z= 0.179 Angle : 0.650 59.184 34076 Z= 0.371 Chirality : 0.040 0.590 3839 Planarity : 0.003 0.051 4272 Dihedral : 14.936 179.186 4203 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.48 % Favored : 94.49 % Rotamer: Outliers : 1.60 % Allowed : 17.37 % Favored : 81.04 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 2959 helix: 1.54 (0.17), residues: 957 sheet: 0.16 (0.23), residues: 474 loop : -1.75 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 193 HIS 0.013 0.001 HIS C 29 PHE 0.014 0.001 PHE C 44 TYR 0.010 0.001 TYR A 179 ARG 0.016 0.000 ARG B 315 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4840.85 seconds wall clock time: 89 minutes 10.80 seconds (5350.80 seconds total)