Starting phenix.real_space_refine (version: dev) on Tue Dec 13 03:27:00 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ltn_0975/12_2022/6ltn_0975.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ltn_0975/12_2022/6ltn_0975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ltn_0975/12_2022/6ltn_0975.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ltn_0975/12_2022/6ltn_0975.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ltn_0975/12_2022/6ltn_0975.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ltn_0975/12_2022/6ltn_0975.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "E ASP 35": "OD1" <-> "OD2" Residue "E ARG 75": "NH1" <-> "NH2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "E TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "E TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 261": "OD1" <-> "OD2" Residue "E PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 300": "NH1" <-> "NH2" Residue "E TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 337": "OE1" <-> "OE2" Residue "E GLU 341": "OE1" <-> "OE2" Residue "A ASP 35": "OD1" <-> "OD2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ASP 81": "OD1" <-> "OD2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 337": "OE1" <-> "OE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "B ASP 35": "OD1" <-> "OD2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ASP 81": "OD1" <-> "OD2" Residue "B TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 261": "OD1" <-> "OD2" Residue "B PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 337": "OE1" <-> "OE2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "C ASP 35": "OD1" <-> "OD2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "C GLU 197": "OE1" <-> "OE2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 261": "OD1" <-> "OD2" Residue "C PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 300": "NH1" <-> "NH2" Residue "C TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 337": "OE1" <-> "OE2" Residue "C GLU 341": "OE1" <-> "OE2" Residue "D ASP 35": "OD1" <-> "OD2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "D ASP 81": "OD1" <-> "OD2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 128": "NH1" <-> "NH2" Residue "D GLU 197": "OE1" <-> "OE2" Residue "D TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 261": "OD1" <-> "OD2" Residue "D PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 300": "NH1" <-> "NH2" Residue "D TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 337": "OE1" <-> "OE2" Residue "D GLU 341": "OE1" <-> "OE2" Residue "F ASP 35": "OD1" <-> "OD2" Residue "F ARG 75": "NH1" <-> "NH2" Residue "F ASP 81": "OD1" <-> "OD2" Residue "F TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 128": "NH1" <-> "NH2" Residue "F GLU 197": "OE1" <-> "OE2" Residue "F TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 261": "OD1" <-> "OD2" Residue "F PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 300": "NH1" <-> "NH2" Residue "F TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 337": "OE1" <-> "OE2" Residue "F GLU 341": "OE1" <-> "OE2" Residue "G ASP 35": "OD1" <-> "OD2" Residue "G ARG 75": "NH1" <-> "NH2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 128": "NH1" <-> "NH2" Residue "G GLU 197": "OE1" <-> "OE2" Residue "G TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 261": "OD1" <-> "OD2" Residue "G PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 300": "NH1" <-> "NH2" Residue "G TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 337": "OE1" <-> "OE2" Residue "G GLU 341": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 13615 Number of models: 1 Model: "" Number of chains: 7 Chain: "E" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1945 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 233} Chain breaks: 3 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1945 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 233} Chain breaks: 3 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1945 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 233} Chain breaks: 3 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1945 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 233} Chain breaks: 3 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1945 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 233} Chain breaks: 3 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1945 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 233} Chain breaks: 3 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1945 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 233} Chain breaks: 3 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 7.95, per 1000 atoms: 0.58 Number of scatterers: 13615 At special positions: 0 Unit cell: (110.874, 108.7, 110.874, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 2338 8.00 N 2079 7.00 C 9128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.26 