Starting phenix.real_space_refine on Sat Sep 12 20:57:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6urt_20862/09_2026/6urt_20862.cif Found real_map, /net/cci-nas-00/data/ceres_data/6urt_20862/09_2026/6urt_20862.map 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 { model { file = "/net/cci-nas-00/data/ceres_data/6urt_20862/09_2026/6urt_20862.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6urt_20862/09_2026/6urt_20862.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6urt_20862/09_2026/6urt_20862.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6urt_20862/09_2026/6urt_20862.map" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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. Time to flip 66 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'GLU:plan': 1, 'PHE:plan': 4, '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: {'GLU:plan': 1, 'PHE:plan': 4, '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: {'GLU:plan': 1, 'PHE:plan': 4, '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: {'GLU:plan': 1, 'PHE:plan': 4, '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: {'GLU:plan': 1, 'PHE:plan': 4, '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: {'GLU:plan': 1, 'PHE:plan': 4, '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: {'GLU:plan': 1, 'PHE:plan': 4, '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: 4.09, per 1000 atoms: 0.22 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 - 3.00 Amino acid : True - 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: 1.68 Conformation dependent library (CDL) restraints added in 800.2 milliseconds 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... Secondary structure from input PDB file: 77 helices and 14 sheets defined 59.0% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'G' and resid 4 through 12 Processing helix chain 'G' and resid 12 through 31 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 40 through 68 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 75 through 108 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) removed outlier: 3.870A pdb=" N LYS G 108 " --> pdb=" O GLN G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 134 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 141 through 160 Processing helix chain 'G' and resid 160 through 176 removed outlier: 3.558A pdb=" N LEU G 164 " --> pdb=" O GLY G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 223 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 232 Processing helix chain 'G' and resid 250 through 264 removed outlier: 3.619A pdb=" N ARG G 259 " --> pdb=" O VAL G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 318 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 12 Processing helix chain 'A' and resid 12 through 31 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 40 through 68 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 75 through 108 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) removed outlier: 3.870A pdb=" N LYS A 108 " --> pdb=" O GLN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 134 removed outlier: 3.783A pdb=" N ILE A 117 " --> pdb=" O THR A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 160 Processing helix chain 'A' and resid 160 through 176 removed outlier: 3.558A pdb=" N LEU A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 223 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 232 Processing helix chain 'A' and resid 250 through 264 removed outlier: 3.619A pdb=" N ARG A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 318 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 12 Processing helix chain 'B' and resid 12 through 31 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 40 through 68 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 75 through 108 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) removed outlier: 3.870A pdb=" N LYS B 108 " --> pdb=" O GLN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 134 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 141 through 160 Processing helix chain 'B' and resid 160 through 176 removed outlier: 3.558A pdb=" N LEU B 164 " --> pdb=" O GLY B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 223 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 232 Processing helix chain 'B' and resid 250 through 264 removed outlier: 3.618A pdb=" N ARG B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 318 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 12 Processing helix chain 'C' and resid 12 through 31 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 40 through 68 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 75 through 108 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) removed outlier: 3.869A pdb=" N LYS C 108 " --> pdb=" O GLN C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 134 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 