Starting phenix.real_space_refine on Sat Feb 17 09:33:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6urt_20862/02_2024/6urt_20862_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6urt_20862/02_2024/6urt_20862.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6urt_20862/02_2024/6urt_20862_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6urt_20862/02_2024/6urt_20862_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6urt_20862/02_2024/6urt_20862_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6urt_20862/02_2024/6urt_20862.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6urt_20862/02_2024/6urt_20862.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6urt_20862/02_2024/6urt_20862_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6urt_20862/02_2024/6urt_20862_updated.pdb" } resolution = 3.27 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 70 5.16 5 C 11893 2.51 5 N 3059 2.21 5 O 3234 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ARG 110": "NH1" <-> "NH2" Residue "G PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 235": "NH1" <-> "NH2" Residue "G ARG 236": "NH1" <-> "NH2" Residue "G TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 323": "OD1" <-> "OD2" Residue "A ARG 110": "NH1" <-> "NH2" Residue "A PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 323": "OD1" <-> "OD2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 110": "NH1" <-> "NH2" Residue "B PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "B TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "B PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 235": "NH1" <-> "NH2" Residue "C ARG 236": "NH1" <-> "NH2" Residue "C TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 323": "OD1" <-> "OD2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "D PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 235": "NH1" <-> "NH2" Residue "D ARG 236": "NH1" <-> "NH2" Residue "D TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 323": "OD1" <-> "OD2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 235": "NH1" <-> "NH2" Residue "E ARG 236": "NH1" <-> "NH2" Residue "E TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 323": "OD1" <-> "OD2" Residue "E PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 235": "NH1" <-> "NH2" Residue "F ARG 236": "NH1" <-> "NH2" Residue "F TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 323": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18263 Number of models: 1 Model: "" Number of chains: 14 Chain: "G" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2559 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 8, 'TRANS': 322} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "A" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2559 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 8, 'TRANS': 322} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2559 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 8, 'TRANS': 322} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "C" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2559 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 8, 'TRANS': 322} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "D" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2559 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 8, 'TRANS': 322} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "E" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2559 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 8, 'TRANS': 322} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "F" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2559 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 8, 'TRANS': 322} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'QGD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'QGD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'QGD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'QGD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'QGD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'QGD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'QGD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 9.58, per 1000 atoms: 0.52 Number of scatterers: 18263 At special positions: 0 Unit cell: (120.096, 119.232, 137.376, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 P 7 15.00 O 3234 8.00 N 3059 7.00 C 11893 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.52 Conformation dependent library (CDL) restraints added in 3.5 seconds 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4312 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 77 helices and 14 sheets defined 53.5% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'G' and resid 5 through 11 Processing helix chain 'G' and resid 13 through 30 removed outlier: 3.834A pdb=" N PHE G 17 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLY G 18 " --> pdb=" O VAL G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 67 removed outlier: 3.630A pdb=" N ILE G 49 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TYR G 50 " --> pdb=" O GLN G 46 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR G 51 " --> pdb=" O PHE G 47 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE G 52 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE G 53 " --> pdb=" O ILE G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 107 removed outlier: 3.665A pdb=" N ILE G 86 " --> pdb=" O CYS G 82 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 133 removed outlier: 3.606A pdb=" N ARG G 116 " --> pdb=" O ILE G 112 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE G 117 " --> pdb=" O THR G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 159 Processing helix chain 'G' and resid 161 through 175 Processing helix chain 'G' and resid 218 through 222 removed outlier: 3.716A pdb=" N SER G 222 " --> pdb=" O SER G 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 231 No H-bonds generated for 'chain 'G' and resid 229 through 231' Processing helix chain 'G' and resid 251 through 263 removed outlier: 3.619A pdb=" N ARG G 259 " --> pdb=" O VAL G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 317 removed outlier: 3.778A pdb=" N ASP G 315 " --> pdb=" O LEU G 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 11 Processing helix chain 'A' and resid 13 through 30 removed outlier: 3.834A pdb=" N PHE A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLY A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 67 removed outlier: 3.630A pdb=" N ILE A 49 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N TYR A 50 " --> pdb=" O GLN A 46 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR A 51 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 107 removed outlier: 3.665A pdb=" N ILE A 86 " --> pdb=" O CYS A 82 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 133 removed outlier: 3.783A pdb=" N ILE A 117 " --> pdb=" O THR A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 159 Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.716A pdb=" N SER A 222 " --> pdb=" O SER A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 251 through 263 removed outlier: 3.619A pdb=" N ARG A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 317 removed outlier: 3.778A pdb=" N ASP A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 13 through 30 removed outlier: 3.834A pdb=" N PHE B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLY B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 67 removed outlier: 3.631A pdb=" N ILE B 49 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N TYR B 50 " --> pdb=" O GLN B 46 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR B 51 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE B 52 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE B 53 " --> pdb=" O ILE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 107 removed outlier: 3.665A pdb=" N ILE B 86 " --> pdb=" O CYS B 82 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 133 removed outlier: 3.604A pdb=" N ARG B 116 " --> pdb=" O ILE B 112 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE B 117 " --> pdb=" O THR B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 Processing helix chain 'B' and resid 161 through 175 Processing helix chain 'B' and resid 218 through 222 removed outlier: 3.717A pdb=" N SER B 222 " --> pdb=" O SER B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 251 through 263 removed outlier: 3.618A pdb=" N ARG B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 317 removed outlier: 3.778A pdb=" N ASP B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 11 Processing helix chain 'C' and resid 13 through 30 removed outlier: 3.835A pdb=" N PHE C 17 " --> pdb=" O LEU C 13 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLY C 18 " --> pdb=" O VAL C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 67 removed outlier: 3.630A pdb=" N ILE C 49 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TYR C 50 " --> pdb=" O GLN C 46 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR C 51 " --> pdb=" O PHE C 47 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 107 removed outlier: 3.665A pdb=" N ILE C 86 " --> pdb=" O CYS C 82 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 133 removed outlier: 3.605A pdb=" N ARG C 116 " --> pdb=" O ILE C 112 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE C 117 " --> pdb=" O THR C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 159 Processing helix chain 'C' and resid 161 through 175 Processing helix chain 'C' and resid 218 through 222 removed outlier: 3.716A pdb=" N SER C 222 " --> pdb=" O SER C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 231 No H-bonds generated for 'chain 'C' and resid 229 through 231' Processing helix chain 'C' and resid 251 through 263 removed outlier: 3.619A pdb=" N ARG C 259 " --> pdb=" O VAL C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 317 removed outlier: 3.778A pdb=" N ASP C 315 " --> pdb=" O LEU C 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 11 Processing helix chain 'D' and resid 13 through 30 removed outlier: 3.835A pdb=" N PHE D 17 " --> pdb=" O LEU D 13 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLY D 18 " --> pdb=" O VAL D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 67 removed outlier: 3.630A pdb=" N ILE D 49 " --> pdb=" O VAL D 45 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TYR D 50 " --> pdb=" O GLN D 46 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR D 51 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE D 52 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE D 53 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 107 removed outlier: 3.665A pdb=" N ILE D 86 " --> pdb=" O CYS D 82 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 133 removed outlier: 3.606A pdb=" N ARG D 116 " --> pdb=" O ILE D 112 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE D 117 " --> pdb=" O THR D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 159 Processing helix chain 'D' and resid 161 through 175 Processing helix chain 'D' and resid 218 through 222 removed outlier: 3.716A pdb=" N SER D 222 " --> pdb=" O SER D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 231 No H-bonds generated for 'chain 'D' and resid 229 through 231' Processing helix chain 'D' and resid 251 through 263 removed outlier: 3.619A pdb=" N ARG D 259 " --> pdb=" O VAL D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 317 removed outlier: 3.778A pdb=" N ASP D 315 " --> pdb=" O LEU D 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 11 Processing helix chain 'E' and resid 13 through 30 removed outlier: 3.834A pdb=" N PHE E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLY E 18 " --> pdb=" O VAL E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 67 removed outlier: 3.630A pdb=" N ILE E 49 " --> pdb=" O VAL E 45 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N TYR E 50 " --> pdb=" O GLN E 46 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR E 51 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE E 53 " --> pdb=" O ILE E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 107 removed outlier: 3.665A pdb=" N ILE E 86 " --> pdb=" O CYS E 82 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 133 removed outlier: 3.604A pdb=" N ARG E 116 " --> pdb=" O ILE E 112 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE E 117 " --> pdb=" O THR E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 159 Processing helix chain 'E' and resid 161 through 175 Processing helix chain 'E' and resid 218 through 222 removed outlier: 3.716A pdb=" N SER E 222 " --> pdb=" O SER E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 231 No H-bonds generated for 'chain 'E' and resid 229 through 231' Processing helix chain 'E' and resid 251 through 263 removed outlier: 3.618A pdb=" N ARG E 259 " --> pdb=" O VAL E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 317 removed outlier: 3.778A pdb=" N ASP E 315 " --> pdb=" O LEU E 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 11 Processing helix chain 'F' and resid 13 through 30 removed outlier: 3.834A pdb=" N PHE F 17 " --> pdb=" O LEU F 13 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLY F 18 " --> pdb=" O VAL F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 67 removed outlier: 3.630A pdb=" N ILE F 49 " --> pdb=" O VAL F 45 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TYR F 50 " --> pdb=" O GLN F 46 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR F 51 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE F 53 " --> pdb=" O ILE F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 107 removed outlier: 3.665A pdb=" N ILE F 86 " --> pdb=" O CYS F 82 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 133 removed outlier: 3.748A pdb=" N ARG F 116 " --> pdb=" O ILE F 112 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE F 117 " --> pdb=" O THR F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 159 Processing helix chain 'F' and resid 161 through 175 Processing helix chain 'F' and resid 218 through 222 removed outlier: 3.716A pdb=" N SER F 222 " --> pdb=" O SER F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 231 No H-bonds generated for 'chain 'F' and resid 229 through 231' Processing helix chain 'F' and resid 251 through 263 removed outlier: 3.619A pdb=" N ARG F 259 " --> pdb=" O VAL F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 317 removed outlier: 3.778A pdb=" N ASP F 315 " --> pdb=" O LEU F 311 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'G' and resid 213 through 217 removed outlier: 5.616A pdb=" N THR G 207 " --> pdb=" O VAL G 196 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N VAL G 196 " --> pdb=" O THR G 207 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 236 through 239 Processing sheet with id= C, first strand: chain 'A' and resid 213 through 217 removed outlier: 5.616A pdb=" N THR A 207 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N VAL A 196 " --> pdb=" O THR A 207 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 236 through 239 Processing sheet with id= E, first strand: chain 'B' and resid 