Conformation dependent library (CDL) restraints added in 1.9 seconds 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3332 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 7 sheets defined 72.1% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'E' and resid 37 through 42 Processing helix chain 'E' and resid 43 through 61 removed outlier: 3.653A pdb=" N ILE E 60 " --> pdb=" O GLN E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 87 removed outlier: 3.764A pdb=" N ASP E 81 " --> pdb=" O ALA E 77 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP E 85 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 119 removed outlier: 3.673A pdb=" N LEU E 105 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS E 106 " --> pdb=" O PRO E 102 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS E 107 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE E 108 " --> pdb=" O TRP E 104 " (cutoff:3.500A) Proline residue: E 110 - end of helix Processing helix chain 'E' and resid 121 through 131 removed outlier: 3.702A pdb=" N PHE E 129 " --> pdb=" O LEU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 151 removed outlier: 4.290A pdb=" N SER E 137 " --> pdb=" O PRO E 133 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASP E 138 " --> pdb=" O HIS E 134 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU E 139 " --> pdb=" O ILE E 135 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASP E 147 " --> pdb=" O MET E 143 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS E 148 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL E 149 " --> pdb=" O GLU E 145 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR E 150 " --> pdb=" O LEU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 204 removed outlier: 3.866A pdb=" N THR E 202 " --> pdb=" O GLN E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 238 removed outlier: 3.890A pdb=" N THR E 220 " --> pdb=" O CYS E 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU E 237 " --> pdb=" O TYR E 233 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N SER E 238 " --> pdb=" O TYR E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 280 removed outlier: 3.555A pdb=" N LEU E 275 " --> pdb=" O GLY E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 287 removed outlier: 3.647A pdb=" N TYR E 284 " --> pdb=" O ASN E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 294 removed outlier: 3.527A pdb=" N VAL E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 335 removed outlier: 4.334A pdb=" N LEU E 333 " --> pdb=" O SER E 329 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE E 334 " --> pdb=" O LEU E 330 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU E 335 " --> pdb=" O TYR E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 341 No H-bonds generated for 'chain 'E' and resid 339 through 341' Processing helix chain 'E' and resid 342 through 351 removed outlier: 3.945A pdb=" N LYS E 346 " --> pdb=" O VAL E 342 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS E 347 " --> pdb=" O LYS E 343 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU E 351 " --> pdb=" O CYS E 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 43 through 61 removed outlier: 3.653A pdb=" N ILE A 60 " --> pdb=" O GLN A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 87 removed outlier: 3.765A pdb=" N ASP A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 119 removed outlier: 3.673A pdb=" N LEU A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS A 106 " --> pdb=" O PRO A 102 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE A 108 " --> pdb=" O TRP A 104 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 121 through 131 removed outlier: 3.702A pdb=" N PHE A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 151 removed outlier: 4.290A pdb=" N SER A 137 " --> pdb=" O PRO A 133 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP A 138 " --> pdb=" O HIS A 134 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP A 147 " --> pdb=" O MET A 143 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 removed outlier: 3.866A pdb=" N THR A 202 " --> pdb=" O GLN A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 238 removed outlier: 3.891A pdb=" N THR A 220 " --> pdb=" O CYS A 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 237 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER A 238 " --> pdb=" O TYR A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 280 removed outlier: 3.556A pdb=" N LEU A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 287 removed outlier: 3.647A pdb=" N TYR A 284 " --> pdb=" O ASN A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 294 removed outlier: 3.526A pdb=" N VAL A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 335 removed outlier: 4.333A pdb=" N LEU A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU A 335 " --> pdb=" O TYR A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 