141 through 160 Processing helix chain 'C' and resid 160 through 176 removed outlier: 3.557A pdb=" N LEU C 164 " --> pdb=" O GLY C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 223 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 232 Processing helix chain 'C' and resid 250 through 264 removed outlier: 3.619A pdb=" N ARG C 259 " --> pdb=" O VAL C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 318 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 12 Processing helix chain 'D' and resid 12 through 31 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 40 through 68 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 75 through 108 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) removed outlier: 3.869A pdb=" N LYS D 108 " --> pdb=" O GLN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 134 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 141 through 160 Processing helix chain 'D' and resid 160 through 176 removed outlier: 3.558A pdb=" N LEU D 164 " --> pdb=" O GLY D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 223 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 232 Processing helix chain 'D' and resid 250 through 264 removed outlier: 3.619A pdb=" N ARG D 259 " --> pdb=" O VAL D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 318 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 12 Processing helix chain 'E' and resid 12 through 31 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 40 through 68 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 75 through 108 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) removed outlier: 3.870A pdb=" N LYS E 108 " --> pdb=" O GLN E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 134 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 141 through 160 Processing helix chain 'E' and resid 160 through 176 removed outlier: 3.558A pdb=" N LEU E 164 " --> pdb=" O GLY E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 223 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 232 Processing helix chain 'E' and resid 250 through 264 removed outlier: 3.618A pdb=" N ARG E 259 " --> pdb=" O VAL E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 318 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 12 Processing helix chain 'F' and resid 12 through 31 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 40 through 68 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 75 through 108 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) removed outlier: 3.870A pdb=" N LYS F 108 " --> pdb=" O GLN F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 134 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 141 through 160 Processing helix chain 'F' and resid 160 through 176 removed outlier: 3.558A pdb=" N LEU F 164 " --> pdb=" O GLY F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 223 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 232 Processing helix chain 'F' and resid 250 through 264 removed outlier: 3.619A pdb=" N ARG F 259 " --> pdb=" O VAL F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 318 removed outlier: 3.778A pdb=" N ASP F 315 " --> pdb=" O LEU F 311 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 184 through 185 removed outlier: 6.893A pdb=" N LYS G 205 " --> pdb=" O ALA G 197 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE G 199 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE G 203 " --> pdb=" O ILE G 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 226 through 227 removed outlier: 7.204A pdb=" N ILE A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE A 199 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LYS A 205 " --> pdb=" O ALA A 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 236 through 240 Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 227 removed outlier: 7.203A pdb=" N ILE B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE B 199 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS B 205 " --> pdb=" O ALA B 197 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 236 through 240 Processing sheet with id=AA6, first strand: chain 'B' and resid 226 through 227 removed outlier: 7.204A pdb=" N ILE C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE C 199 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LYS C 205 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 236 through 240 Processing sheet with id=AA8, first strand: chain 'C' and resid 226 through 227 removed outlier: 7.204A pdb=" N ILE D 203 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ILE D 199 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LYS D 205 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 236 through 240 Processing sheet with id=AB1, first strand: chain 'D' and resid 226 through 227 removed outlier: 7.203A pdb=" N ILE E 203 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE E 199 " --> pdb=" O ILE E 203 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS E 205 " --> pdb=" O ALA E 197 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 236 through 240 Processing sheet with id=AB3, first strand: chain 'E' and resid 226 through 227 removed outlier: 7.204A pdb=" N ILE F 203 " --> pdb=" O ILE F 199 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE F 199 " --> pdb=" O ILE F 203 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LYS F 205 " --> pdb=" O ALA F 197 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 236 through 240 Processing sheet with id=AB5, first strand: chain 'F' and resid 236 through 240 1094 hydrogen bonds defined for protein. 