213 through 217 removed outlier: 5.615A pdb=" N THR B 207 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N VAL B 196 " --> pdb=" O THR B 207 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 236 through 239 Processing sheet with id= G, first strand: chain 'C' and resid 213 through 217 removed outlier: 5.615A pdb=" N THR C 207 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N VAL C 196 " --> pdb=" O THR C 207 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 236 through 239 Processing sheet with id= I, first strand: chain 'D' and resid 213 through 217 removed outlier: 5.616A pdb=" N THR D 207 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N VAL D 196 " --> pdb=" O THR D 207 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 236 through 239 Processing sheet with id= K, first strand: chain 'E' and resid 213 through 217 removed outlier: 5.615A pdb=" N THR E 207 " --> pdb=" O VAL E 196 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N VAL E 196 " --> pdb=" O THR E 207 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 236 through 239 Processing sheet with id= M, first strand: chain 'F' and resid 213 through 217 removed outlier: 5.616A pdb=" N THR F 207 " --> pdb=" O VAL F 196 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N VAL F 196 " --> pdb=" O THR F 207 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 236 through 239 946 hydrogen bonds defined for protein. 2796 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: 5.24 Time building geometry restraints manager: 8.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2922 1.32 - 1.44: 4904 1.44 - 1.56: 10628 1.56 - 1.68: 26 1.68 - 1.80: 126 Bond restraints: 18606 Sorted by residual: bond pdb=" O3 QGD F 401 " pdb=" P1 QGD F 401 " ideal model delta sigma weight residual 1.667 1.580 0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" N ASP F 111 " pdb=" CA ASP F 111 " ideal model delta sigma weight residual 1.457 1.502 -0.045 1.29e-02 6.01e+03 1.21e+01 bond pdb=" C20 QGD F 401 " pdb=" O1 QGD F 401 " ideal model delta sigma weight residual 1.420 1.351 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" N ASP C 111 " pdb=" CA ASP C 111 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.29e-02 6.01e+03 1.01e+01 bond pdb=" N ILE E 112 " pdb=" CA ILE E 112 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.17e-02 7.31e+03 1.00e+01 ... (remaining 18601 not shown) Histogram of bond angle deviations from ideal: 99.51 - 106.40: 379 106.40 - 113.30: 10256 113.30 - 120.20: 7497 120.20 - 127.09: 6832 127.09 - 133.99: 173 Bond angle restraints: 25137 Sorted by residual: angle pdb=" C15 QGD G 401 " pdb=" C16 QGD G 401 " pdb=" C17 QGD G 401 " ideal model delta sigma weight residual 109.48 130.73 -21.25 3.00e+00 1.11e-01 5.02e+01 angle pdb=" C15 QGD B 401 " pdb=" C16 QGD B 401 " pdb=" C17 QGD B 401 " ideal model delta sigma weight residual 109.48 130.70 -21.22 3.00e+00 1.11e-01 5.00e+01 angle pdb=" C15 QGD D 401 " pdb=" C16 QGD D 401 " pdb=" C17 QGD D 401 " ideal model delta sigma weight residual 109.48 130.70 -21.22 3.00e+00 1.11e-01 5.00e+01 angle pdb=" C15 QGD E 401 " pdb=" C16 QGD E 401 " pdb=" C17 QGD E 401 " ideal model delta sigma weight residual 109.48 130.69 -21.21 3.00e+00 1.11e-01 5.00e+01 angle pdb=" C15 QGD C 401 " pdb=" C16 QGD C 401 " pdb=" C17 QGD C 401 " ideal model delta sigma weight residual 109.48 130.68 -21.20 3.00e+00 1.11e-01 4.99e+01 ... (remaining 25132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.20: 10434 27.20 - 54.40: 506 54.40 - 81.61: 79 81.61 - 108.81: 21 108.81 - 136.01: 20 Dihedral angle restraints: 11060 sinusoidal: 4361 harmonic: 6699 Sorted by residual: dihedral pdb=" CA PRO E 327 " pdb=" C PRO E 327 " pdb=" N SER E 328 " pdb=" CA SER E 328 " ideal model delta harmonic sigma weight residual 180.00 151.94 28.06 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA PRO A 327 " pdb=" C PRO A 327 " pdb=" N SER A 328 " pdb=" CA SER A 328 " ideal model delta harmonic sigma weight residual 180.00 151.95 28.05 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA PRO C 327 " pdb=" C PRO C 327 " pdb=" N SER C 328 " pdb=" CA SER C 328 " ideal model delta harmonic sigma weight residual 180.00 151.96 28.04 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 11057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2450 0.087 - 0.173: 428 0.173 - 0.260: 33 0.260 - 0.346: 7 0.346 - 0.433: 1 Chirality restraints: 2919 Sorted by residual: chirality pdb=" CA ASP B 323 " pdb=" N ASP B 323 " pdb=" C ASP B 323 " pdb=" CB ASP B 323 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" CG LEU B 146 " pdb=" CB LEU B 146 " pdb=" CD1 LEU B 146 " pdb=" CD2 LEU B 146 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CG LEU F 146 " pdb=" CB LEU F 146 " pdb=" CD1 LEU F 146 " pdb=" CD2 LEU F 146 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 2916 not shown) Planarity restraints: 3115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 325 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C ALA A 325 " 0.060 2.00e-02 2.50e+03 pdb=" O ALA A 325 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE A 326 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA F 325 " 0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C ALA F 325 " -0.057 2.00e-02 2.50e+03 pdb=" O ALA F 325 " 0.022 2.00e-02 2.50e+03 pdb=" N PHE F 326 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 325 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.43e+00 pdb=" C ALA D 325 " -0.053 2.00e-02 2.50e+03 pdb=" O ALA D 325 " 0.020 2.00e-02 2.50e+03 pdb=" N PHE D 326 " 0.018 2.00e-02 2.50e+03 ... (remaining 3112 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 5533 2.81 - 3.33: 17865 3.33 - 3.85: 30546 3.85 - 4.38: 34172 4.38 - 4.90: 57918 Nonbonded interactions: 146034 Sorted by model distance: nonbonded pdb=" CZ PHE A 281 " pdb=" CE2 PHE B 324 " model vdw 2.285 3.640 nonbonded pdb=" N ASP C 247 " pdb=" OD1 ASP C 247 " model vdw 2.304 2.520 nonbonded pdb=" N ASP E 247 " pdb=" OD1 ASP E 247 " model vdw 2.304 2.520 nonbonded pdb=" N ASP F 247 " pdb=" OD1 ASP F 247 " model vdw 2.304 2.520 nonbonded pdb=" N ASP D 247 " pdb=" OD1 ASP D 247 " model vdw 2.304 2.520 ... (remaining 146029 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: 0.010 Normalize map: mean=0, sd=1: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.750 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 48.810 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 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 : 0.008 0.087 18606 Z= 0.518 Angle : 1.357 21.246 25137 Z= 0.675 Chirality : 0.062 0.433 2919 Planarity : 0.007 0.072 3115 Dihedral : 17.608 136.012 6748 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 3.41 % Allowed : 6.49 % Favored : 90.10 % Cbeta Deviations : 0.05 % 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: -4.88 (0.13), residues: 2303 helix: -2.67 (0.11), residues: 1267 sheet: -3.35 (0.26), residues: 259 loop : -3.87 (0.18), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP F 184 HIS 0.006 0.002 HIS F 137 PHE 0.032 0.003 PHE G 324 TYR 0.014 0.002 TYR F 215 ARG 0.005 0.001 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 254 time to evaluate : 2.