342 through 351 removed outlier: 3.946A pdb=" N LYS A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 43 through 61 removed outlier: 3.651A pdb=" N ILE B 60 " --> pdb=" O GLN B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 87 removed outlier: 3.765A pdb=" N ASP B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 119 removed outlier: 3.673A pdb=" N LEU B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS B 106 " --> pdb=" O PRO B 102 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE B 108 " --> pdb=" O TRP B 104 " (cutoff:3.500A) Proline residue: B 110 - end of helix Processing helix chain 'B' and resid 121 through 131 removed outlier: 3.702A pdb=" N PHE B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 151 removed outlier: 4.290A pdb=" N SER B 137 " --> pdb=" O PRO B 133 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASP B 138 " --> pdb=" O HIS B 134 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP B 147 " --> pdb=" O MET B 143 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TYR B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 204 removed outlier: 3.866A pdb=" N THR B 202 " --> pdb=" O GLN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 238 removed outlier: 3.890A pdb=" N THR B 220 " --> pdb=" O CYS B 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER B 238 " --> pdb=" O TYR B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 280 removed outlier: 3.556A pdb=" N LEU B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 287 removed outlier: 3.646A pdb=" N TYR B 284 " --> pdb=" O ASN B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 294 removed outlier: 3.526A pdb=" N VAL B 292 " --> pdb=" O ALA B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 335 removed outlier: 4.334A pdb=" N LEU B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU B 335 " --> pdb=" O TYR B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'B' and resid 342 through 351 removed outlier: 3.946A pdb=" N LYS B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS B 347 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 351 " --> pdb=" O CYS B 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 42 Processing helix chain 'C' and resid 43 through 61 removed outlier: 3.652A pdb=" N ILE C 60 " --> pdb=" O GLN C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 87 removed outlier: 3.764A pdb=" N ASP C 81 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 119 removed outlier: 3.673A pdb=" N LEU C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS C 106 " --> pdb=" O PRO C 102 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS C 107 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE C 108 " --> pdb=" O TRP C 104 " (cutoff:3.500A) Proline residue: C 110 - end of helix Processing helix chain 'C' and resid 121 through 131 removed outlier: 3.702A pdb=" N PHE C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 151 removed outlier: 4.290A pdb=" N SER C 137 " --> pdb=" O PRO C 133 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP C 138 " --> pdb=" O HIS C 134 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASP C 147 " --> pdb=" O MET C 143 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS C 148 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 204 removed outlier: 3.865A pdb=" N THR C 202 " --> pdb=" O GLN C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 238 removed outlier: 3.891A pdb=" N THR C 220 " --> pdb=" O CYS C 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 237 " --> pdb=" O TYR C 233 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N SER C 238 " --> pdb=" O TYR C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 280 removed outlier: 3.556A pdb=" N LEU C 275 " --> pdb=" O GLY C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 287 removed outlier: 3.647A pdb=" N TYR C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 294 removed outlier: 3.526A pdb=" N VAL C 292 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 335 removed outlier: 4.334A pdb=" N LEU C 333 " --> pdb=" O SER C 329 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE C 334 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU C 335 " --> pdb=" O TYR C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 341 No H-bonds generated for 'chain 'C' and resid 339 through 341' Processing helix chain 'C' and resid 342 through 351 removed outlier: 3.945A pdb=" N LYS C 346 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS C 347 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU C 351 " --> pdb=" O CYS C 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 42 Processing helix chain 'D' and resid 43 through 61 removed outlier: 3.653A pdb=" N ILE D 60 " --> pdb=" O GLN D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 87 removed outlier: 3.764A pdb=" N ASP D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 119 removed outlier: 3.673A