3177 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.05 Time building geometry restraints manager: 2.20 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=" 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=" O3 QGD F 401 " pdb=" P1 QGD F 401 " ideal model delta sigma weight residual 1.646 1.580 0.066 2.00e-02 2.50e+03 1.10e+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 bond pdb=" N ASP G 111 " pdb=" CA ASP G 111 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.29e-02 6.01e+03 9.98e+00 ... (remaining 18601 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 24480 3.45 - 6.89: 532 6.89 - 10.34: 80 10.34 - 13.78: 33 13.78 - 17.23: 12 Bond angle restraints: 25137 Sorted by residual: angle pdb=" C PHE F 324 " pdb=" CA PHE F 324 " pdb=" CB PHE F 324 " ideal model delta sigma weight residual 115.89 107.97 7.92 1.32e+00 5.74e-01 3.60e+01 angle pdb=" C15 QGD G 401 " pdb=" C16 QGD G 401 " pdb=" C17 QGD G 401 " ideal model delta sigma weight residual 113.50 130.73 -17.23 3.00e+00 1.11e-01 3.30e+01 angle pdb=" C15 QGD B 401 " pdb=" C16 QGD B 401 " pdb=" C17 QGD B 401 " ideal model delta sigma weight residual 113.50 130.70 -17.20 3.00e+00 1.11e-01 3.29e+01 angle pdb=" C15 QGD D 401 " pdb=" C16 QGD D 401 " pdb=" C17 QGD D 401 " ideal model delta sigma weight residual 113.50 130.70 -17.20 3.00e+00 1.11e-01 3.29e+01 angle pdb=" C15 QGD E 401 " pdb=" C16 QGD E 401 " pdb=" C17 QGD E 401 " ideal model delta sigma weight residual 113.50 130.69 -17.19 3.00e+00 1.11e-01 3.28e+01 ... (remaining 25132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 10764 35.45 - 70.89: 364 70.89 - 106.34: 28 106.34 - 141.78: 23 141.78 - 177.23: 7 Dihedral angle restraints: 11186 sinusoidal: 4487 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 11183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2442 0.087 - 0.173: 422 0.173 - 0.260: 41 0.260 - 0.346: 13 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=" C2 QGD D 401 " pdb=" C3 QGD D 401 " pdb=" C4 QGD D 401 " pdb=" O2 QGD D 401 " both_signs ideal model delta sigma weight residual False 2.36 2.67 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" C2 QGD A 401 " pdb=" C3 QGD A 401 " pdb=" C4 QGD A 401 " pdb=" O2 QGD A 401 " both_signs ideal model delta sigma weight residual False 2.36 2.67 -0.31 2.00e-01 2.50e+01 2.47e+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: 5511 2.81 - 3.33: 17746 3.33 - 3.85: 30369 3.85 - 4.38: 33932 4.38 - 4.90: 57884 Nonbonded interactions: 145442 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 3.120 nonbonded pdb=" N ASP E 247 " pdb=" OD1 ASP E 247 " model vdw 2.304 3.120 nonbonded pdb=" N ASP F 247 " pdb=" OD1 ASP F 247 " model vdw 2.304 3.120 nonbonded pdb=" N ASP D 247 " pdb=" OD1 ASP D 247 " model vdw 2.304 3.120 ... (remaining 145437 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.240 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 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 0.066 18606 Z= 0.391 Angle : 1.316 17.226 25137 Z= 0.666 Chirality : 0.064 0.433 2919 Planarity : 0.007 0.072 3115 Dihedral : 19.177 177.227 6874 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.001 ARG A 236 TYR 0.014 0.002 TYR F 215 PHE 0.032 0.003 PHE G 324 TRP 0.017 0.003 TRP F 184 HIS 0.006 0.002 HIS F 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00760 / 0.39 (18606) covalent geometry : angle 1.31628 / 0.67 (25137) hydrogen bonds : bond 0.15840 / 10.37 ( 1094) hydrogen bonds : angle 6.85955 / 4.77 ( 3177) *********************** 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 to be fit. rotamer outliers: 63 poor density : 254 time to evaluate : 0.802 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: 0.7491 (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: 0.8657 (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: 0.9136 (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: 0.1228 time to fit residues: 62.2979 Evaluate side-chains 216 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 216 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 60.0000 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 20.