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 140 MET cc_start: 0.7493 (mtt) cc_final: 0.7289 (mpp) REVERT: G 193 GLU cc_start: 0.9178 (tt0) cc_final: 0.8714 (tt0) REVERT: G 227 GLU cc_start: 0.8463 (tt0) cc_final: 0.8212 (tt0) REVERT: G 246 GLU cc_start: 0.9171 (pp20) cc_final: 0.8957 (pp20) REVERT: G 284 SER cc_start: 0.9391 (OUTLIER) cc_final: 0.8850 (t) REVERT: G 289 MET cc_start: 0.8980 (ttt) cc_final: 0.8773 (ttp) REVERT: A 140 MET cc_start: 0.7479 (mtt) cc_final: 0.7217 (mpp) REVERT: A 146 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8762 (tt) REVERT: A 193 GLU cc_start: 0.9182 (tt0) cc_final: 0.8640 (tt0) REVERT: A 284 SER cc_start: 0.9397 (OUTLIER) cc_final: 0.8890 (t) REVERT: A 289 MET cc_start: 0.8975 (ttt) cc_final: 0.8726 (ptm) REVERT: B 193 GLU cc_start: 0.9157 (tt0) cc_final: 0.8756 (tt0) REVERT: B 227 GLU cc_start: 0.8472 (tt0) cc_final: 0.8257 (tt0) REVERT: B 271 ARG cc_start: 0.9287 (ptp-110) cc_final: 0.9046 (mtm-85) REVERT: B 284 SER cc_start: 0.9427 (OUTLIER) cc_final: 0.8991 (t) REVERT: C 140 MET cc_start: 0.7492 (mtt) cc_final: 0.7245 (mpp) REVERT: C 146 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8708 (tt) REVERT: C 193 GLU cc_start: 0.9152 (tt0) cc_final: 0.8640 (tp30) REVERT: C 227 GLU cc_start: 0.8485 (tt0) cc_final: 0.8165 (tt0) REVERT: C 284 SER cc_start: 0.9417 (OUTLIER) cc_final: 0.8860 (t) REVERT: D 193 GLU cc_start: 0.9169 (tt0) cc_final: 0.8658 (tt0) REVERT: D 227 GLU cc_start: 0.8352 (tt0) cc_final: 0.7845 (tt0) REVERT: D 284 SER cc_start: 0.9401 (OUTLIER) cc_final: 0.8932 (t) REVERT: E 140 MET cc_start: 0.7440 (mtt) cc_final: 0.7182 (mpp) REVERT: E 193 GLU cc_start: 0.9143 (tt0) cc_final: 0.8746 (tt0) REVERT: E 284 SER cc_start: 0.9386 (OUTLIER) cc_final: 0.8881 (t) REVERT: F 146 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8714 (tt) REVERT: F 154 LEU cc_start: 0.9514 (tt) cc_final: 0.9290 (tt) REVERT: F 193 GLU cc_start: 0.9137 (tt0) cc_final: 0.8638 (tt0) REVERT: F 246 GLU cc_start: 0.9189 (pp20) cc_final: 0.8862 (pp20) REVERT: F 271 ARG cc_start: 0.9313 (ptp-110) cc_final: 0.9097 (mtm-85) REVERT: F 284 SER cc_start: 0.9358 (OUTLIER) cc_final: 0.8852 (t) REVERT: F 333 MET cc_start: 0.8933 (ttm) cc_final: 0.8704 (mtp) outliers start: 63 outliers final: 14 residues processed: 312 average time/residue: 0.2538 time to fit residues: 126.3151 Evaluate side-chains 216 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 192 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 284 SER Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 284 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 0.8980 chunk 175 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 181 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 134 optimal weight: 20.0000 chunk 209 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 46 GLN G 62 ASN G 137 HIS G 211 ASN G 270 GLN G 280 GLN G 287 ASN A 46 GLN A 62 ASN A 105 GLN A 211 ASN A 270 GLN A 280 GLN A 287 ASN B 46 GLN B 62 ASN B 137 HIS B 211 ASN B 270 GLN B 280 GLN B 287 ASN C 46 GLN C 62 ASN C 211 ASN C 270 GLN C 280 GLN C 287 ASN D 46 GLN D 62 ASN D 137 HIS D 211 ASN D 270 GLN D 280 GLN D 287 ASN E 46 GLN E 62 ASN E 137 HIS E 211 ASN E 270 GLN E 280 GLN E 287 ASN F 46 GLN F 62 ASN F 137 HIS F 211 ASN F 270 GLN F 280 GLN F 287 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18606 Z= 0.170 Angle : 0.614 7.107 25137 Z= 0.324 Chirality : 0.042 0.133 2919 Planarity : 0.004 0.052 3115 Dihedral : 15.164 99.404 2799 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 3.63 % Allowed : 12.45 % Favored : 83.93 % 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: -3.11 (0.16), residues: 2303 helix: -0.87 (0.13), residues: 1281 sheet: -3.02 (0.30), residues: 259 loop : -3.68 (0.19), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 201 HIS 0.002 0.001 HIS A 137 PHE 0.023 0.001 PHE G 148 TYR 0.011 0.001 TYR G 215 ARG 0.003 0.000 ARG G 271 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 207 time to evaluate : 2.053 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: G 46 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8336 (tm-30) REVERT: G 146 LEU cc_start: 0.8864 (tt) cc_final: 0.8443 (mt) REVERT: G 193 GLU cc_start: 0.9101 (tt0) cc_final: 0.8730 (tt0) REVERT: G 227 GLU cc_start: 0.8315 (tt0) cc_final: 0.8078 (tt0) REVERT: G 246 GLU cc_start: 0.9099 (pp20) cc_final: 0.8830 (pp20) REVERT: A 46 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8302 (tm-30) REVERT: A 146 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8738 (mt) REVERT: A 193 GLU cc_start: 0.9116 (tt0) cc_final: 0.8568 (tp30) REVERT: A 289 MET cc_start: 0.8983 (ttt) cc_final: 0.8753 (ptm) REVERT: B 46 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8213 (tm-30) REVERT: B 193 GLU cc_start: 0.9134 (tt0) cc_final: 0.8856 (tt0) REVERT: B 227 GLU cc_start: 0.8316 (tt0) cc_final: 0.8054 (tt0) REVERT: B 271 ARG cc_start: 0.9255 (ptp-110) cc_final: 0.9054 (mtm-85) REVERT: C 46 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8404 (tm-30) REVERT: C 146 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8607 (mt) REVERT: C 154 LEU cc_start: 0.9566 (tt) cc_final: 0.9354 (tt) REVERT: C 193 GLU cc_start: 0.9125 (tt0) cc_final: 0.8628 (tt0) REVERT: C 227 GLU cc_start: 0.8283 (tt0) cc_final: 0.7933 (tt0) REVERT: D 46 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8387 (tm-30) REVERT: D 111 ASP cc_start: 0.7466 (t0) cc_final: 0.7262 (t0) REVERT: D 193 GLU cc_start: 0.9118 (tt0) cc_final: 0.8554 (tp30) REVERT: D 227 GLU cc_start: 0.8268 (tt0) cc_final: 0.7908 (tt0) REVERT: D 261 MET cc_start: 0.9449 (tmm) cc_final: 0.9244 (tmm) REVERT: D 289 MET cc_start: 0.9091 (ttp) cc_final: 0.8401 (ptm) REVERT: E 46 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8474 (tm-30) REVERT: E 146 LEU cc_start: 0.8858 (tt) cc_final: 0.8368 (mt) REVERT: E 193 GLU cc_start: 0.9099 (tt0) cc_final: 0.8655 (tt0) REVERT: E 256 GLU cc_start: 0.9201 (tp30) cc_final: 0.8917 (mm-30) REVERT: E 261 MET cc_start: 0.9439 (tmm) cc_final: 0.9237 (tmm) REVERT: F 46 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8386 (tm-30) REVERT: F 146 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8707 (mt) REVERT: F 154 LEU cc_start: 0.9555 (tt) cc_final: 0.9314 (tt) REVERT: F 193 GLU cc_start: 0.9096 (tt0) cc_final: 0.8602 (tt0) REVERT: F 333 MET cc_start: 0.8975 (ttm) cc_final: 0.8762 (mtp) outliers start: 67 outliers final: 32 residues processed: 250 average time/residue: 0.2591 time to fit residues: 104.4562 Evaluate side-chains 221 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 179 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 GLN Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 63 TYR Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 TYR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain D residue 63 TYR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 63 TYR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain F residue 46 GLN Chi-restraints excluded: chain F residue 63 TYR Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 225 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 168 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 46 GLN A 46 GLN A 320 HIS B 46 GLN B 320 HIS C 46 GLN D 46 GLN E 46 GLN F 46 GLN F 320 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 18606 Z= 0.235 Angle : 0.603 7.343 25137 Z= 0.316 Chirality : 0.042 0.147 2919 Planarity : 0.004 0.051 3115 Dihedral : 12.638 87.718 2786 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 3.84 % Allowed : 16.40 % Favored : 79.76 % 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: -2.00 (0.17), residues: 2303 helix: 0.22 (0.14), residues: 1274 sheet: -2.64 (0.32), residues: 259 loop : -3.52 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 184 HIS 0.003 0.001 HIS D 43 PHE 0.019 0.001 PHE G 148 TYR 0.012 0.001 TYR A 291 ARG 0.002 0.000 ARG E 236 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 203 time to evaluate : 2.135 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: G 46 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8488 (pp30) REVERT: G 146 LEU cc_start: 0.8881 (tt) cc_final: 0.8435 (mt) REVERT: G 193 GLU cc_start: 0.9051 (tt0) cc_final: 0.8703 (tt0) REVERT: G 227 GLU cc_start: 0.8334 (tt0) cc_final: 0.8105 (tt0) REVERT: G 301 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8883 (mp0) REVERT: A 146 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8729 (mt) REVERT: A 193 GLU cc_start: 0.9089 (tt0) cc_final: 0.8558 (tt0) REVERT: A 333 MET cc_start: 0.8924 (mtp) cc_final: 0.8606 (mtp) REVERT: B 63 TYR cc_start: 0.8592 (OUTLIER) cc_final: 0.8349 (t80) REVERT: B 146 LEU cc_start: 0.8863 (tt) cc_final: 0.8417 (mt) REVERT: B 193 GLU cc_start: 0.9085 (tt0) cc_final: 0.8853 (tt0) REVERT: B 227 GLU cc_start: 0.8371 (tt0) cc_final: 0.8087 (tt0) REVERT: B 271 ARG cc_start: 0.9260 (ptp-110) cc_final: 0.9057 (mtm-85) REVERT: B 289 MET cc_start: 0.9185 (ttp) cc_final: 0.8875 (ptm) REVERT: C 193 GLU cc_start: 0.9082 (tt0) cc_final: 0.8580 (tt0) REVERT: C 227 GLU cc_start: 0.8314 (tt0) cc_final: 0.7947 (tt0) REVERT: D 193 GLU cc_start: 0.9077 (tt0) cc_final: 0.8523 (tt0) REVERT: D 227 GLU cc_start: 0.8336 (tt0) cc_final: 0.7950 (tt0) REVERT: E 142 LEU cc_start: 0.8760 (tt) cc_final: 0.8282 (mm) REVERT: E 146 LEU cc_start: 0.8890 (tt) cc_final: 0.8471 (mt) REVERT: E 193 GLU cc_start: 0.9032 (tt0) cc_final: 0.8622 (tt0) REVERT: E 261 MET cc_start: 0.9479 (tmm) cc_final: 0.9247 (tmm) REVERT: E 289 MET cc_start: 0.9193 (ttp) cc_final: 0.8685 (ptm) REVERT: E 301 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8935 (pt0) REVERT: F 146 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8915 (mt) REVERT: F 154 LEU cc_start: 0.9544 (tt) cc_final: 0.9316 (tt) REVERT: F 193 GLU cc_start: 0.9062 (tt0) cc_final: 0.8528 (tp30) outliers start: 71 outliers final: 29 residues processed: 248 average time/residue: 0.2424 time to fit residues: 97.7906 Evaluate side-chains 207 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 174 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 GLN Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 320 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 100 optimal weight: 50.0000 chunk 141 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 chunk 223 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 46 GLN A 320 HIS ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 HIS C 46 GLN C 320 HIS D 46 GLN D 320 HIS E 320 HIS F 320 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 18606 Z= 0.414 Angle : 0.685 6.475 25137 Z= 0.359 Chirality : 0.044 0.152 2919 Planarity : 0.004 0.058 3115 Dihedral : 11.776 89.345 2769 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 4.38 % Allowed : 17.26 % Favored : 78.35 % 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: -1.30 (0.18), residues: 2303 helix: 0.76 (0.15), residues: 1309 sheet: -2.49 (0.32), residues: 266 loop : -3.27 (0.19), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 184 HIS 0.011 0.002 HIS B 320 PHE 0.018 0.001 PHE D 42 TYR 0.014 0.001 TYR A 291 ARG 0.002 0.000 ARG F 244 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 191 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 142 LEU cc_start: 0.8731 (tt) cc_final: 0.8221 (mm) REVERT: G 146 LEU cc_start: 0.8965 (tt) cc_final: 0.8437 (mt) REVERT: G 193 GLU cc_start: 0.9054 (tt0) cc_final: 0.8705 (tt0) REVERT: G 227 GLU cc_start: 0.8356 (tt0) cc_final: 0.8110 (tt0) REVERT: G 289 MET cc_start: 0.9273 (ttp) cc_final: 0.8982 (ptm) REVERT: A 111 ASP cc_start: 0.7057 (t0) cc_final: 0.6829 (t0) REVERT: A 140 MET cc_start: 0.7187 (mtt) cc_final: 0.6959 (mtp) REVERT: A 146 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8753 (mt) REVERT: A 193 GLU cc_start: 0.9083 (tt0) cc_final: 0.8634 (tt0) REVERT: A 333 MET cc_start: 0.8980 (mtp) cc_final: 0.8753 (mtp) REVERT: B 43 HIS cc_start: 0.8539 (OUTLIER) cc_final: 0.8153 (t70) REVERT: B 146 LEU cc_start: 0.8974 (tt) cc_final: 0.8431 (mt) REVERT: B 193 GLU cc_start: 0.9067 (tt0) cc_final: 0.8845 (tt0) REVERT: B 227 GLU cc_start: 0.8427 (tt0) cc_final: 0.8146 (tt0) REVERT: B 271 ARG cc_start: 0.9251 (ptp-110) cc_final: 0.9036 (mtm-85) REVERT: B 289 MET cc_start: 0.9235 (ttp) cc_final: 0.8916 (ptm) REVERT: B 301 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8944 (pt0) REVERT: C 146 LEU cc_start: 0.8973 (mt) cc_final: 0.8667 (mt) REVERT: C 193 GLU cc_start: 0.9075 (tt0) cc_final: 0.8547 (tt0) REVERT: D 142 LEU cc_start: 0.8723 (tt) cc_final: 0.8319 (mm) REVERT: D 146 LEU cc_start: 0.8992 (tt) cc_final: 0.8512 (mt) REVERT: D 193 GLU cc_start: 0.9081 (tt0) cc_final: 0.8533 (tt0) REVERT: D 227 GLU cc_start: 0.8426 (tt0) cc_final: 0.8052 (tt0) REVERT: E 43 HIS cc_start: 0.8497 (OUTLIER) cc_final: 0.8190 (t70) REVERT: E 142 LEU cc_start: 0.8770 (tt) cc_final: 0.8225 (mm) REVERT: E 146 LEU cc_start: 0.8978 (tt) cc_final: 0.8480 (mt) REVERT: E 193 GLU cc_start: 0.9017 (tt0) cc_final: 0.8604 (tt0) REVERT: E 261 MET cc_start: 0.9478 (tmm) cc_final: 0.9235 (tmm) REVERT: E 289 MET cc_start: 0.9239 (ttp) cc_final: 0.8821 (ptm) REVERT: F 43 HIS cc_start: 0.8449 (OUTLIER) cc_final: 0.8073 (t70) REVERT: F 118 MET cc_start: 0.9488 (tpp) cc_final: 0.9252 (tpp) REVERT: F 193 GLU cc_start: 0.9075 (tt0) cc_final: 0.8555 (tt0) REVERT: F 333 MET cc_start: 0.8925 (mtp) cc_final: 0.8700 (mtp) outliers start: 81 outliers final: 49 residues processed: 257 average time/residue: 0.2382 time to fit residues: 99.9305 Evaluate side-chains 231 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 178 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 GLN Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 198 GLU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 320 HIS Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain E residue 43 HIS Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 320 HIS Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain F residue 43 HIS Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 331 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 166 optimal weight: 50.0000 chunk 92 optimal weight: 0.2980 chunk 190 optimal weight: 0.8980 chunk 154 optimal weight: 0.6980 chunk 0 optimal weight: 70.0000 chunk 114 optimal weight: 2.9990 chunk 200 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 46 GLN G 320 HIS A 137 HIS ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN C 137 HIS C 320 HIS D 46 GLN D 320 HIS ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 18606 Z= 0.141 Angle : 0.575 7.662 25137 Z= 0.295 Chirality : 0.042 0.135 2919 Planarity : 0.003 0.053 3115 Dihedral : 11.183 88.749 2767 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 3.79 % Allowed : 18.72 % Favored : 77.49 % 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: -0.84 (0.18), residues: 2303 helix: 1.26 (0.15), residues: 1267 sheet: -2.08 (0.34), residues: 259 loop : -3.20 (0.19), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 302 HIS 0.008 0.001 HIS D 320 PHE 0.024 0.001 PHE C 42 TYR 0.011 0.001 TYR G 291 ARG 0.002 0.000 ARG G 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 190 time to evaluate : 2.009 Fit side-chains revert: symmetry clash REVERT: G 140 MET cc_start: 0.6932 (mtt) cc_final: 0.6691 (mtm) REVERT: G 142 LEU cc_start: 0.8631 (tt) cc_final: 0.8290 (mm) REVERT: G 146 LEU cc_start: 0.8950 (tt) cc_final: 0.8460 (mt) REVERT: G 193 GLU cc_start: 0.9077 (tt0) cc_final: 0.8725 (tt0) REVERT: G 227 GLU cc_start: 0.8348 (tt0) cc_final: 0.8124 (tt0) REVERT: G 232 MET cc_start: 0.8961 (ptt) cc_final: 0.8722 (ptt) REVERT: G 289 MET cc_start: 0.9229 (ttp) cc_final: 0.8935 (ptm) REVERT: G 333 MET cc_start: 0.8852 (mtp) cc_final: 0.8442 (mtp) REVERT: A 111 ASP cc_start: 0.7152 (t0) cc_final: 0.6825 (t0) REVERT: A 140 MET cc_start: 0.6951 (mtt) cc_final: 0.6674 (mtp) REVERT: A 193 GLU cc_start: 0.9102 (tt0) cc_final: 0.8549 (tp30) REVERT: A 232 MET cc_start: 0.9433 (ptm) cc_final: 0.9038 (ptm) REVERT: A 333 MET cc_start: 0.8888 (mtp) cc_final: 0.8631 (mtp) REVERT: B 43 HIS cc_start: 0.8440 (OUTLIER) cc_final: 0.8143 (t70) REVERT: B 146 LEU cc_start: 0.8945 (tt) cc_final: 0.8445 (mt) REVERT: B 193 GLU cc_start: 0.9105 (tt0) cc_final: 0.8823 (tt0) REVERT: B 227 GLU cc_start: 0.8346 (tt0) cc_final: 0.8061 (tt0) REVERT: B 271 ARG cc_start: 0.9237 (ptp-110) cc_final: 0.9024 (mtm-85) REVERT: B 289 MET cc_start: 0.9203 (ttp) cc_final: 0.8913 (ptm) REVERT: B 301 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8903 (pt0) REVERT: C 138 PHE cc_start: 0.7344 (m-80) cc_final: 0.7117 (m-80) REVERT: C 140 MET cc_start: 0.6818 (mtt) cc_final: 0.6589 (mtp) REVERT: C 146 LEU cc_start: 0.8982 (mt) cc_final: 0.8677 (mt) REVERT: C 193 GLU cc_start: 0.9098 (tt0) cc_final: 0.8590 (tp30) REVERT: C 227 GLU cc_start: 0.8145 (tt0) cc_final: 0.7909 (tt0) REVERT: C 301 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8878 (mp0) REVERT: C 333 MET cc_start: 0.8802 (mtp) cc_final: 0.8334 (tpp) REVERT: D 146 LEU cc_start: 0.8964 (tt) cc_final: 0.8478 (mt) REVERT: D 193 GLU cc_start: 0.9111 (tt0) cc_final: 0.8560 (tt0) REVERT: D 227 GLU cc_start: 0.8368 (tt0) cc_final: 0.7974 (tt0) REVERT: D 301 GLU cc_start: 0.9182 (mt-10) cc_final: 0.8860 (mp0) REVERT: E 43 HIS cc_start: 0.8403 (OUTLIER) cc_final: 0.8171 (t70) REVERT: E 142 LEU cc_start: 0.8692 (tt) cc_final: 0.8139 (mm) REVERT: E 146 LEU cc_start: 0.8996 (tt) cc_final: 0.8526 (mt) REVERT: E 193 GLU cc_start: 0.9068 (tt0) cc_final: 0.8665 (tt0) REVERT: E 289 MET cc_start: 0.9225 (ttp) cc_final: 0.8799 (ptm) REVERT: E 301 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8855 (mp0) REVERT: F 43 HIS cc_start: 0.8320 (OUTLIER) cc_final: 0.8018 (t70) REVERT: F 118 MET cc_start: 0.9463 (tpp) cc_final: 0.9235 (tpp) REVERT: F 140 MET cc_start: 0.6973 (mtt) cc_final: 0.6729 (mtp) REVERT: F 193 GLU cc_start: 0.9083 (tt0) cc_final: 0.8581 (tp30) REVERT: F 289 MET cc_start: 0.9193 (ttp) cc_final: 0.8956 (ttp) REVERT: F 333 MET cc_start: 0.8808 (mtp) cc_final: 0.8425 (mtp) outliers start: 70 outliers final: 38 residues processed: 249 average time/residue: 0.2351 time to fit residues: 95.9606 Evaluate side-chains 208 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 167 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 43 HIS Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 320 HIS Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain E residue 43 HIS Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain F residue 43 HIS Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 330 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 7.9990 chunk 201 optimal weight: 0.0670 chunk 44 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 223 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 320 HIS ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18606 Z= 0.279 Angle : 0.606 7.577 25137 Z= 0.316 Chirality : 0.043 0.144 2919 Planarity : 0.003 0.055 3115 Dihedral : 10.953 89.427 2765 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 3.95 % Allowed : 19.16 % Favored : 76.89 % 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: -0.67 (0.18), residues: 2303 helix: 1.42 (0.15), residues: 1267 sheet: -2.13 (0.33), residues: 266 loop : -3.13 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 184 HIS 0.010 0.001 HIS G 320 PHE 0.018 0.001 PHE C 42 TYR 0.012 0.001 TYR G 291 ARG 0.002 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 176 time to evaluate : 2.081 Fit side-chains REVERT: G 138 PHE cc_start: 0.7493 (m-80) cc_final: 0.7279 (m-80) REVERT: G 142 LEU cc_start: 0.8639 (tt) cc_final: 0.8295 (mm) REVERT: G 146 LEU cc_start: 0.8953 (tt) cc_final: 0.8474 (mt) REVERT: G 193 GLU cc_start: 0.9036 (tt0) cc_final: 0.8680 (tt0) REVERT: G 227 GLU cc_start: 0.8418 (tt0) cc_final: 0.8174 (tt0) REVERT: G 289 MET cc_start: 0.9283 (ttp) cc_final: 0.9006 (ptm) REVERT: G 333 MET cc_start: 0.8893 (mtp) cc_final: 0.8492 (mtp) REVERT: A 111 ASP cc_start: 0.7213 (t0) cc_final: 0.6932 (t0) REVERT: A 140 MET cc_start: 0.7016 (mtt) cc_final: 0.6768 (mtp) REVERT: A 193 GLU cc_start: 0.9077 (tt0) cc_final: 0.8590 (tt0) REVERT: A 333 MET cc_start: 0.8960 (mtp) cc_final: 0.8755 (mtp) REVERT: B 43 HIS cc_start: 0.8464 (OUTLIER) cc_final: 0.8254 (t70) REVERT: B 146 LEU cc_start: 0.8935 (tt) cc_final: 0.8409 (mt) REVERT: B 193 GLU cc_start: 0.9079 (tt0) cc_final: 0.8823 (tt0) REVERT: B 227 GLU cc_start: 0.8406 (tt0) cc_final: 0.8157 (tt0) REVERT: B 271 ARG cc_start: 0.9232 (ptp-110) cc_final: 0.9015 (mtm-85) REVERT: B 289 MET cc_start: 0.9262 (ttp) cc_final: 0.8730 (ptm) REVERT: C 140 MET cc_start: 0.6963 (mtt) cc_final: 0.6572 (mtm) REVERT: C 146 LEU cc_start: 0.8973 (mt) cc_final: 0.8664 (mt) REVERT: C 193 GLU cc_start: 0.9063 (tt0) cc_final: 0.8562 (tt0) REVERT: C 198 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7291 (tm-30) REVERT: C 227 GLU cc_start: 0.8294 (tt0) cc_final: 0.8061 (tt0) REVERT: C 333 MET cc_start: 0.8934 (mtp) cc_final: 0.8470 (tpp) REVERT: D 142 LEU cc_start: 0.8686 (tt) cc_final: 0.8336 (mm) REVERT: D 146 LEU cc_start: 0.8954 (tt) cc_final: 0.8485 (mt) REVERT: D 193 GLU cc_start: 0.9072 (tt0) cc_final: 0.8512 (tp30) REVERT: D 227 GLU cc_start: 0.8453 (tt0) cc_final: 0.8026 (tt0) REVERT: D 301 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8958 (pt0) REVERT: E 142 LEU cc_start: 0.8743 (tt) cc_final: 0.8333 (mm) REVERT: E 146 LEU cc_start: 0.9010 (tt) cc_final: 0.8530 (mt) REVERT: E 193 GLU cc_start: 0.9022 (tt0) cc_final: 0.8595 (tt0) REVERT: E 289 MET cc_start: 0.9247 (ttp) cc_final: 0.8869 (ptm) REVERT: F 118 MET cc_start: 0.9489 (tpp) cc_final: 0.9256 (tpp) REVERT: F 138 PHE cc_start: 0.7396 (m-80) cc_final: 0.7143 (m-80) REVERT: F 140 MET cc_start: 0.6981 (mtt) cc_final: 0.6755 (ptp) REVERT: F 193 GLU cc_start: 0.9058 (tt0) cc_final: 0.8529 (tp30) REVERT: F 333 MET cc_start: 0.8920 (mtp) cc_final: 0.8613 (mtp) outliers start: 73 outliers final: 40 residues processed: 245 average time/residue: 0.2351 time to fit residues: 94.7456 Evaluate side-chains 209 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 168 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 43 HIS Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 330 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 127 optimal weight: 0.5980 chunk 163 optimal weight: 0.5980 chunk 126 optimal weight: 0.8980 chunk 188 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 222 optimal weight: 4.9990 chunk 139 optimal weight: 0.0980 chunk 135 optimal weight: 1.9990 chunk 102 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 46 GLN ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18606 Z= 0.130 Angle : 0.591 12.071 25137 Z= 0.292 Chirality : 0.041 0.131 2919 Planarity : 0.003 0.051 3115 Dihedral : 10.504 86.740 2765 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.14 % Allowed : 20.62 % Favored : 76.24 % 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: -0.47 (0.18), residues: 2303 helix: 1.61 (0.15), residues: 1260 sheet: -1.87 (0.34), residues: 259 loop : -3.10 (0.19), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 302 HIS 0.002 0.000 HIS D 137 PHE 0.017 0.001 PHE D 42 TYR 0.012 0.001 TYR G 291 ARG 0.002 