pdb=" N LEU D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS D 106 " --> pdb=" O PRO D 102 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE D 108 " --> pdb=" O TRP D 104 " (cutoff:3.500A) Proline residue: D 110 - end of helix Processing helix chain 'D' and resid 121 through 131 removed outlier: 3.701A pdb=" N PHE D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 151 removed outlier: 4.290A pdb=" N SER D 137 " --> pdb=" O PRO D 133 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASP D 138 " --> pdb=" O HIS D 134 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 139 " --> pdb=" O ILE D 135 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP D 147 " --> pdb=" O MET D 143 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 removed outlier: 3.865A pdb=" N THR D 202 " --> pdb=" O GLN D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 238 removed outlier: 3.891A pdb=" N THR D 220 " --> pdb=" O CYS D 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU D 237 " --> pdb=" O TYR D 233 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER D 238 " --> pdb=" O TYR D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 280 removed outlier: 3.556A pdb=" N LEU D 275 " --> pdb=" O GLY D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 287 removed outlier: 3.646A pdb=" N TYR D 284 " --> pdb=" O ASN D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 294 removed outlier: 3.527A pdb=" N VAL D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 335 removed outlier: 4.334A pdb=" N LEU D 333 " --> pdb=" O SER D 329 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU D 335 " --> pdb=" O TYR D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 341 No H-bonds generated for 'chain 'D' and resid 339 through 341' Processing helix chain 'D' and resid 342 through 351 removed outlier: 3.946A pdb=" N LYS D 346 " --> pdb=" O VAL D 342 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS D 347 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU D 351 " --> pdb=" O CYS D 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 42 Processing helix chain 'F' and resid 43 through 61 removed outlier: 3.652A pdb=" N ILE F 60 " --> pdb=" O GLN F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 87 removed outlier: 3.764A pdb=" N ASP F 81 " --> pdb=" O ALA F 77 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP F 85 " --> pdb=" O ASP F 81 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA F 86 " --> pdb=" O SER F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 119 removed outlier: 3.673A pdb=" N LEU F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS F 106 " --> pdb=" O PRO F 102 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE F 108 " --> pdb=" O TRP F 104 " (cutoff:3.500A) Proline residue: F 110 - end of helix Processing helix chain 'F' and resid 121 through 131 removed outlier: 3.701A pdb=" N PHE F 129 " --> pdb=" O LEU F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 151 removed outlier: 4.289A pdb=" N SER F 137 " --> pdb=" O PRO F 133 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASP F 138 " --> pdb=" O HIS F 134 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU F 139 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP F 147 " --> pdb=" O MET F 143 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS F 148 " --> pdb=" O GLU F 144 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL F 149 " --> pdb=" O GLU F 145 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR F 150 " --> pdb=" O LEU F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 204 removed outlier: 3.865A pdb=" N THR F 202 " --> pdb=" O GLN F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 238 removed outlier: 3.890A pdb=" N THR F 220 " --> pdb=" O CYS F 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU F 237 " --> pdb=" O TYR F 233 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER F 238 " --> pdb=" O TYR F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 280 removed outlier: 3.556A pdb=" N LEU F 275 " --> pdb=" O GLY F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 287 removed outlier: 3.647A pdb=" N TYR F 284 " --> pdb=" O ASN F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 294 removed outlier: 3.526A pdb=" N VAL F 292 " --> pdb=" O ALA F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 335 removed outlier: 4.334A pdb=" N LEU F 333 " --> pdb=" O SER F 329 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE F 334 " --> pdb=" O LEU F 330 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU F 335 " --> pdb=" O TYR F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 341 No H-bonds generated for 'chain 'F' and resid 339 through 341' Processing helix chain 'F' and resid 342 through 351 removed outlier: 3.945A pdb=" N LYS F 346 " --> pdb=" O VAL F 342 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS F 347 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU F 351 " --> pdb=" O CYS F 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 42 Processing helix chain 'G' and resid 43 through 61 removed outlier: 3.652A pdb=" N ILE G 60 " --> pdb=" O GLN G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 87 removed outlier: 3.764A pdb=" N ASP G 81 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP G 85 " --> pdb=" O ASP G 81 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA G 86 " --> pdb=" O SER G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 119 removed outlier: 3.673A pdb=" N LEU G 105 " --> pdb=" O LEU G 101 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS G 106 " --> pdb=" O PRO G 102 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS G 107 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE G 108 " --> pdb=" O TRP G 104 " (cutoff:3.500A) Proline residue: G 110 - end of helix Processing helix chain 'G' and resid 121 through 131 removed outlier: 3.702A pdb=" N PHE G 129 " --> pdb=" O LEU G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 151 removed outlier: 4.289A pdb=" N SER G 137 " --> pdb=" O PRO G 133 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASP G 138 " --> pdb=" O HIS G 134 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU G 139 " --> pdb=" O ILE G 135 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASP G 147 " --> pdb=" O MET G 143 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS G 148 " --> pdb=" O GLU G 144 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL G 149 " --> pdb=" O GLU G 145 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TYR G 150 " --> pdb=" O LEU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 204 removed outlier: 3.865A pdb=" N THR G 202 " --> pdb=" O GLN G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 238 removed outlier: 3.890A pdb=" N THR G 220 " --> pdb=" O CYS G 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU G 237 " --> pdb=" O TYR G 233 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER G 238 " --> pdb=" O TYR G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 280 removed outlier: 3.556A pdb=" N LEU G 275 " --> pdb=" O GLY G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 287 removed outlier: 3.647A pdb=" N TYR G 284 " --> pdb=" O ASN G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 294 removed outlier: 3.527A pdb=" N VAL G 292 " --> pdb=" O ALA G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 335 removed outlier: 4.334A pdb=" N LEU G 333 " --> pdb=" O SER G 329 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE G 334 " --> pdb=" O LEU G 330 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU G 335 " --> pdb=" O TYR G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 341 No H-bonds generated for 'chain 'G' and resid 339 through 341' Processing helix chain 'G' and resid 342 through 351 removed outlier: 3.945A pdb=" N LYS G 346 " --> pdb=" O VAL G 342 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS G 347 " --> pdb=" O LYS G 343 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU G 351 " --> pdb=" O CYS G 347 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 243 through 246 Processing sheet with id=AA2, first strand: chain 'A' and resid 243 through 246 Processing sheet with id=AA3, first strand: chain 'B' and resid 243 through 246 Processing sheet with id=AA4, first strand: chain 'C' and resid 243 through 246 Processing sheet with id=AA5, first strand: chain 'D' and resid 243 through 246 Processing sheet with id=AA6, first strand: chain 'F' and resid 243 through 246 Processing sheet with id=AA7, first strand: chain 'G' and resid 243 through 246 651 hydrogen bonds defined for protein. 1932 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.53 Time building geometry restraints manager: 5.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3920 1.34 - 1.46: 2959 1.46 - 1.57: 6981 1.57 - 1.69: 0 1.69 - 1.81: 77 Bond restraints: 13937 Sorted by residual: bond pdb=" CB GLU D 341 " pdb=" CG GLU D 341 " ideal model delta sigma weight residual 1.520 1.572 -0.052 3.00e-02 1.11e+03 3.01e+00 bond pdb=" CB GLU A 341 " pdb=" CG GLU A 341 " ideal model delta sigma weight residual 1.520 1.572 -0.052 3.00e-02 1.11e+03 3.00e+00 bond pdb=" CB GLU C 341 " pdb=" CG GLU C 341 " ideal model delta sigma weight residual 1.520 1.572 -0.052 3.00e-02 1.11e+03 2.99e+00 bond pdb=" CB GLU G 341 " pdb=" CG GLU G 341 " ideal model delta sigma weight residual 1.520 1.572 -0.052 3.00e-02 1.11e+03 2.99e+00 bond pdb=" CB GLU B 341 " pdb=" CG GLU B 341 " ideal model delta sigma weight residual 1.520 1.572 -0.052 3.00e-02 1.11e+03 2.95e+00 ... (remaining 13932 not shown) Histogram of bond angle deviations from ideal: 100.63 - 107.31: 392 107.31 - 114.00: 8008 114.00 - 120.68: 6240 120.68 - 127.37: 4183 127.37 - 134.06: 140 Bond angle restraints: 18963 Sorted by residual: angle pdb=" N VAL G 297 " pdb=" CA VAL G 297 " pdb=" C VAL G 297 " ideal model delta sigma weight residual 108.88 116.96 -8.08 2.16e+00 2.14e-01 1.40e+01 angle pdb=" N VAL E 297 " pdb=" CA VAL E 297 " pdb=" C VAL E 297 " ideal model delta sigma weight residual 108.88 116.95 -8.07 2.16e+00 2.14e-01 1.40e+01 angle pdb=" N VAL B 297 " pdb=" CA VAL B 297 " pdb=" C VAL B 297 " ideal model delta sigma weight residual 108.88 116.95 -8.07 2.16e+00 2.14e-01 1.40e+01 angle pdb=" N VAL D 297 " pdb=" CA VAL D 297 " pdb=" C VAL D 297 " ideal model delta sigma weight residual 108.88 116.95 -8.07 2.16e+00 2.14e-01 1.40e+01 angle pdb=" N VAL F 297 " pdb=" CA VAL F 297 " pdb=" C VAL F 297 " ideal model delta sigma weight residual 108.88 116.94 -8.06 2.16e+00 2.14e-01 1.39e+01 ... (remaining 18958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.54: 7160 15.54 - 31.07: 715 31.07 - 46.61: 287 46.61 - 62.15: 49 62.15 - 77.69: 42 Dihedral angle restraints: 8253 sinusoidal: 3150 harmonic: 5103 Sorted by residual: dihedral pdb=" CA SER A 239 " pdb=" C SER A 239 " pdb=" N LEU A 240 " pdb=" CA LEU A 240 " ideal model delta harmonic sigma weight residual 180.00 161.70 18.30 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA SER G 239 " pdb=" C SER G 239 " pdb=" N LEU G 240 " pdb=" CA LEU G 240 " ideal model delta harmonic sigma weight residual 180.00 161.73 18.27 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA SER B 239 " pdb=" C SER B 239 " pdb=" N LEU B 240 " pdb=" CA LEU B 240 " ideal model delta harmonic sigma weight residual 180.00 161.76 18.24 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 8250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1067 0.033 - 0.066: 814 0.066 - 0.098: 240 0.098 - 0.131: 133 0.131 - 0.164: 35 Chirality restraints: 2289 Sorted by residual: chirality pdb=" CA LEU G 122 " pdb=" N LEU G 122 " pdb=" C LEU G 122 " pdb=" CB LEU G 122 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" CA LEU E 122 " pdb=" N LEU E 122 " pdb=" C LEU E 122 " pdb=" CB LEU E 122 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" CA LEU C 122 " pdb=" N LEU C 122 " pdb=" C LEU C 122 " pdb=" CB LEU C 122 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.58e-01 ... (remaining 2286 not shown) Planarity restraints: 2268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 122 " -0.047 5.00e-02 4.00e+02 7.07e-02 7.99e+00 pdb=" N PRO A 123 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 123 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 123 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 122 " -0.047 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO C 123 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO C 123 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 123 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 122 " 0.047 5.00e-02 4.00e+02 7.05e-02 7.94e+00 pdb=" N PRO E 123 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO E 123 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 123 " 0.039 5.00e-02 4.00e+02 ... (remaining 2265 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3736 2.78 - 3.31: 11937 3.31 - 3.84: 20885 3.84 - 4.37: 24678 4.37 - 4.90: 41404 Nonbonded interactions: 102640 Sorted by model distance: nonbonded pdb=" OG SER B 59 " pdb=" OE2 GLU G 57 " model vdw 2.254 2.440 nonbonded pdb=" OE2 GLU B 57 " pdb=" OG SER D 59 " model vdw 2.291 2.440 nonbonded pdb=" O SER C 65 " pdb=" OG SER C 65 " model vdw 2.342 2.440 nonbonded pdb=" O SER D 65 " pdb=" OG SER D 65 " model vdw 2.343 2.440 nonbonded pdb=" O SER G 65 " pdb=" OG SER G 65 " model vdw 2.343 2.440 ... (remaining 102635 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 9128 2.51 5 N 2079 2.21 5 O 2338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.960 Check model and map are aligned: 0.210 Convert atoms to be neutral: 0.100 Process input model: 35.240 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 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 : 0.006 0.052 13937 Z= 0.384 Angle : 0.949 12.903 18963 Z= 0.484 Chirality : 0.052 0.164 2289 Planarity : 0.010 0.071 2268 Dihedral : 16.291 77.685 4900 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -6.39 (0.12), residues: 1652 helix: -4.37 (0.06), residues: 1162 sheet: -3.08 (0.57), residues: 91 loop : -2.99 (0.24), residues: 399 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 390 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 411 average time/residue: 0.2150 time to fit residues: 132.3564 Evaluate side-chains 293 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 282 time to evaluate : 1.601 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1188 time to fit residues: 4.5846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 68 optimal weight: 0.1980 chunk 131 optimal weight: 0.0170 chunk 50 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 GLN E 205 ASN ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN A 76 GLN A 205 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN B 76 GLN B 205 ASN ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN C 76 GLN C 205 ASN ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN D 76 GLN D 205 ASN ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN D 338 ASN F 76 GLN F 205 ASN ** F 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN G 76 GLN G 205 ASN ** G 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 13937 Z= 0.143 Angle : 0.623 7.037 18963 Z= 0.312 Chirality : 0.038 0.122 2289 Planarity : 0.007 0.065 2268 Dihedral : 4.243 13.017 1806 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer Outliers : 3.