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 62 ASN G 137 HIS G 211 ASN G 270 GLN G 287 ASN A 62 ASN A 211 ASN A 270 GLN A 287 ASN B 62 ASN B 137 HIS B 211 ASN B 270 GLN B 287 ASN C 62 ASN C 211 ASN C 270 GLN C 287 ASN D 62 ASN D 137 HIS D 211 ASN D 270 GLN D 287 ASN E 62 ASN E 137 HIS E 211 ASN E 270 GLN E 287 ASN F 62 ASN F 137 HIS F 211 ASN F 270 GLN F 287 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.083423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.058517 restraints weight = 61493.276| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.00 r_work: 0.2804 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18606 Z= 0.157 Angle : 0.667 7.610 25137 Z= 0.352 Chirality : 0.044 0.135 2919 Planarity : 0.005 0.052 3115 Dihedral : 18.689 136.836 2925 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 2.87 % Allowed : 13.15 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.16), residues: 2303 helix: -0.82 (0.13), residues: 1309 sheet: -3.12 (0.29), residues: 259 loop : -3.58 (0.19), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 244 TYR 0.012 0.001 TYR A 291 PHE 0.024 0.002 PHE B 324 TRP 0.010 0.002 TRP E 201 HIS 0.003 0.001 HIS E 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 (18606) covalent geometry : angle 0.66662 / 0.35 (25137) hydrogen bonds : bond 0.04005 / 2.70 ( 1094) hydrogen bonds : angle 4.77084 / 3.30 ( 3177) *********************** 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 279 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 226 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 73 ILE cc_start: 0.7100 (OUTLIER) cc_final: 0.6800 (mp) REVERT: G 142 LEU cc_start: 0.8495 (tt) cc_final: 0.8045 (mp) REVERT: G 146 LEU cc_start: 0.8931 (tt) cc_final: 0.8508 (mt) REVERT: A 73 ILE cc_start: 0.7149 (OUTLIER) cc_final: 0.6932 (mp) REVERT: A 146 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8686 (mt) REVERT: A 193 GLU cc_start: 0.9201 (tt0) cc_final: 0.8952 (tt0) REVERT: B 73 ILE cc_start: 0.7270 (OUTLIER) cc_final: 0.7004 (mp) REVERT: B 333 MET cc_start: 0.8912 (mtp) cc_final: 0.8700 (mtp) REVERT: C 193 GLU cc_start: 0.9183 (tt0) cc_final: 0.8921 (tt0) REVERT: C 256 GLU cc_start: 0.9410 (tp30) cc_final: 0.9116 (mm-30) REVERT: D 73 ILE cc_start: 0.7259 (OUTLIER) cc_final: 0.6943 (mp) REVERT: D 111 ASP cc_start: 0.7628 (t0) cc_final: 0.7415 (t0) REVERT: D 289 MET cc_start: 0.9492 (ttp) cc_final: 0.9075 (ptm) REVERT: E 73 ILE cc_start: 0.7109 (OUTLIER) cc_final: 0.6831 (mp) REVERT: E 142 LEU cc_start: 0.8577 (tt) cc_final: 0.7996 (mm) REVERT: E 146 LEU cc_start: 0.8915 (tt) cc_final: 0.8467 (mt) REVERT: F 73 ILE cc_start: 0.7100 (OUTLIER) cc_final: 0.6761 (mp) REVERT: F 142 LEU cc_start: 0.8414 (tt) cc_final: 0.8085 (mm) REVERT: F 146 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8757 (mt) REVERT: F 154 LEU cc_start: 0.9634 (tt) cc_final: 0.9429 (tt) REVERT: F 333 MET cc_start: 0.9009 (ttm) cc_final: 0.8795 (mtp) outliers start: 53 outliers final: 22 residues processed: 266 average time/residue: 0.1293 time to fit residues: 55.0041 Evaluate side-chains 203 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain A residue 73 ILE 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 146 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 225 SER 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 225 SER Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 146 LEU 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 25 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 229 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 171 optimal weight: 8.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.085813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.060293 restraints weight = 61499.867| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.08 r_work: 0.2876 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18606 Z= 0.121 Angle : 0.614 8.346 25137 Z= 0.318 Chirality : 0.042 0.140 2919 Planarity : 0.004 0.049 3115 Dihedral : 17.141 133.031 2902 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 3.30 % Allowed : 15.96 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.16), residues: 2303 helix: 0.10 (0.14), residues: 1295 sheet: -2.69 (0.30), residues: 259 loop : -3.48 (0.19), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 244 TYR 0.011 0.001 TYR B 291 PHE 0.017 0.001 PHE G 148 TRP 0.010 0.001 TRP E 184 HIS 0.002 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (18606) covalent geometry : angle 0.61425 / 0.32 (25137) hydrogen bonds : bond 0.03625 / 2.43 ( 1094) hydrogen bonds : angle 4.27047 / 2.94 ( 3177) *********************** 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 242 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 181 time to evaluate : 0.673 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 73 ILE cc_start: 0.6971 (OUTLIER) cc_final: 0.6741 (mp) REVERT: G 142 LEU cc_start: 0.8399 (tt) cc_final: 0.7920 (mm) REVERT: G 146 LEU cc_start: 0.8907 (tt) cc_final: 0.8374 (mt) REVERT: G 289 MET cc_start: 