0.000 ARG D 236 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 185 time to evaluate : 2.507 Fit side-chains REVERT: G 142 LEU cc_start: 0.8516 (tt) cc_final: 0.8197 (mp) REVERT: G 146 LEU cc_start: 0.8909 (tt) cc_final: 0.8418 (mt) REVERT: G 193 GLU cc_start: 0.9073 (tt0) cc_final: 0.8724 (tt0) REVERT: G 227 GLU cc_start: 0.8339 (tt0) cc_final: 0.8126 (tt0) REVERT: G 289 MET cc_start: 0.9202 (ttp) cc_final: 0.8885 (ptm) REVERT: A 111 ASP cc_start: 0.7098 (t0) cc_final: 0.6786 (t0) REVERT: A 193 GLU cc_start: 0.9098 (tt0) cc_final: 0.8545 (tp30) REVERT: A 289 MET cc_start: 0.8810 (ptm) cc_final: 0.8586 (ptm) REVERT: A 333 MET cc_start: 0.8862 (mtp) cc_final: 0.8548 (mmm) REVERT: B 138 PHE cc_start: 0.7971 (m-10) cc_final: 0.7554 (m-10) REVERT: B 140 MET cc_start: 0.7617 (pmm) cc_final: 0.7232 (pmm) REVERT: B 146 LEU cc_start: 0.8870 (tt) cc_final: 0.8368 (mt) REVERT: B 193 GLU cc_start: 0.9108 (tt0) cc_final: 0.8804 (tt0) REVERT: B 227 GLU cc_start: 0.8367 (tt0) cc_final: 0.8156 (tt0) REVERT: B 271 ARG cc_start: 0.9230 (ptp-110) cc_final: 0.9028 (mtm-85) REVERT: B 289 MET cc_start: 0.9216 (ttp) cc_final: 0.8783 (ptm) REVERT: B 333 MET cc_start: 0.8545 (mtp) cc_final: 0.8162 (mtp) REVERT: C 140 MET cc_start: 0.6449 (mtt) cc_final: 0.6239 (mtp) REVERT: C 193 GLU cc_start: 0.9094 (tt0) cc_final: 0.8614 (tp30) REVERT: C 198 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7281 (tm-30) REVERT: C 227 GLU cc_start: 0.8205 (tt0) cc_final: 0.7964 (tt0) REVERT: C 301 GLU cc_start: 0.9113 (mt-10) cc_final: 0.8902 (mp0) REVERT: C 333 MET cc_start: 0.8710 (mtp) cc_final: 0.8351 (tpp) REVERT: D 138 PHE cc_start: 0.7865 (m-10) cc_final: 0.7571 (m-10) REVERT: D 140 MET cc_start: 0.7665 (pmm) cc_final: 0.6960 (pmm) REVERT: D 146 LEU cc_start: 0.8888 (tt) cc_final: 0.8391 (mt) REVERT: D 193 GLU cc_start: 0.9114 (tt0) cc_final: 0.8681 (tt0) REVERT: D 227 GLU cc_start: 0.8368 (tt0) cc_final: 0.7949 (tt0) REVERT: E 146 LEU cc_start: 0.8977 (tt) cc_final: 0.8463 (mt) REVERT: E 193 GLU cc_start: 0.9060 (tt0) cc_final: 0.8565 (tt0) REVERT: E 289 MET cc_start: 0.9262 (ttp) cc_final: 0.8876 (ptm) REVERT: E 301 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8871 (mp0) REVERT: F 118 MET cc_start: 0.9461 (tpp) cc_final: 0.9219 (tpp) REVERT: F 138 PHE cc_start: 0.7434 (m-80) cc_final: 0.7196 (m-80) REVERT: F 193 GLU cc_start: 0.9082 (tt0) cc_final: 0.8596 (tp30) REVERT: F 198 GLU cc_start: 0.8295 (pt0) cc_final: 0.7929 (tm-30) REVERT: F 333 MET cc_start: 0.8744 (mtp) cc_final: 0.8435 (mtp) outliers start: 58 outliers final: 48 residues processed: 234 average time/residue: 0.2621 time to fit residues: 100.3102 Evaluate side-chains 222 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 174 time to evaluate : 3.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 43 HIS Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 43 HIS Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain F residue 43 HIS Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 330 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 137 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 132 optimal weight: 70.0000 chunk 67 optimal weight: 4.9990 chunk 43 optimal weight: 0.1980 chunk 141 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 202 optimal weight: 0.0770 overall best weight: 2.0544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 46 GLN ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18606 Z= 0.246 Angle : 0.623 12.708 25137 Z= 0.315 Chirality : 0.042 0.142 2919 Planarity : 0.003 0.053 3115 Dihedral : 10.442 87.547 2765 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.14 % Allowed : 20.56 % Favored : 76.30 % 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: -0.35 (0.18), residues: 2303 helix: 1.71 (0.15), residues: 1260 sheet: -1.88 (0.34), residues: 266 loop : -3.04 (0.19), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 184 HIS 0.003 0.001 HIS C 43 PHE 0.018 0.001 PHE D 42 TYR 0.012 0.001 TYR G 291 ARG 0.002 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 179 time to evaluate : 1.915 Fit side-chains REVERT: G 142 LEU cc_start: 0.8577 (tt) cc_final: 0.8238 (mp) REVERT: G 146 LEU cc_start: 0.8918 (tt) cc_final: 0.8422 (mt) REVERT: G 193 GLU cc_start: 0.9019 (tt0) cc_final: 0.8682 (tt0) REVERT: G 227 GLU cc_start: 0.8407 (tt0) cc_final: 0.8185 (tt0) REVERT: G 289 MET cc_start: 0.9287 (ttp) cc_final: 0.9044 (ptm) REVERT: A 111 ASP cc_start: 0.7233 (t0) cc_final: 0.6927 (t0) REVERT: A 193 GLU cc_start: 0.9062 (tt0) cc_final: 0.8570 (tt0) REVERT: A 333 MET cc_start: 0.8921 (mtp) cc_final: 0.8630 (mmm) REVERT: B 142 LEU cc_start: 0.8692 (tt) cc_final: 0.8358 (mp) REVERT: B 146 LEU cc_start: 0.8878 (tt) cc_final: 0.8396 (mt) REVERT: B 193 GLU cc_start: 0.9073 (tt0) cc_final: 0.8802 (tt0) REVERT: B 198 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7377 (tm-30) REVERT: B 271 ARG cc_start: 0.9229 (ptp-110) cc_final: 0.9013 (mtm-85) REVERT: B 289 MET cc_start: 0.9278 (ttp) cc_final: 0.8809 (ptm) REVERT: B 333 MET cc_start: 0.8749 (mtp) cc_final: 0.8545 (mtp) REVERT: C 140 MET cc_start: 0.6454 (mtt) cc_final: 0.6172 (mtm) REVERT: C 193 GLU cc_start: 0.9048 (tt0) cc_final: 0.8531 (tp30) REVERT: C 198 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7284 (tm-30) REVERT: C 227 GLU cc_start: 0.8287 (tt0) cc_final: 0.8051 (tt0) REVERT: C 301 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8856 (mp0) REVERT: C 333 MET cc_start: 0.8867 (mtp) cc_final: 0.8399 (tpp) REVERT: D 146 LEU cc_start: 0.8894 (tt) cc_final: 0.8375 (mt) REVERT: D 193 GLU cc_start: 0.9084 (tt0) cc_final: 0.8517 (tt0) REVERT: D 198 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7278 (tm-30) REVERT: D 227 GLU cc_start: 0.8439 (tt0) cc_final: 0.7991 (tt0) REVERT: E 140 MET cc_start: 0.6485 (OUTLIER) cc_final: 0.6285 (ptp) REVERT: E 146 LEU cc_start: 0.8950 (tt) cc_final: 0.8429 (mt) REVERT: E 193 GLU cc_start: 0.9018 (tt0) cc_final: 0.8575 (tt0) REVERT: E 198 GLU cc_start: 0.8255 (pt0) cc_final: 0.7904 (tm-30) REVERT: E 301 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8845 (mp0) REVERT: F 118 MET cc_start: 0.9489 (tpp) cc_final: 0.9272 (tpp) REVERT: F 193 GLU cc_start: 0.9031 (tt0) cc_final: 0.8532 (tt0) REVERT: F 333 MET cc_start: 0.8885 (mtp) cc_final: 0.8564 (mtp) outliers start: 58 outliers final: 52 residues processed: 231 average time/residue: 0.2464 time to fit residues: 93.3343 Evaluate side-chains 223 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 170 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 43 HIS Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 43 HIS Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 330 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 187 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 ASN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18606 Z= 0.175 Angle : 0.612 12.800 25137 Z= 0.305 Chirality : 0.041 0.139 2919 Planarity : 0.003 0.052 3115 Dihedral : 10.284 88.015 2765 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.35 % Allowed : 20.24 % Favored : 76.41 % 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: -0.30 (0.18), residues: 2303 helix: 1.72 (0.15), residues: 1260 sheet: -1.68 (0.35), residues: 259 loop : -3.03 (0.19), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 302 HIS 0.002 0.000 HIS C 43 PHE 0.020 0.001 PHE G 42 TYR 0.012 0.001 TYR G 291 ARG 0.002 0.000 ARG F 235 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 176 time to evaluate : 2.324 Fit side-chains REVERT: G 138 PHE cc_start: 0.7575 (m-80) cc_final: 0.7308 (m-80) REVERT: G 142 LEU