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.13 (0.18), residues: 1652 helix: -1.75 (0.13), residues: 1183 sheet: -2.24 (0.62), residues: 91 loop : -2.36 (0.28), residues: 378 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 344 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 21 residues processed: 370 average time/residue: 0.2040 time to fit residues: 117.1123 Evaluate side-chains 318 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 297 time to evaluate : 1.693 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1202 time to fit residues: 6.8014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 165 optimal weight: 20.0000 chunk 136 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 GLN B 205 ASN ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN F 205 ASN ** F 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN ** G 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 13937 Z= 0.272 Angle : 0.680 12.218 18963 Z= 0.329 Chirality : 0.041 0.183 2289 Planarity : 0.006 0.071 2268 Dihedral : 4.295 17.177 1806 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 5.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.52 (0.21), residues: 1652 helix: -0.44 (0.16), residues: 1141 sheet: -1.90 (0.65), residues: 91 loop : -2.04 (0.28), residues: 420 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 302 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 40 residues processed: 359 average time/residue: 0.1948 time to fit residues: 109.2392 Evaluate side-chains 330 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 290 time to evaluate : 1.656 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.1189 time to fit residues: 11.1372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 153 optimal weight: 30.0000 chunk 162 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 ASN ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 ASN ** F 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 13937 Z= 0.172 Angle : 0.645 12.471 18963 Z= 0.298 Chirality : 0.039 0.175 2289 Planarity : 0.006 0.057 2268 Dihedral : 3.936 14.285 1806 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.96 (0.22), residues: 1652 helix: -0.06 (0.17), residues: 1141 sheet: -1.84 (0.65), residues: 91 loop : -1.63 (0.30), residues: 420 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 311 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 13 residues processed: 330 average time/residue: 0.2031 time to fit residues: 104.4992 Evaluate side-chains 301 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 288 time to evaluate : 1.520 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1603 time to fit residues: 5.7539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.3980 chunk 92 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 145 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 ASN ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN ** G 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 13937 Z= 0.203 Angle : 0.641 11.080 18963 Z= 0.301 Chirality : 0.040 0.185 2289 Planarity : 0.005 0.057 2268 Dihedral : 3.911 14.804 1806 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.60 (0.23), residues: 1652 helix: 0.20 (0.17), residues: 1141 sheet: -1.79 (0.65), residues: 91 loop : -1.44 (0.32), residues: 420 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 299 time to evaluate : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 14 residues processed: 314 average time/residue: 0.1985 time to fit residues: 97.1261 Evaluate side-chains 295 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 281 time to evaluate : 1.745 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1605 time to fit residues: 6.1018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN ** G 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 13937 Z= 0.165 Angle : 0.624 10.671 18963 Z= 0.291 Chirality : 0.039 0.142 2289 Planarity : 0.005 0.058 2268 Dihedral : 3.782 13.229 1806 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.38 (0.22), residues: 1652 helix: 0.38 (0.17), residues: 1141 sheet: -4.56 (0.53), residues: 49 loop : -1.10 (0.31), residues: 462 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 286 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 10 residues processed: 299 average time/residue: 0.1867 