0.9443 (ttp) cc_final: 0.9215 (ptm) REVERT: G 333 MET cc_start: 0.8803 (mtp) cc_final: 0.8597 (mtp) REVERT: A 63 TYR cc_start: 0.7823 (t80) cc_final: 0.7495 (t80) REVERT: A 142 LEU cc_start: 0.8369 (tt) cc_final: 0.8091 (mm) REVERT: A 146 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8775 (mt) REVERT: B 73 ILE cc_start: 0.7041 (OUTLIER) cc_final: 0.6815 (mp) REVERT: B 138 PHE cc_start: 0.8108 (m-80) cc_final: 0.7381 (m-80) REVERT: B 140 MET cc_start: 0.8479 (mpp) cc_final: 0.8006 (ptp) REVERT: D 111 ASP cc_start: 0.7605 (t0) cc_final: 0.7398 (t0) REVERT: D 142 LEU cc_start: 0.8555 (pp) cc_final: 0.8111 (mp) REVERT: D 146 LEU cc_start: 0.8964 (tt) cc_final: 0.8451 (mt) REVERT: D 289 MET cc_start: 0.9491 (ttp) cc_final: 0.9121 (ptm) REVERT: E 73 ILE cc_start: 0.6960 (OUTLIER) cc_final: 0.6758 (mp) REVERT: E 193 GLU cc_start: 0.9158 (tt0) cc_final: 0.8870 (tt0) REVERT: E 260 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8788 (tm-30) REVERT: E 289 MET cc_start: 0.9476 (ttp) cc_final: 0.9135 (ptm) REVERT: F 63 TYR cc_start: 0.7969 (t80) cc_final: 0.7696 (t80) REVERT: F 73 ILE cc_start: 0.6887 (OUTLIER) cc_final: 0.6686 (mp) REVERT: F 146 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8894 (mt) outliers start: 61 outliers final: 34 residues processed: 236 average time/residue: 0.1100 time to fit residues: 43.9696 Evaluate side-chains 207 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 317 VAL 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 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 B residue 73 ILE 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 C residue 51 THR Chi-restraints excluded: chain C residue 82 CYS 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 D residue 82 CYS Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 128 VAL 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 E residue 51 THR Chi-restraints excluded: chain E residue 73 ILE 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 73 ILE Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 146 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 196 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 164 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 168 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 137 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.084103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.061021 restraints weight = 59444.398| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.97 r_work: 0.2831 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18606 Z= 0.115 Angle : 0.590 8.367 25137 Z= 0.305 Chirality : 0.041 0.139 2919 Planarity : 0.003 0.050 3115 Dihedral : 16.133 130.646 2895 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.90 % Allowed : 16.99 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.17), residues: 2303 helix: 0.66 (0.14), residues: 1302 sheet: -2.17 (0.33), residues: 259 loop : -3.38 (0.19), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 186 TYR 0.017 0.001 TYR C 63 PHE 0.017 0.001 PHE F 148 TRP 0.011 0.001 TRP B 184 HIS 0.003 0.001 HIS D 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 (18606) covalent geometry : angle 0.58973 / 0.31 (25137) hydrogen bonds : bond 0.03362 / 2.24 ( 1094) hydrogen bonds : angle 4.06035 / 2.80 ( 3177) *********************** 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 255 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 183 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 73 ILE cc_start: 0.6825 (OUTLIER) cc_final: 0.6587 (mp) REVERT: G 142 LEU cc_start: 0.8440 (tt) cc_final: 0.8088 (mm) REVERT: G 146 LEU cc_start: 0.8965 (tt) cc_final: 0.8413 (mt) REVERT: G 256 GLU cc_start: 0.9479 (tp30) cc_final: 0.9180 (mm-30) REVERT: A 63 TYR cc_start: 0.7814 (t80) cc_final: 0.7445 (t80) REVERT: A 111 ASP cc_start: 0.7527 (t0) cc_final: 0.7241 (t0) REVERT: A 140 MET cc_start: 0.7204 (mtt) cc_final: 0.6816 (mtp) REVERT: A 146 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8762 (mt) REVERT: B 73 ILE cc_start: 0.7009 (OUTLIER) cc_final: 0.6772 (mp) REVERT: B 138 PHE cc_start: 0.8009 (m-80) cc_final: 0.7533 (m-80) REVERT: B 142 LEU cc_start: 0.8564 (tt) cc_final: 0.8204 (mm) REVERT: B 146 LEU cc_start: 0.8981 (tt) cc_final: 0.8457 (mt) REVERT: C 136 GLU cc_start: 0.8925 (pp20) cc_final: 0.8719 (pp20) REVERT: C 138 PHE cc_start: 0.7700 (m-80) cc_final: 0.7480 (m-80) REVERT: C 142 LEU cc_start: 0.8745 (mm) cc_final: 0.8520 (tt) REVERT: C 256 GLU cc_start: 0.9468 (tp30) cc_final: 0.9191 (mm-30) REVERT: C 333 MET cc_start: 0.8869 (mtp) cc_final: 0.8603 (tpp) REVERT: D 142 LEU cc_start: 0.8612 (pp) cc_final: 0.7987 (tt) REVERT: D 146 LEU cc_start: 0.9007 (tt) cc_final: 0.8456 (mt) REVERT: E 73 ILE cc_start: 0.6903 (OUTLIER) cc_final: 0.6678 (mp) REVERT: E 142 LEU cc_start: 0.8693 (mm) cc_final: 0.7903 (tt) REVERT: E 146 LEU cc_start: 0.8926 (tt) cc_final: 0.8393 (mt) REVERT: E 162 