cc_start: 0.8565 (tt) cc_final: 0.8224 (mp) REVERT: G 146 LEU cc_start: 0.8873 (tt) cc_final: 0.8353 (mt) REVERT: G 193 GLU cc_start: 0.9051 (tt0) cc_final: 0.8702 (tt0) REVERT: G 227 GLU cc_start: 0.8382 (tt0) cc_final: 0.8159 (tt0) REVERT: G 289 MET cc_start: 0.9270 (ttp) cc_final: 0.8961 (ptm) REVERT: A 111 ASP cc_start: 0.7178 (t0) cc_final: 0.6856 (t0) REVERT: A 193 GLU cc_start: 0.9082 (tt0) cc_final: 0.8544 (tp30) REVERT: A 333 MET cc_start: 0.8914 (mtp) cc_final: 0.8616 (mmm) REVERT: B 193 GLU cc_start: 0.9092 (tt0) cc_final: 0.8808 (tt0) REVERT: B 198 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7332 (tm-30) REVERT: B 271 ARG cc_start: 0.9223 (ptp-110) cc_final: 0.9015 (mtm-85) REVERT: B 289 MET cc_start: 0.9262 (ttp) cc_final: 0.8799 (ptm) REVERT: B 333 MET cc_start: 0.8643 (mtp) cc_final: 0.8257 (mtp) REVERT: C 140 MET cc_start: 0.6283 (mtt) cc_final: 0.6056 (mtm) REVERT: C 193 GLU cc_start: 0.9072 (tt0) cc_final: 0.8552 (tp30) REVERT: C 198 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7280 (tm-30) REVERT: C 227 GLU cc_start: 0.8279 (tt0) cc_final: 0.8039 (tt0) REVERT: C 333 MET cc_start: 0.8820 (mtp) cc_final: 0.8442 (tpp) REVERT: D 138 PHE cc_start: 0.7972 (m-10) cc_final: 0.7607 (m-10) REVERT: D 140 MET cc_start: 0.7542 (pmm) cc_final: 0.7116 (pmm) REVERT: D 146 LEU cc_start: 0.8862 (tt) cc_final: 0.8340 (mt) REVERT: D 162 ASP cc_start: 0.8443 (p0) cc_final: 0.8228 (p0) REVERT: D 193 GLU cc_start: 0.9093 (tt0) cc_final: 0.8594 (tt0) REVERT: D 198 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7308 (tm-30) REVERT: D 227 GLU cc_start: 0.8406 (tt0) cc_final: 0.7964 (tt0) REVERT: E 146 LEU cc_start: 0.8975 (tt) cc_final: 0.8428 (mt) REVERT: E 193 GLU cc_start: 0.9039 (tt0) cc_final: 0.8615 (tt0) REVERT: E 198 GLU cc_start: 0.8239 (pt0) cc_final: 0.7900 (tm-30) REVERT: E 289 MET cc_start: 0.9227 (ttp) cc_final: 0.8919 (ttp) REVERT: E 301 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8857 (mp0) REVERT: F 118 MET cc_start: 0.9479 (tpp) cc_final: 0.9262 (tpp) REVERT: F 193 GLU cc_start: 0.9064 (tt0) cc_final: 0.8560 (tp30) REVERT: F 333 MET cc_start: 0.8867 (mtp) cc_final: 0.8539 (mtp) outliers start: 62 outliers final: 57 residues processed: 227 average time/residue: 0.2380 time to fit residues: 88.3522 Evaluate side-chains 231 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 174 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 43 HIS Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 43 HIS Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain F residue 43 HIS Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 330 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 230 optimal weight: 0.8980 chunk 211 optimal weight: 8.9990 chunk 183 optimal weight: 0.2980 chunk 19 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 145 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18606 Z= 0.136 Angle : 0.607 13.435 25137 Z= 0.298 Chirality : 0.041 0.139 2919 Planarity : 0.003 0.052 3115 Dihedral : 10.051 89.142 2765 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.98 % Allowed : 21.10 % Favored : 75.92 % 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: -0.24 (0.18), residues: 2303 helix: 1.80 (0.15), residues: 1253 sheet: -1.65 (0.35), residues: 259 loop : -3.02 (0.19), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 302 HIS 0.002 0.000 HIS D 137 PHE 0.020 0.001 PHE G 42 TYR 0.012 0.001 TYR G 291 ARG 0.002 0.000 ARG F 235 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 185 time to evaluate : 2.289 Fit side-chains REVERT: G 138 PHE cc_start: 0.7637 (m-80) cc_final: 0.7337 (m-80) REVERT: G 146 LEU cc_start: 0.8818 (tt) cc_final: 0.8251 (mt) REVERT: G 193 GLU cc_start: 0.9054 (tt0) cc_final: 0.8731 (tt0) REVERT: G 198 GLU cc_start: 0.8354 (pt0) cc_final: 0.8056 (tm-30) REVERT: G 227 GLU cc_start: 0.8376 (tt0) cc_final: 0.8166 (tt0) REVERT: G 289 MET cc_start: 0.9199 (ttp) cc_final: 0.8925 (ptm) REVERT: G 333 MET cc_start: 0.8646 (mtp) cc_final: 0.8055 (mtp) REVERT: A 111 ASP cc_start: 0.7190 (t0) cc_final: 0.6849 (t0) REVERT: A 193 GLU cc_start: 0.9083 (tt0) cc_final: 0.8531 (tp30) REVERT: A 333 MET cc_start: 0.8794 (mtp) cc_final: 0.8480 (tpp) REVERT: B 136 GLU cc_start: 0.8042 (pp20) cc_final: 0.7700 (pp20) REVERT: B 140 MET cc_start: 0.7180 (pmm) cc_final: 0.6776 (pmm) REVERT: B 193 GLU cc_start: 0.9095 (tt0) cc_final: 0.8803 (tt0) REVERT: B 198 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7298 (tm-30) REVERT: B 271 ARG cc_start: 0.9213 (ptp-110) cc_final: 0.9013 (mtm-85) REVERT: B 289 MET cc_start: 0.9241 (ttp) cc_final: 0.8801 (ptm) REVERT: C 193 GLU cc_start: 0.9069 (tt0) cc_final: 0.8591 (tp30) REVERT: C 198 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7320 (tm-30) REVERT: D 138 PHE cc_start: 0.7977 (m-10) cc_final: 0.7652 (m-10) REVERT: D 140 MET cc_start: 0.7286 (pmm) cc_final: 0.7012 (pmm) REVERT: D 146 LEU cc_start: 0.8821 (tt) cc_final: 0.8309 (mt) REVERT: D 162 ASP cc_start: 0.8389 (p0) cc_final: 0.8181 (p0) REVERT: D 193 GLU cc_start: 0.9088 (tt0) cc_final: 0.8588 (tt0) REVERT: D 198 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7310 (tm-30) REVERT: D 227 GLU cc_start: 0.8379 (tt0) cc_final: 0.7941 (tt0) REVERT: D 289 MET cc_start: 0.9307 (ttp) cc_final: 0.8269 (ppp) REVERT: E 146 LEU cc_start: 0.8938 (tt) cc_final: 0.8388 (mt) REVERT: E 193 GLU cc_start: 0.9043 (tt0) cc_final: 0.8562 (tt0) REVERT: E 198 GLU cc_start: 0.8251 (pt0) cc_final: 0.7911 (tm-30) REVERT: E 289 MET cc_start: 0.9238 (ttp) cc_final: 0.8187 (ppp) REVERT: F 193 GLU cc_start: 0.9062 (tt0) cc_final: 0.8605 (tt0) REVERT: F 198 GLU cc_start: 0.8305 (pt0) cc_final: 0.7995 (tm-30) REVERT: F 333 MET cc_start: 0.8816 (mtp) cc_final: 0.8498 (mtp) outliers start: 55 outliers final: 49 residues processed: 233 average time/residue: 0.2460 time to fit residues: 93.8924 Evaluate side-chains 222 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 173 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 43 HIS Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain F residue 43 HIS Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 330 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 0.6980 chunk 56 optimal weight: 0.4980 chunk 168 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 0.0570 chunk 183 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 33 optimal weight: 80.0000 chunk 161 optimal weight: 0.2980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 234 ASN ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 GLN D 137 HIS ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 ASN F 329 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.084744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.060022 restraints weight = 60817.294| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 3.16 r_work: 0.2829 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18606 Z= 0.136 Angle : 0.605 13.034 25137 Z= 0.295 Chirality : 0.041 0.159 2919 Planarity : 0.003 0.051 3115 Dihedral : 9.909 89.664 2765 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.71 % Allowed : 21.43 % Favored : 75.87 % 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: -0.15 (0.18), residues: 2303 helix: 1.87 (0.15), residues: 1253 sheet: -1.58 (0.36), residues: 259 loop : -2.99 (0.19), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 302 HIS 0.004 0.000 HIS D 137 PHE 0.021 0.001 PHE G 42 TYR 0.012 0.001 TYR G 291 ARG 0.002 0.000 ARG E 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3594.96 seconds wall clock time: 66 minutes 40.91 seconds (4000.91 seconds total)