Starting phenix.real_space_refine on Sat Mar 16 03:47:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ltn_0975/03_2024/6ltn_0975.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ltn_0975/03_2024/6ltn_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_0975/03_2024/6ltn_0975.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ltn_0975/03_2024/6ltn_0975.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ltn_0975/03_2024/6ltn_0975.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ltn_0975/03_2024/6ltn_0975.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 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. 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 7.37, per 1000 atoms: 0.54 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: 5.08 Conformation dependent library (CDL) restraints added in 2.3 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: 1.31 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: 5.53 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 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: 0.360 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: 2.600 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 36.240 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.080 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.38 % Allowed : 11.73 % Favored : 86.89 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 85 HIS 0.003 0.001 HIS E 106 PHE 0.030 0.002 PHE B 72 TYR 0.008 0.001 TYR F 199 ARG 0.002 0.000 ARG G 75 *********************** 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 : 1.687 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 REVERT: E 37 MET cc_start: 0.8494 (ppp) cc_final: 0.8172 (ppp) REVERT: E 121 TYR cc_start: 0.8448 (t80) cc_final: 0.8180 (t80) REVERT: E 138 ASP cc_start: 0.7988 (m-30) cc_final: 0.7719 (t0) REVERT: E 199 TYR cc_start: 0.6817 (t80) cc_final: 0.6617 (t80) REVERT: E 223 ILE cc_start: 0.9017 (tt) cc_final: 0.8791 (tt) REVERT: A 37 MET cc_start: 0.8794 (ppp) cc_final: 0.8544 (ppp) REVERT: A 56 GLN cc_start: 0.8391 (tp40) cc_final: 0.7904 (mm-40) REVERT: A 57 GLU cc_start: 0.6637 (tm-30) cc_final: 0.6318 (tm-30) REVERT: A 63 GLN cc_start: 0.8368 (mp10) cc_final: 0.8024 (mp10) REVERT: A 138 ASP cc_start: 0.8262 (m-30) cc_final: 0.7903 (t0) REVERT: A 197 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7267 (tp30) REVERT: A 199 TYR cc_start: 0.6542 (t80) cc_final: 0.6164 (t80) REVERT: A 280 ASN cc_start: 0.9184 (t0) cc_final: 0.8842 (t0) REVERT: B 37 MET cc_start: 0.8598 (ppp) cc_final: 0.8302 (ppp) REVERT: B 63 GLN cc_start: 0.8520 (mp10) cc_final: 0.7971 (mp10) REVERT: B 197 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7127 (tp30) REVERT: B 280 ASN cc_start: 0.9231 (t0) cc_final: 0.9018 (t0) REVERT: C 36 LYS cc_start: 0.7886 (mmtp) cc_final: 0.6786 (mptt) REVERT: C 37 MET cc_start: 0.8662 (ppp) cc_final: 0.8334 (ppp) REVERT: C 56 GLN cc_start: 0.8455 (tp40) cc_final: 0.8160 (pp30) REVERT: C 111 TYR cc_start: 0.8861 (m-80) cc_final: 0.8571 (m-80) REVERT: C 121 TYR cc_start: 0.8659 (t80) cc_final: 0.8267 (t80) REVERT: C 126 PHE cc_start: 0.8229 (t80) cc_final: 0.7987 (t80) REVERT: C 197 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7555 (tp30) REVERT: C 299 PHE cc_start: 0.8271 (t80) cc_final: 0.8053 (t80) REVERT: C 331 TYR cc_start: 0.7026 (t80) cc_final: 0.6755 (t80) REVERT: D 36 LYS cc_start: 0.7807 (mmtp) cc_final: 0.7194 (mptt) REVERT: D 101 LEU cc_start: 0.8345 (tp) cc_final: 0.8144 (mp) REVERT: D 299 PHE cc_start: 0.8192 (t80) cc_final: 0.7756 (t80) REVERT: F 36 LYS cc_start: 0.7936 (mmtp) cc_final: 0.6962 (mptt) REVERT: F 37 MET cc_start: 0.8802 (ppp) cc_final: 0.8402 (ppp) REVERT: F 56 GLN cc_start: 0.8509 (tp40) cc_final: 0.8067 (mm-40) REVERT: F 63 GLN cc_start: 0.8286 (mp10) cc_final: 0.7888 (mp10) REVERT: F 124 PRO cc_start: 0.8545 (Cg_exo) cc_final: 0.8278 (Cg_endo) REVERT: F 138 ASP cc_start: 0.8208 (m-30) cc_final: 0.7936 (t0) REVERT: F 197 GLU cc_start: 0.7902 (mm-30) cc_final: 0.6927 (tp30) REVERT: F 299 PHE cc_start: 0.8024 (t80) cc_final: 0.7737 (t80) REVERT: F 331 TYR cc_start: 0.7170 (t80) cc_final: 0.6248 (t80) REVERT: G 63 GLN cc_start: 0.8146 (mp10) cc_final: 0.7592 (mp10) REVERT: G 138 ASP cc_start: 0.7961 (m-30) cc_final: 0.7727 (t0) REVERT: G 197 GLU cc_start: 0.7617 (mm-30) cc_final: 0.6855 (tp30) REVERT: G 199 TYR cc_start: 0.6632 (t80) cc_final: 0.5905 (t80) outliers start: 21 outliers final: 11 residues processed: 411 average time/residue: 0.2148 time to fit residues: 132.5285 Evaluate side-chains 300 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 289 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 341 GLU 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: 0.9980 chunk 70 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 152 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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** B 76 GLN B 205 ASN ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13937 Z= 0.174 Angle : 0.627 7.206 18963 Z= 0.317 Chirality : 0.039 0.120 2289 Planarity : 0.007 0.068 2268 Dihedral : 5.799 90.033 1828 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.01 % Allowed : 19.20 % Favored : 77.79 % 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: -3.19 (0.18), residues: 1652 helix: -1.73 (0.13), residues: 1190 sheet: -2.24 (0.62), residues: 91 loop : -2.64 (0.26), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 127 HIS 0.003 0.001 HIS G 134 PHE 0.012 0.001 PHE A 72 TYR 0.016 0.001 TYR G 150 ARG 0.003 0.000 ARG B 254 *********************** 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 382 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 336 time to evaluate : 1.573 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: E 48 LEU cc_start: 0.9389 (tp) cc_final: 0.8989 (mt) REVERT: E 56 GLN cc_start: 0.8452 (tp40) cc_final: 0.8104 (mm-40) REVERT: E 121 TYR cc_start: 0.8102 (t80) cc_final: 0.7898 (t80) REVERT: A 37 MET cc_start: 0.8683 (ppp) cc_final: 0.8372 (ppp) REVERT: A 56 GLN cc_start: 0.8449 (tp40) cc_final: 0.8225 (mm-40) REVERT: A 63 GLN cc_start: 0.8399 (mp10) cc_final: 0.7999 (mp10) REVERT: A 124 PRO cc_start: 0.8371 (Cg_exo) cc_final: 0.8008 (Cg_endo) REVERT: A 142 ILE cc_start: 0.7860 (mm) cc_final: 0.7603 (mt) REVERT: A 197 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7259 (tp30) REVERT: B 37 MET cc_start: 0.8544 (ppp) cc_final: 0.8305 (ppp) REVERT: B 56 GLN cc_start: 0.8579 (tp40) cc_final: 0.8304 (mm-40) REVERT: B 63 GLN cc_start: 0.8518 (mp10) cc_final: 0.7912 (mp10) REVERT: B 124 PRO cc_start: 0.8287 (Cg_exo) cc_final: 0.8021 (Cg_endo) REVERT: B 197 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7141 (tp30) REVERT: B 237 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7462 (pp) REVERT: C 36 LYS cc_start: 0.7951 (mmtp) cc_final: 0.7046 (mptt) REVERT: C 111 TYR cc_start: 0.8737 (m-80) cc_final: 0.8292 (m-80) REVERT: C 121 TYR cc_start: 0.8412 (t80) cc_final: 0.8027 (t80) REVERT: C 124 PRO cc_start: 0.8309 (Cg_exo) cc_final: 0.8006 (Cg_endo) REVERT: C 197 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7540 (tp30) REVERT: C 237 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7834 (pp) REVERT: C 299 PHE cc_start: 0.8225 (t80) cc_final: 0.7980 (t80) REVERT: C 331 TYR cc_start: 0.7045 (t80) cc_final: 0.6739 (t80) REVERT: D 124 PRO cc_start: 0.8345 (Cg_exo) cc_final: 0.8086 (Cg_endo) REVERT: D 216 CYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7719 (t) REVERT: F 36 LYS cc_start: 0.7969 (mmtp) cc_final: 0.6978 (mptt) REVERT: F 56 GLN cc_start: 0.8505 (tp40) cc_final: 0.8144 (mm-40) REVERT: F 63 GLN cc_start: 0.8378 (mp10) cc_final: 0.7822 (mp10) REVERT: F 124 PRO cc_start: 0.8547 (Cg_exo) cc_final: 0.8253 (Cg_endo) REVERT: F 138 ASP cc_start: 0.8063 (m-30) cc_final: 0.7572 (t0) REVERT: F 197 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7213 (tp30) REVERT: F 237 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7919 (pp) REVERT: F 280 ASN cc_start: 0.9339 (OUTLIER) cc_final: 0.9044 (t0) REVERT: F 299 PHE cc_start: 0.8054 (t80) cc_final: 0.7763 (t80) REVERT: F 331 TYR cc_start: 0.7061 (t80) cc_final: 0.5964 (t80) REVERT: G 63 GLN cc_start: 0.8449 (mp10) cc_final: 0.7853 (mp10) REVERT: G 121 TYR cc_start: 0.7924 (t80) cc_final: 0.7595 (t80) REVERT: G 146 LEU cc_start: 0.6189 (OUTLIER) cc_final: 0.5617 (mm) REVERT: G 197 GLU cc_start: 0.7823 (mm-30) cc_final: 0.6973 (tp30) REVERT: G 199 TYR cc_start: 0.6574 (t80) cc_final: 0.6303 (t80) outliers start: 46 outliers final: 25 residues processed: 368 average time/residue: 0.2104 time to fit residues: 119.8337 Evaluate side-chains 330 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 299 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 280 ASN Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 216 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 0.7980 chunk 47 optimal weight: 0.0980 chunk 126 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 152 optimal weight: 20.0000 chunk 165 optimal weight: 20.0000 chunk 136 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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** D 280 ASN 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13937 Z= 0.125 Angle : 0.597 12.672 18963 Z= 0.279 Chirality : 0.038 0.160 2289 Planarity : 0.006 0.058 2268 Dihedral : 3.808 12.871 1807 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.46 % Allowed : 19.79 % Favored : 75.75 % 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: -1.50 (0.21), residues: 1652 helix: -0.47 (0.16), residues: 1141 sheet: -1.65 (0.66), residues: 91 loop : -1.93 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 85 HIS 0.001 0.000 HIS B 106 PHE 0.017 0.001 PHE D 299 TYR 0.011 0.001 TYR E 150 ARG 0.002 0.000 ARG B 254 *********************** 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: 68 poor density : 312 time to evaluate : 1.678 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: E 56 GLN cc_start: 0.8419 (tp40) cc_final: 0.8199 (mm-40) REVERT: E 146 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6335 (mm) REVERT: E 151 ASN cc_start: 0.7197 (m-40) cc_final: 0.6991 (m-40) REVERT: A 63 GLN cc_start: 0.8406 (mp10) cc_final: 0.7970 (mp10) REVERT: A 101 LEU cc_start: 0.8439 (tt) cc_final: 0.8137 (mt) REVERT: A 124 PRO