time to fit residues: 89.0073 Evaluate side-chains 285 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 275 time to evaluate : 1.551 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1161 time to fit residues: 4.4281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 161 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 GLN ** F 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 13937 Z= 0.219 Angle : 0.645 9.895 18963 Z= 0.304 Chirality : 0.040 0.140 2289 Planarity : 0.005 0.057 2268 Dihedral : 3.934 14.120 1806 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.23 (0.23), residues: 1652 helix: 0.50 (0.17), residues: 1141 sheet: -1.80 (0.63), residues: 91 loop : -1.32 (0.33), residues: 420 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 279 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 15 residues processed: 288 average time/residue: 0.1910 time to fit residues: 87.0182 Evaluate side-chains 284 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 269 time to evaluate : 1.712 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1277 time to fit residues: 5.7791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 205 ASN ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN ** G 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 13937 Z= 0.183 Angle : 0.632 10.191 18963 Z= 0.295 Chirality : 0.039 0.125 2289 Planarity : 0.005 0.057 2268 Dihedral : 3.825 13.204 1806 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.10 (0.23), residues: 1652 helix: 0.61 (0.17), residues: 1141 sheet: -4.46 (0.53), residues: 49 loop : -1.06 (0.31), residues: 462 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 273 time to evaluate : 1.637 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 280 average time/residue: 0.2008 time to fit residues: 90.0300 Evaluate side-chains 276 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 266 time to evaluate : 1.409 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1177 time to fit residues: 4.2174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 118 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 136 optimal weight: 5.9990 chunk 142 optimal weight: 0.0670 chunk 99 optimal weight: 0.3980 chunk 159 optimal weight: 10.0000 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 205 ASN ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 13937 Z= 0.141 Angle : 0.626 10.106 18963 Z= 0.286 Chirality : 0.039 0.160 2289 Planarity : 0.005 0.058 2268 Dihedral : 3.605 12.862 1806 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.23), residues: 1652 helix: 0.76 (0.17), residues: 1134 sheet: -4.22 (0.54), residues: 49 loop : -1.06 (0.31), residues: 469 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 279 time to evaluate : 1.606 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 282 average time/residue: 0.1915 time to fit residues: 86.1558 Evaluate side-chains 270 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 267 time to evaluate : 1.661 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1393 time to fit residues: 2.8025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.6980 chunk 75 optimal weight: 0.3980 chunk 110 optimal weight: 0.7980 chunk 167 optimal weight: 20.0000 chunk 154 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 205 ASN ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 13937 Z= 0.240 Angle : 0.653 9.536 18963 Z= 0.309 Chirality : 0.041 0.144 2289 Planarity : 0.005 0.058 2268 Dihedral : 3.875 13.339 1806 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.11 (0.23), residues: 1652 helix: 0.77 (0.17), residues: 1141 sheet: -1.72 (0.62), residues: 91 loop : -1.23 (0.33), residues: 420 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 262 time to evaluate : 1.634 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 263 average time/residue: 0.1856 time to fit residues: 78.4614 Evaluate side-chains 266 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 260 time to evaluate : 1.560 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1146 time to fit residues: 3.4666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 205 ASN ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.165487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.116533 restraints weight = 22368.975| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.53 r_work: 0.3338 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 13937 Z= 0.238 Angle : 0.658 9.603 18963 Z= 0.311 Chirality : 0.041 0.136 2289 Planarity : 0.005 0.058 2268 Dihedral : 3.967 14.013 1806 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.04 (0.23), residues: 1652 helix: 0.70 (0.17), residues: 1148 sheet: -1.89 (0.62), residues: 91 loop : -1.21 (0.33), residues: 413 =============================================================================== Job complete usr+sys time: 2715.25 seconds wall clock time: 50 minutes 41.86 seconds (3041.86 seconds total)