ASP cc_start: 0.8581 (p0) cc_final: 0.8333 (p0) REVERT: E 193 GLU cc_start: 0.9120 (tt0) cc_final: 0.8828 (tt0) REVERT: E 260 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8712 (tm-30) REVERT: E 289 MET cc_start: 0.9518 (ttp) cc_final: 0.9208 (ptm) REVERT: F 63 TYR cc_start: 0.7977 (t80) cc_final: 0.7675 (t80) REVERT: F 73 ILE cc_start: 0.6757 (OUTLIER) cc_final: 0.6544 (mp) REVERT: F 118 MET cc_start: 0.9549 (tpp) cc_final: 0.9334 (tpp) REVERT: F 136 GLU cc_start: 0.8892 (pp20) cc_final: 0.8674 (pp20) REVERT: F 142 LEU cc_start: 0.8680 (mm) cc_final: 0.8279 (tt) REVERT: F 146 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8884 (mt) REVERT: F 193 GLU cc_start: 0.9114 (tt0) cc_final: 0.8891 (tt0) outliers start: 72 outliers final: 46 residues processed: 247 average time/residue: 0.1103 time to fit residues: 46.3155 Evaluate side-chains 218 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 166 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 320 HIS 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 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 320 HIS Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 73 ILE 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 320 HIS Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 164 LEU 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 D residue 51 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 226 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 73 ILE 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 320 HIS Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 146 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 320 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 113 optimal weight: 7.9990 chunk 159 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 209 optimal weight: 0.8980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 320 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.081568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.058208 restraints weight = 59592.927| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.93 r_work: 0.2789 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18606 Z= 0.248 Angle : 0.664 6.617 25137 Z= 0.348 Chirality : 0.044 0.162 2919 Planarity : 0.004 0.056 3115 Dihedral : 15.883 131.848 2895 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 5.63 % Allowed : 16.77 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.18), residues: 2303 helix: 0.98 (0.14), residues: 1288 sheet: -1.97 (0.34), residues: 259 loop : -3.20 (0.19), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 186 TYR 0.013 0.001 TYR G 291 PHE 0.017 0.001 PHE C 148 TRP 0.014 0.002 TRP B 184 HIS 0.004 0.001 HIS E 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.25 (18606) covalent geometry : angle 0.66415 / 0.35 (25137) hydrogen bonds : bond 0.03598 / 2.39 ( 1094) hydrogen bonds : angle 4.04730 / 2.79 ( 3177) *********************** 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 282 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 178 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 73 ILE cc_start: 0.6821 (OUTLIER) cc_final: 0.6573 (mp) REVERT: G 142 LEU cc_start: 0.8580 (tt) cc_final: 0.8218 (mm) REVERT: G 146 LEU cc_start: 0.9006 (tt) cc_final: 0.8441 (mt) REVERT: A 43 HIS cc_start: 0.8745 (OUTLIER) cc_final: 0.8477 (t70) REVERT: A 63 TYR cc_start: 0.7818 (t80) cc_final: 0.7426 (t80) REVERT: A 111 ASP cc_start: 0.7805 (t0) cc_final: 0.7457 (t0) REVERT: A 140 MET cc_start: 0.7343 (mtt) cc_final: 0.6952 (mtp) REVERT: A 146 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8750 (mt) REVERT: B 43 HIS cc_start: 0.8777 (OUTLIER) cc_final: 0.8354 (t70) REVERT: B 73 ILE cc_start: 0.6999 (OUTLIER) cc_final: 0.6765 (mp) REVERT: B 146 LEU cc_start: 0.8996 (tt) cc_final: 0.8450 (mt) REVERT: C 142 LEU cc_start: 0.8788 (mm) cc_final: 0.8270 (tt) REVERT: C 146 LEU cc_start: 0.8960 (tt) cc_final: 0.8403 (mt) REVERT: D 43 HIS cc_start: 0.8739 (OUTLIER) cc_final: 0.8269 (t70) REVERT: D 111 ASP cc_start: 0.7782 (t0) cc_final: 0.7561 (t0) REVERT: D 118 MET cc_start: 0.9540 (tpp) cc_final: 0.9325 (tpp) REVERT: D 142 LEU cc_start: 0.8719 (pp) cc_final: 0.8247 (mm) REVERT: D 146 LEU cc_start: 0.9032 (tt) cc_final: 0.8483 (mt) REVERT: D 162 ASP cc_start: 0.8702 (p0) cc_final: 0.8484 (p0) REVERT: E 43 HIS cc_start: 0.8758 (OUTLIER) cc_final: 0.8291 (t70) REVERT: E 63 TYR cc_start: 0.8000 (t80) cc_final: 0.7740 (t80) REVERT: E 73 ILE cc_start: 0.6853 (OUTLIER) cc_final: 0.6614 (mp) REVERT: E 142 LEU cc_start: 0.8751 (mm) cc_final: 0.8512 (tt) REVERT: E 260 GLU cc_start: 0.9037 (tm-30) cc_final: 0.8781 (tm-30) REVERT: F 43 HIS cc_start: 0.8800 (OUTLIER) cc_final: 0.8344 (t70) REVERT: F 63 TYR cc_start: 0.8010 (t80) cc_final: 0.7691 (t80) REVERT: F 73 ILE cc_start: 0.6682 (OUTLIER) cc_final: 0.6461 (mp) REVERT: F 118 MET cc_start: 0.9603 (tpp) cc_final: 0.9380 (tpp) REVERT: F 140 MET