cc_start: 0.8209 (Cg_exo) cc_final: 0.7901 (Cg_endo) REVERT: A 146 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.6200 (mm) REVERT: A 147 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.7164 (p0) REVERT: A 197 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7301 (tp30) REVERT: B 37 MET cc_start: 0.8579 (ppp) cc_final: 0.8242 (ppp) REVERT: B 63 GLN cc_start: 0.8415 (mp10) cc_final: 0.8062 (mp10) REVERT: B 124 PRO cc_start: 0.8294 (Cg_exo) cc_final: 0.8065 (Cg_endo) REVERT: B 128 ARG cc_start: 0.8044 (ptt180) cc_final: 0.7755 (tmm-80) REVERT: B 146 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6543 (mm) REVERT: B 197 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7040 (tp30) REVERT: C 56 GLN cc_start: 0.8474 (tp40) cc_final: 0.8035 (pp30) REVERT: C 146 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6372 (mm) REVERT: C 197 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7507 (tp30) REVERT: C 216 CYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7820 (t) REVERT: C 299 PHE cc_start: 0.8166 (t80) cc_final: 0.7909 (t80) REVERT: C 331 TYR cc_start: 0.7262 (t80) cc_final: 0.6929 (t80) REVERT: D 146 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6779 (mm) REVERT: D 197 GLU cc_start: 0.6767 (tp30) cc_final: 0.6530 (tp30) REVERT: D 216 CYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7981 (t) REVERT: F 56 GLN cc_start: 0.8576 (tp40) cc_final: 0.8170 (mm-40) REVERT: F 63 GLN cc_start: 0.8354 (mp10) cc_final: 0.7890 (mp10) REVERT: F 121 TYR cc_start: 0.8261 (t80) cc_final: 0.7835 (t80) REVERT: F 124 PRO cc_start: 0.8659 (Cg_exo) cc_final: 0.8437 (Cg_endo) REVERT: F 138 ASP cc_start: 0.7928 (m-30) cc_final: 0.7485 (t0) REVERT: F 146 LEU cc_start: 0.6678 (OUTLIER) cc_final: 0.6245 (mm) REVERT: F 197 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7233 (tp30) REVERT: F 216 CYS cc_start: 0.7498 (OUTLIER) cc_final: 0.6813 (t) REVERT: F 299 PHE cc_start: 0.8054 (t80) cc_final: 0.7734 (t80) REVERT: F 331 TYR cc_start: 0.7068 (t80) cc_final: 0.6112 (t80) REVERT: G 63 GLN cc_start: 0.8377 (mp10) cc_final: 0.7781 (mp10) REVERT: G 121 TYR cc_start: 0.7827 (t80) cc_final: 0.7481 (t80) REVERT: G 124 PRO cc_start: 0.8469 (Cg_exo) cc_final: 0.8216 (Cg_endo) REVERT: G 197 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7015 (tp30) REVERT: G 280 ASN cc_start: 0.9311 (t0) cc_final: 0.8946 (t0) outliers start: 68 outliers final: 34 residues processed: 354 average time/residue: 0.1942 time to fit residues: 107.4493 Evaluate side-chains 329 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 285 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 331 TYR Chi-restraints excluded: chain G residue 348 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 102 optimal weight: 0.6980 chunk 153 optimal weight: 20.0000 chunk 162 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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** E 280 ASN ** 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** F 280 ASN ** G 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13937 Z= 0.165 Angle : 0.627 12.746 18963 Z= 0.289 Chirality : 0.039 0.132 2289 Planarity : 0.005 0.056 2268 Dihedral : 3.792 12.095 1806 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 5.11 % Allowed : 19.79 % Favored : 75.10 % 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: -0.72 (0.23), residues: 1652 helix: 0.13 (0.17), residues: 1113 sheet: -1.68 (0.65), residues: 91 loop : -1.52 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 85 HIS 0.001 0.000 HIS B 106 PHE 0.018 0.001 PHE E 299 TYR 0.007 0.001 TYR D 111 ARG 0.002 0.000 ARG B 254 *********************** 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 372 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 294 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 56 GLN cc_start: 0.8415 (tp40) cc_final: 0.8081 (mm-40) REVERT: E 146 LEU cc_start: 0.6689 (OUTLIER) cc_final: 0.6233 (mm) REVERT: A 63 GLN cc_start: 0.8445 (mp10) cc_final: 0.8000 (mp10) REVERT: A 101 LEU cc_start: 0.8461 (tt) cc_final: 0.8145 (mt) REVERT: A 124 PRO cc_start: 0.8197 (Cg_exo) cc_final: 0.7878 (Cg_endo) REVERT: A 146 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6765 (mm) REVERT: A 197 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7230 (tp30) REVERT: A 331 TYR cc_start: 0.7873 (OUTLIER) cc_final: 0.7517 (t80) REVERT: B 63 GLN cc_start: 0.8449 (mp10) cc_final: 0.7847 (mp10) REVERT: B 124 PRO cc_start: 0.8208 (Cg_exo) cc_final: 0.7997 (Cg_endo) REVERT: B 128 ARG cc_start: 0.7991 (ptt180) cc_final: 0.7700 (tmm-80) REVERT: B 197 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7179 (tp30) REVERT: C 56 GLN cc_start: 0.8330 (tp40) cc_final: 0.7972 (pp30) REVERT: C 146 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6497 (mm) REVERT: C 197 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7588 (tp30) REVERT: C 216 CYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7773 (t) REVERT: C 299 PHE cc_start: 0.8198 (t80) cc_final: 0.7922 (t80) REVERT: D 146 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6654 (mm) REVERT: D 216 CYS cc_start: 0.8242 (OUTLIER) cc_final: 0.8018 (t) REVERT: F 56 GLN cc_start: 0.8565 (tp40) cc_final: 0.8151 (pp30) REVERT: F 63 GLN cc_start: 0.8280 (mp10) cc_final: 0.7814 (mp10) REVERT: F 121 TYR cc_start: 0.8225 (t80) cc_final: 0.7794 (t80) REVERT: F 124 PRO cc_start: 0.8626 (Cg_exo) cc_final: 0.8391 (Cg_endo) REVERT: F 138 ASP cc_start: 0.7844 (m-30) cc_final: 0.7370 (t0) REVERT: F 146 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6422 (mm) REVERT: F 197 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7168 (tp30) REVERT: F 280 ASN cc_start: 0.9280 (OUTLIER) cc_final: 0.8966 (t0) REVERT: F 299 PHE cc_start: 0.8062 (t80) cc_final: 0.7743 (t80) REVERT: F 331 TYR cc_start: 0.7091 (t80) cc_final: 0.6161 (t80) REVERT: G 63 GLN cc_start: 0.8506 (mp10) cc_final: 0.7876 (mp10) REVERT: G 121 TYR cc_start: 0.7908 (t80) cc_final: 0.7516 (t80) REVERT: G 124 PRO cc_start: 0.8619 (Cg_exo) cc_final: 0.8356 (Cg_endo) REVERT: G 138 ASP cc_start: 0.7316 (t0) cc_final: 0.6859 (t0) REVERT: G 146 LEU cc_start: 0.6132 (OUTLIER) cc_final: 0.5512 (mm) REVERT: G 197 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7082 (tp30) REVERT: G 199 TYR cc_start: 0.6557 (OUTLIER) cc_final: 0.6324 (t80) outliers start: 78 outliers final: 45 residues processed: 338 average time/residue: 0.1864 time to fit residues: 100.2314 Evaluate side-chains 333 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 277 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 280 ASN Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 128 ARG Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 331 TYR Chi-restraints excluded: chain G residue 348 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.5980 chunk 92 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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** 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: 0.7842 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13937 Z= 0.194 Angle : 0.639 11.390 18963 Z= 0.295 Chirality : 0.039 0.116 2289 Planarity : 0.005 0.056 2268 Dihedral : 3.843 13.030 1806 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 5.24 % Allowed : 21.49 % Favored : 73.26 % 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: -0.42 (0.23), residues: 1652 helix: 0.36 (0.17), residues: 1134 sheet: -1.73 (0.65), residues: 91 loop : -1.45 (0.33), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 85 HIS 0.001 0.000 HIS B 106 PHE 0.019 0.001 PHE G 299 TYR 0.009 0.001 TYR B 213 ARG 0.001 0.000 ARG B 254 *********************** 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 376 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 296 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 56 GLN cc_start: 0.8449 (tp40) cc_final: 0.8111 (mm-40) REVERT: E 146 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6537 (mm) REVERT: A 56 GLN cc_start: 0.8722 (tp-100) cc_final: 0.8057 (pp30) REVERT: A 63 GLN cc_start: 0.8467 (mp10) cc_final: 0.8011 (mp10) REVERT: A 101 LEU cc_start: 0.8473 (tt) cc_final: 0.8156 (mt) REVERT: A 124 PRO cc_start: 0.8244 (Cg_exo) cc_final: 0.7949 (Cg_endo) REVERT: A 146 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6783 (mm) REVERT: A 197 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7169 (tp30) REVERT: A 331 TYR cc_start: 0.7864 (OUTLIER) cc_final: 0.7442 (t80) REVERT: B 63 GLN cc_start: 0.8520 (mp10) cc_final: 0.7926 (mp10) REVERT: B 124 PRO cc_start: 0.8275 (Cg_exo) cc_final: 0.8058 (Cg_endo) REVERT: B 146 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6480 (mm) REVERT: B 197 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7274 (tp30) REVERT: C 56 GLN cc_start: 0.8339 (tp40) cc_final: 0.7924 (pp30) REVERT: C 124 PRO cc_start: 0.8531 (Cg_exo) cc_final: 0.8311 (Cg_endo) REVERT: C 146 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6476 (mm) REVERT: C 197 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7524 (tp30) REVERT: C 216 CYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7703 (t) REVERT: C 299 PHE cc_start: 0.8241 (t80) cc_final: 0.7958 (t80) REVERT: D 146 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6694 (mm) REVERT: D 197 GLU cc_start: 0.6794 (tp30) cc_final: 0.6550 (tp30) REVERT: D 216 CYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7932 (t) REVERT: F 56 GLN cc_start: 0.8601 (tp40) cc_final: 0.8208 (tm-30) REVERT: F 63 GLN cc_start: 0.8251 (mp10) cc_final: 0.7774 (mp10) REVERT: F 121 TYR cc_start: 0.8235 (t80) cc_final: 0.7838 (t80) REVERT: F 124 PRO cc_start: 0.8602 (Cg_exo) cc_final: 0.8377 (Cg_endo) REVERT: F 138 ASP cc_start: 0.7670 (m-30) cc_final: 0.7320 (t0) REVERT: F 146 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6380 (mm) REVERT: F 197 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7239 (tp30) REVERT: F 216 CYS cc_start: 0.7486 (OUTLIER) cc_final: 0.6864 (t) REVERT: F 299 PHE cc_start: 0.8088 (t80) cc_final: 0.7781 (t80) REVERT: F 331 TYR cc_start: 0.7343 (t80) cc_final: 0.6887 (t80) REVERT: G 63 GLN cc_start: 0.8542 (mp10) cc_final: 0.7866 (mp10) REVERT: G 121 TYR cc_start: 0.7989 (t80) cc_final: 0.7567 (t80) REVERT: G 124 PRO cc_start: 0.8672 (Cg_exo) cc_final: 0.8426 (Cg_endo) REVERT: G 146 LEU cc_start: 0.6625 (OUTLIER) cc_final: 0.6210 (mm) REVERT: G 197 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7146 (tp30) outliers start: 80 outliers final: 52 residues processed: 347 average time/residue: 0.1956 time to fit residues: 106.7010 Evaluate side-chains 348 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 285 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 128 ARG Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 228 CYS Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 331 TYR Chi-restraints excluded: chain G residue 348 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 4.9990 chunk 146 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 53 optimal weight: 0.4980 chunk 85 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 205 ASN ** 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** F 280 ASN ** G 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3595 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= 0.160 Angle : 0.624 10.645 18963 Z= 0.286 Chirality : 0.039 0.189 2289 Planarity : 0.005 0.057 2268 Dihedral : 3.716 12.288 1806 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.98 % Allowed : 22.21 % Favored : 72.80 % 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: -0.22 (0.23), residues: 1652 helix: 0.49 (0.17), residues: 1141 sheet: -4.47 (0.52), residues: 49 loop : -1.00 (0.32), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 85 HIS 0.001 0.000 HIS B 106 PHE 0.014 0.001 PHE G 299 TYR 0.008 0.001 TYR D 111 ARG 0.001 0.000 ARG G 254 *********************** 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 368 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 292 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 56 GLN cc_start: 0.8457 (tp40) cc_final: 0.8185 (mm-40) REVERT: E 146 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6519 (mm) REVERT: A 56 GLN cc_start: 0.8718 (tp-100) cc_final: 0.8061 (pp30) REVERT: A 63 GLN cc_start: 0.8462 (mp10) cc_final: 0.8002 (mp10) REVERT: A 124 PRO cc_start: 0.8230 (Cg_exo) cc_final: 0.7941 (Cg_endo) REVERT: A 146 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6864 (mm) REVERT: A 197 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7369 (tp30) REVERT: A 331 TYR cc_start: 0.7757 (OUTLIER) cc_final: 0.7413 (t80) REVERT: B 63 GLN cc_start: 0.8508 (mp10) cc_final: 0.7950 (mp10) REVERT: B 124 PRO cc_start: 0.8253 (Cg_exo) cc_final: 0.8038 (Cg_endo) REVERT: B 146 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6395 (mm) REVERT: B 197 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7254 (tp30) REVERT: C 56 GLN cc_start: 0.8201 (tp40) cc_final: 0.7867 (pp30) REVERT: C 124 PRO cc_start: 0.8517 (Cg_exo) cc_final: 0.8305 (Cg_endo) REVERT: C 146 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6402 (mm) REVERT: C 197 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7445 (tp30) REVERT: C 299 PHE cc_start: 0.8250 (t80) cc_final: 0.7936 (t80) REVERT: D 116 PHE cc_start: 0.8260 (m-80) cc_final: 0.8036 (m-80) REVERT: D 146 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6676 (mm) REVERT: D 197 GLU cc_start: 0.6807 (tp30) cc_final: 0.6598 (tp30) REVERT: F 56 GLN cc_start: 0.8594 (tp40) cc_final: 0.8275 (tm-30) REVERT: F 63 GLN cc_start: 0.8232 (mp10) cc_final: 0.7758 (mp10) REVERT: F 101 LEU cc_start: 0.8423 (tt) cc_final: 0.8176 (mp) REVERT: F 121 TYR cc_start: 0.8245 (t80) cc_final: 0.7791 (t80) REVERT: F 124 PRO cc_start: 0.8533 (Cg_exo) cc_final: 0.8319 (Cg_endo) REVERT: F 146 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6440 (mm) REVERT: F 197 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7280 (tp30) REVERT: F 216 CYS cc_start: 0.7527 (OUTLIER) cc_final: 0.6896 (t) REVERT: F 299 PHE cc_start: 0.8085 (t80) cc_final: 0.7760 (t80) REVERT: G 63 GLN cc_start: 0.8535 (mp10) cc_final: 0.7849 (mp10) REVERT: G 121 TYR cc_start: 0.7963 (t80) cc_final: 0.7595 (t80) REVERT: G 146 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.5913 (mm) REVERT: G 197 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7285 (tp30) outliers start: 76 outliers final: 54 residues processed: 340 average time/residue: 0.1939 time to fit residues: 104.1938 Evaluate side-chains 342 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 279 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 128 ARG Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 331 TYR Chi-restraints excluded: chain G residue 348 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 20.0000 chunk 18 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 205 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3690 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= 0.188 Angle : 0.632 9.878 18963 Z= 0.293 Chirality : 0.039 0.169 2289 Planarity : 0.005 0.056 2268 Dihedral : 3.822 12.754 1806 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 5.24 % Allowed : 22.54 % Favored : 72.21 % 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: -0.05 (0.23), residues: 1652 helix: 0.59 (0.17), residues: 1141 sheet: -1.74 (0.63), residues: 91 loop : -1.11 (0.34), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 85 HIS 0.001 0.000 HIS B 106 PHE 0.014 0.001 PHE E 244 TYR 0.008 0.001 TYR