cc_start: 0.7180 (mtt) cc_final: 0.6821 (mtm) REVERT: F 142 LEU cc_start: 0.8723 (mm) cc_final: 0.8299 (tt) REVERT: F 146 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8881 (mt) REVERT: F 333 MET cc_start: 0.8871 (mtp) cc_final: 0.8534 (mtp) outliers start: 104 outliers final: 55 residues processed: 271 average time/residue: 0.1075 time to fit residues: 49.3999 Evaluate side-chains 234 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 168 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 128 VAL 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 320 HIS Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain A residue 43 HIS 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 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 51 THR Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 130 LEU 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 51 THR Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 140 MET 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 330 THR Chi-restraints excluded: chain D residue 43 HIS 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 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 317 VAL Chi-restraints excluded: chain E residue 43 HIS Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 73 ILE 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 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 73 ILE Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 146 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 320 HIS 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 94 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 172 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 0 optimal weight: 70.0000 chunk 63 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 320 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.082790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.059625 restraints weight = 58979.597| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.92 r_work: 0.2830 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18606 Z= 0.154 Angle : 0.622 11.076 25137 Z= 0.320 Chirality : 0.043 0.136 2919 Planarity : 0.003 0.054 3115 Dihedral : 15.447 131.831 2895 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 4.71 % Allowed : 18.18 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.18), residues: 2303 helix: 1.11 (0.14), residues: 1288 sheet: -1.83 (0.34), residues: 259 loop : -3.20 (0.19), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 202 TYR 0.011 0.001 TYR B 291 PHE 0.016 0.001 PHE C 148 TRP 0.010 0.001 TRP F 184 HIS 0.003 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (18606) covalent geometry : angle 0.62191 / 0.32 (25137) hydrogen bonds : bond 0.03398 / 2.25 ( 1094) hydrogen bonds : angle 3.90633 / 2.69 ( 3177) *********************** 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 271 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 184 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 73 ILE cc_start: 0.6715 (OUTLIER) cc_final: 0.6474 (mp) REVERT: G 140 MET cc_start: 0.7124 (mtt) cc_final: 0.6817 (mtm) REVERT: G 142 LEU cc_start: 0.8555 (tt) cc_final: 0.8177 (mm) REVERT: G 146 LEU cc_start: 0.8991 (tt) cc_final: 0.8433 (mt) REVERT: G 162 ASP cc_start: 0.8604 (p0) cc_final: 0.8388 (p0) REVERT: A 43 HIS cc_start: 0.8717 (OUTLIER) cc_final: 0.8462 (t70) REVERT: A 63 TYR cc_start: 0.7786 (t80) cc_final: 0.7392 (t80) REVERT: A 111 ASP cc_start: 0.7770 (t0) cc_final: 0.7373 (t0) REVERT: A 146 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8764 (mt) REVERT: B 43 HIS cc_start: 0.8731 (OUTLIER) cc_final: 0.8294 (t70) REVERT: B 73 ILE cc_start: 0.6882 (OUTLIER) cc_final: 0.6640 (mp) REVERT: B 140 MET cc_start: 0.8210 (pmm) cc_final: 0.7785 (pmm) REVERT: B 146 LEU cc_start: 0.8988 (tt) cc_final: 0.8442 (mt) REVERT: C 136 GLU cc_start: 0.8976 (pp20) cc_final: 0.8750 (pp20) REVERT: C 142 LEU cc_start: 0.8798 (mm) cc_final: 0.8298 (tt) REVERT: C 146 LEU cc_start: 0.8928 (tt) cc_final: 0.8370 (mt) REVERT: C 256 GLU cc_start: 0.9450 (tp30) cc_final: 0.9162 (mm-30) REVERT: D 43 HIS cc_start: 0.8744 (OUTLIER) cc_final: 0.8336 (t70) REVERT: D 111 ASP cc_start: 0.7749 (t0) cc_final: 0.7516 (t0) REVERT: D 118 MET cc_start: 0.9520 (tpp) cc_final: 0.9309 (tpp) REVERT: D 140 MET cc_start: 0.7987 (pmm) cc_final: 0.7757 (pmm) REVERT: D 142 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8247 (mt) REVERT: D 146 LEU cc_start: 0.8995 (tt) cc_final: 0.8439 (mt) REVERT: D 162 ASP cc_start: 0.8644 (p0) cc_final: 0.8419 (p0) REVERT: E 43 HIS cc_start: 0.8717 (OUTLIER) cc_final: 0.8223 (t70) REVERT: E 73 ILE cc_start: 0.6824 (OUTLIER) cc_final: 0.6594 (mp) REVERT: E 142 LEU cc_start: 0.8773 (mm) cc_final: 0.8536 (tt) REVERT: E 193 GLU cc_start: 0.9269 (tt0) cc_final: 0.8984 (tp30) REVERT: E 260 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8646 (tm-30) REVERT: F 43 HIS cc_start: 0.8781 (OUTLIER) cc_final: 