B 213 ARG 0.001 0.000 ARG G 254 *********************** 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 366 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 286 time to evaluate : 1.649 Fit side-chains revert: symmetry clash REVERT: E 56 GLN cc_start: 0.8442 (tp40) cc_final: 0.8076 (mm-40) REVERT: E 146 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6730 (mm) REVERT: A 56 GLN cc_start: 0.8823 (tp-100) cc_final: 0.8093 (pp30) REVERT: A 63 GLN cc_start: 0.8486 (mp10) cc_final: 0.8051 (mp10) REVERT: A 124 PRO cc_start: 0.8164 (Cg_exo) cc_final: 0.7873 (Cg_endo) REVERT: A 146 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.6917 (mm) REVERT: A 197 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7362 (tp30) REVERT: A 331 TYR cc_start: 0.7777 (OUTLIER) cc_final: 0.7235 (t80) REVERT: B 63 GLN cc_start: 0.8521 (mp10) cc_final: 0.7968 (mp10) REVERT: B 124 PRO cc_start: 0.8237 (Cg_exo) cc_final: 0.8023 (Cg_endo) REVERT: B 146 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6394 (mm) REVERT: B 197 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7299 (tp30) REVERT: C 56 GLN cc_start: 0.8390 (tp40) cc_final: 0.8028 (tm-30) REVERT: C 124 PRO cc_start: 0.8495 (Cg_exo) cc_final: 0.8252 (Cg_endo) REVERT: C 138 ASP cc_start: 0.7657 (m-30) cc_final: 0.7311 (t0) REVERT: C 146 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.6373 (mm) REVERT: C 197 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7449 (tp30) REVERT: D 146 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6677 (mm) REVERT: D 197 GLU cc_start: 0.6754 (tp30) cc_final: 0.6535 (tp30) REVERT: F 63 GLN cc_start: 0.8256 (mp10) cc_final: 0.7821 (mp10) REVERT: F 101 LEU cc_start: 0.8435 (tt) cc_final: 0.8121 (mt) REVERT: F 121 TYR cc_start: 0.8217 (t80) cc_final: 0.7759 (t80) REVERT: F 124 PRO cc_start: 0.8521 (Cg_exo) cc_final: 0.8290 (Cg_endo) REVERT: F 146 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6462 (mm) REVERT: F 197 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7292 (tp30) REVERT: F 280 ASN cc_start: 0.9317 (OUTLIER) cc_final: 0.9091 (t0) REVERT: F 299 PHE cc_start: 0.8109 (t80) cc_final: 0.7754 (t80) REVERT: G 63 GLN cc_start: 0.8561 (mp10) cc_final: 0.7877 (mp10) REVERT: G 121 TYR cc_start: 0.8020 (t80) cc_final: 0.7615 (t80) REVERT: G 146 LEU cc_start: 0.6558 (OUTLIER) cc_final: 0.6183 (mm) REVERT: G 197 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7378 (tp30) outliers start: 80 outliers final: 59 residues processed: 336 average time/residue: 0.1854 time to fit residues: 99.5943 Evaluate side-chains 349 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 281 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 280 ASN Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 128 ARG Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 331 TYR Chi-restraints excluded: chain G residue 348 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 80 optimal weight: 0.0020 chunk 15 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- 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 205 ASN ** 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** ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 GLN 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13937 Z= 0.130 Angle : 0.618 10.124 18963 Z= 0.280 Chirality : 0.038 0.149 2289 Planarity : 0.005 0.057 2268 Dihedral : 3.590 11.505 1806 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.93 % Allowed : 24.38 % Favored : 71.69 % 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: 0.09 (0.23), residues: 1652 helix: 0.77 (0.17), residues: 1113 sheet: -4.28 (0.51), residues: 49 loop : -0.93 (0.31), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 85 HIS 0.001 0.000 HIS A 134 PHE 0.011 0.001 PHE G 299 TYR 0.009 0.001 TYR C 213 ARG 0.001 0.000 ARG B 254 *********************** 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 352 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 292 time to evaluate : 1.617 Fit side-chains revert: symmetry clash REVERT: E 56 GLN cc_start: 0.8411 (tp40) cc_final: 0.8123 (mm-40) REVERT: E 146 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6498 (mm) REVERT: A 56 GLN cc_start: 0.8799 (tp-100) cc_final: 0.8087 (pp30) REVERT: A 63 GLN cc_start: 0.8464 (mp10) cc_final: 0.8018 (mp10) REVERT: A 146 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6739 (mm) REVERT: A 197 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7423 (tp30) REVERT: A 331 TYR cc_start: 0.7713 (OUTLIER) cc_final: 0.7344 (t80) REVERT: B 63 GLN cc_start: 0.8466 (mp10) cc_final: 0.7938 (mp10) REVERT: B 124 PRO cc_start: 0.8210 (Cg_exo) cc_final: 0.8007 (Cg_endo) REVERT: B 146 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6485 (mm) REVERT: B 197 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7357 (tp30) REVERT: C 56 GLN cc_start: 0.8343 (tp40) cc_final: 0.7991 (pp30) REVERT: C 124 PRO cc_start: 0.8522 (Cg_exo) cc_final: 0.8298 (Cg_endo) REVERT: C 138 ASP cc_start: 0.7655 (m-30) cc_final: 0.7333 (t0) REVERT: C 146 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6411 (mm) REVERT: C 197 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7434 (tp30) REVERT: D 146 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6635 (mm) REVERT: D 197 GLU cc_start: 0.6755 (tp30) cc_final: 0.6521 (tp30) REVERT: D 331 TYR cc_start: 0.7670 (OUTLIER) cc_final: 0.7344 (t80) REVERT: F 56 GLN cc_start: 0.8453 (tp40) cc_final: 0.8042 (pp30) REVERT: F 63 GLN cc_start: 0.8250 (mp10) cc_final: 0.7792 (mp10) REVERT: F 101 LEU cc_start: 0.8373 (tt) cc_final: 0.8055 (mp) REVERT: F 121 TYR cc_start: 0.8130 (t80) cc_final: 0.7668 (t80) REVERT: F 124 PRO cc_start: 0.8629 (Cg_exo) cc_final: 0.8411 (Cg_endo) REVERT: F 138 ASP cc_start: 0.7661 (m-30) cc_final: 0.7297 (t0) REVERT: F 146 LEU cc_start: 0.6737 (OUTLIER) cc_final: 0.6293 (mm) REVERT: F 197 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7405 (tp30) REVERT: F 280 ASN cc_start: 0.9272 (OUTLIER) cc_final: 0.9060 (t0) REVERT: F 299 PHE cc_start: 0.8069 (t80) cc_final: 0.7738 (t80) REVERT: G 63 GLN cc_start: 0.8504 (mp10) cc_final: 0.7837 (mp10) REVERT: G 121 TYR cc_start: 0.7915 (t80) cc_final: 0.7540 (t80) REVERT: G 146 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.6502 (mm) REVERT: G 197 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7460 (tp30) outliers start: 60 outliers final: 41 residues processed: 329 average time/residue: 0.1823 time to fit residues: 96.2501 Evaluate side-chains 329 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 278 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 280 ASN Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 128 ARG Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 331 TYR Chi-restraints excluded: chain G residue 348 LEU 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: 8.9990 chunk 150 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 99 optimal weight: 0.0370 chunk 159 optimal weight: 4.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- 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** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13937 Z= 0.237 Angle : 0.646 9.227 18963 Z= 0.305 Chirality : 0.041 0.154 2289 Planarity : 0.005 0.056 2268 Dihedral : 3.905 13.336 1806 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.33 % Allowed : 23.98 % Favored : 71.69 % 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: 0.12 (0.23), residues: 1652 helix: 0.79 (0.17), residues: 1113 sheet: -1.72 (0.62), residues: 91 loop : -1.16 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 85 HIS 0.001 0.001 HIS G 134 PHE 0.031 0.001 PHE C 299 TYR 0.010 0.001 TYR B 213 ARG 0.001 0.000 ARG E 254 *********************** 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 351 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 285 time to evaluate : 1.564 Fit side-chains revert: symmetry clash REVERT: E 56 GLN cc_start: 0.8372 (tp40) cc_final: 0.7964 (pp30) REVERT: E 146 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6544 (mm) REVERT: A 56 GLN cc_start: 0.8774 (tp-100) cc_final: 0.8182 (pp30) REVERT: A 63 GLN cc_start: 0.8498 (mp10) cc_final: 0.8049 (mp10) REVERT: A 124 PRO cc_start: 0.8143 (Cg_exo) cc_final: 0.7858 (Cg_endo) REVERT: A 146 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6848 (mm) REVERT: A 197 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7372 (tp30) REVERT: A 331 TYR cc_start: 0.7790 (OUTLIER) cc_final: 0.7345 (t80) REVERT: B 63 GLN cc_start: 0.8547 (mp10) cc_final: 0.8012 (mp10) REVERT: B 124 PRO cc_start: 0.8212 (Cg_exo) cc_final: 0.8004 (Cg_endo) REVERT: B 146 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6384 (mm) REVERT: B 197 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7353 (tp30) REVERT: C 56 GLN cc_start: 0.8412 (tp40) cc_final: 0.8055 (tm-30) REVERT: C 124 PRO cc_start: 0.8505 (Cg_exo) cc_final: 0.8267 (Cg_endo) REVERT: C 138 ASP cc_start: 0.7583 (m-30) cc_final: 0.7242 (t0) REVERT: C 146 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.6344 (mm) REVERT: C 197 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7427 (tp30) REVERT: D 146 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6573 (mm) REVERT: D 197 GLU cc_start: 0.6767 (tp30) cc_final: 0.6514 (tp30) REVERT: F 56 GLN cc_start: 0.8476 (tp40) cc_final: 0.8060 (pp30) REVERT: F 63 GLN cc_start: 0.8291 (mp10) cc_final: 0.7840 (mp10) REVERT: F 101 LEU cc_start: 0.8376 (tt) cc_final: 0.7974 (mt) REVERT: F 121 TYR cc_start: 0.8227 (t80) cc_final: 0.7823 (t80) REVERT: F 138 ASP cc_start: 0.7692 (m-30) cc_final: 0.7341 (t0) REVERT: F 146 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6383 (mm) REVERT: F 197 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7305 (tp30) REVERT: F 216 CYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7258 (t) REVERT: F 280 ASN cc_start: 0.9332 (OUTLIER) cc_final: 0.9113 (t0) REVERT: F 299 PHE cc_start: 0.8118 (t80) cc_final: 0.7754 (t80) REVERT: G 63 GLN cc_start: 0.8566 (mp10) cc_final: 0.7829 (mp10) REVERT: G 121 TYR cc_start: 0.8028 (t80) cc_final: 0.7655 (t80) REVERT: G 146 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.6517 (mm) REVERT: G 197 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7345 (tp30) outliers start: 66 outliers final: 53 residues processed: 326 average time/residue: 0.1966 time to fit residues: 101.8701 Evaluate side-chains 343 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 280 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 280 ASN Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 331 TYR Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 128 ARG Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 331 TYR Chi-restraints excluded: chain G residue 348 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 167 optimal weight: 0.0000 chunk 154 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 105 optimal weight: 8.9990 chunk 141 optimal weight: 10.0000 overall best weight: 1.1388 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3975 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= 0.151 Angle : 0.624 10.051 18963 Z= 0.287 Chirality : 0.039 0.140 2289 Planarity : 0.005 0.057 2268 Dihedral : 3.706 11.852 1806 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.00 % Allowed : 24.77 % Favored : 71.23 % 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: 0.19 (0.23), residues: 1652 helix: 0.90 (0.17), residues: 1106 sheet: -4.31 (0.51), residues: 49 loop : -1.01 (0.31), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 85 HIS 0.001 0.000 HIS B 106 PHE 0.011 0.001 PHE A 244 TYR 0.012 0.001 TYR B 213 ARG 0.001 0.000 ARG G 254 ********************** 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 345 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 284 time to evaluate : 1.621 Fit side-chains REVERT: E 56 GLN cc_start: 0.8482 (tp40) cc_final: 0.8009 (pp30) REVERT: E 146 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.6567 (mm) REVERT: A 56 GLN cc_start: 0.8762 (tp-100) cc_final: 0.8172 (pp30) REVERT: A 63 GLN cc_start: 0.8465 (mp10) cc_final: 0.7996 (mp10) REVERT: A 124 PRO cc_start: 0.8285 (Cg_exo) cc_final: 0.8032 (Cg_endo) REVERT: A 146 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6750 (mm) REVERT: A 197 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7505 (tp30) REVERT: A 331 TYR cc_start: 0.7719 (OUTLIER) cc_final: 0.7367 (t80) REVERT: B 63 GLN cc_start: 0.8503 (mp10) cc_final: 0.7979 (mp10) REVERT: B 146 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6443 (mm) REVERT: B 197 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7378 (tp30) REVERT: C 56 GLN cc_start: 0.8407 (tp40) cc_final: 0.8054 (tm-30) REVERT: C 124 PRO cc_start: 0.8468 (Cg_exo) cc_final: 0.8230 (Cg_endo) REVERT: C 138 ASP cc_start: 0.7631 (m-30) cc_final: 0.7302 (t0) REVERT: C 146 LEU cc_start: 0.6788 (OUTLIER) cc_final: 0.6332 (mm) REVERT: C 197 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7435 (tp30) REVERT: D 146 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6696 (mm) REVERT: D 197 GLU cc_start: 0.6764 (tp30) cc_final: 0.5796 (mt-10) REVERT: D 331 TYR cc_start: 0.7785 (OUTLIER) cc_final: 0.7447 (t80) REVERT: F 56 GLN cc_start: 0.8473 (tp40) cc_final: 0.8075 (pp30) REVERT: F 63 GLN cc_start: 0.8276 (mp10) cc_final: 0.7820 (mp10) REVERT: F 101 LEU cc_start: 0.8329 (tt) cc_final: 0.8007 (mp) REVERT: F 121 TYR cc_start: 0.8170 (t80) cc_final: 0.7756 (t80) REVERT: F 138 ASP cc_start: 0.7678 (m-30) cc_final: 0.7285 (t0) REVERT: F 146 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.6368 (mm) REVERT: F 197 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7312 (tp30) REVERT: F 216 CYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7254 (t) REVERT: F 299 PHE cc_start: 0.8085 (t80) cc_final: 0.7802 (t80) REVERT: G 63 GLN cc_start: 0.8531 (mp10) cc_final: 0.7844 (mp10) REVERT: G 121 TYR cc_start: 0.7969 (t80) cc_final: 0.7594 (t80) REVERT: G 146 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6713 (mm) REVERT: G 197 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7400 (tp30) outliers start: 61 outliers final: 49 residues processed: 323 average time/residue: 0.1864 time to fit residues: 96.1434 Evaluate side-chains 336 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 277 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 128 ARG Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 331 TYR Chi-restraints excluded: chain G residue 348 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 117 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.164545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.116035 restraints weight = 22409.146| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.49 r_work: 0.3327 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3927 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= 0.264 Angle : 0.664 9.115 18963 Z= 0.314 Chirality : 0.041 0.155 2289 Planarity : 0.006 0.056 2268 Dihedral : 3.998 13.935 1806 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.39 % Allowed : 24.44 % Favored : 71.17 % 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: 0.81 (0.17), residues: 1113 sheet: -1.82 (0.62), residues: 91 loop : -1.20 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 85 HIS 0.002 0.001 HIS G 134 PHE 0.011 0.001 PHE A 244 TYR 0.012 0.001 TYR B 213 ARG 0.002 0.000 ARG E 254 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2929.32 seconds wall clock time: 53 minutes 37.27 seconds (3217.27 seconds total)