0.8344 (t70) REVERT: F 63 TYR cc_start: 0.7987 (t80) cc_final: 0.7670 (t80) REVERT: F 73 ILE cc_start: 0.6576 (OUTLIER) cc_final: 0.6342 (mp) REVERT: F 118 MET cc_start: 0.9589 (tpp) cc_final: 0.9371 (tpp) REVERT: F 136 GLU cc_start: 0.8852 (pp20) cc_final: 0.8642 (pp20) REVERT: F 142 LEU cc_start: 0.8740 (mm) cc_final: 0.8299 (tt) REVERT: F 146 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8896 (mt) outliers start: 87 outliers final: 53 residues processed: 260 average time/residue: 0.1066 time to fit residues: 46.8531 Evaluate side-chains 232 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 167 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 73 ILE Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 226 VAL 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 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 146 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 121 ILE 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 51 THR Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 140 MET 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 330 THR Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain E residue 43 HIS Chi-restraints excluded: chain E residue 73 ILE 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 320 HIS Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain F residue 43 HIS Chi-restraints excluded: chain F residue 73 ILE 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 146 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 320 HIS 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 130 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 167 optimal weight: 30.0000 chunk 32 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.082758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.059586 restraints weight = 59628.252| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.94 r_work: 0.2833 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18606 Z= 0.157 Angle : 0.642 11.366 25137 Z= 0.330 Chirality : 0.043 0.176 2919 Planarity : 0.004 0.054 3115 Dihedral : 15.342 131.880 2895 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 4.06 % Allowed : 18.99 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.18), residues: 2303 helix: 1.15 (0.14), residues: 1295 sheet: -1.75 (0.34), residues: 259 loop : -3.11 (0.19), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 202 TYR 0.012 0.001 TYR G 291 PHE 0.015 0.001 PHE C 148 TRP 0.009 0.001 TRP A 184 HIS 0.006 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (18606) covalent geometry : angle 0.64212 / 0.33 (25137) hydrogen bonds : bond 0.03352 / 2.23 ( 1094) hydrogen bonds : angle 3.85412 / 2.65 ( 3177) *********************** 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 251 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 176 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 73 ILE cc_start: 0.6729 (OUTLIER) cc_final: 0.6489 (mp) REVERT: G 138 PHE cc_start: 0.7975 (m-80) cc_final: 0.7770 (m-80) REVERT: G 140 MET cc_start: 0.7108 (mtt) cc_final: 0.6770 (mtm) REVERT: G 142 LEU cc_start: 0.8590 (tt) cc_final: 0.8209 (mm) REVERT: G 146 LEU cc_start: 0.8985 (tt) cc_final: 0.8435 (mt) REVERT: G 162 ASP cc_start: 0.8621 (p0) cc_final: 0.8402 (p0) REVERT: A 43 HIS cc_start: 0.8745 (OUTLIER) cc_final: 0.8503 (t70) REVERT: A 63 TYR cc_start: 0.7763 (t80) cc_final: 0.7358 (t80) REVERT: A 111 ASP cc_start: 0.7768 (t0) cc_final: 0.7345 (t0) REVERT: A 146 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8745 (mt) REVERT: A 158 MET cc_start: 0.9326 (ttm) cc_final: 0.9121 (ttp) REVERT: B 43 HIS cc_start: 0.8738 (OUTLIER) cc_final: 0.8302 (t70) REVERT: B 73 ILE cc_start: 0.6864 (OUTLIER) cc_final: 0.6634 (mp) REVERT: B 138 PHE cc_start: 0.8208 (m-80) cc_final: 0.7987 (m-10) REVERT: B 140 MET cc_start: 0.8143 (pmm) cc_final: 0.7754 (pmm) REVERT: B 146 LEU cc_start: 0.8986 (tt) cc_final: 0.8437 (mt) REVERT: C 136 GLU cc_start: 0.8934 (pp20) cc_final: 0.8728 (pp20) REVERT: C 142 LEU cc_start: 0.8833 (mm) cc_final: 0.8337 (tt) REVERT: C 146 LEU cc_start: 0.8931 (tt) cc_final: 0.8332 (mt) REVERT: C 256 GLU cc_start: 0.9452 (tp30) cc_final: 0.9199 (mm-30) REVERT: D 43 HIS cc_start: 0.8754 (OUTLIER) cc_final: 0.8385 (t70) REVERT: D 118 MET cc_start: 0.9520 (tpp) cc_final: 0.9312 (tpp) REVERT: D 137 HIS cc_start: 0.8727 (OUTLIER) cc_final: 0.8500 (m-70) REVERT: D 140 MET cc_start: 0.7984 (pmm) cc_final: 0.7770 (pmm) REVERT: D 142 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8218 (mm) REVERT: D 146 LEU cc_start: 0.8985 (tt) cc_final: 0.8422 (mt) REVERT: E 43 HIS cc_start: 0.8700 (OUTLIER) cc_final: 0.8219 (t70) REVERT: E 73 ILE cc_start: 0.6828 (OUTLIER) cc_final: 0.6605 (mp) REVERT: E 142 LEU cc_start: 0.8803 (mm) cc_final: 0.8569 (tt) REVERT: E 193 GLU cc_start: 0.9259 (tt0) cc_final: 0.8951 (tp30) REVERT: E 260 GLU cc_start: 0.8989 (tm-30) cc_final: 0.8622 (tm-30) REVERT: F 43 HIS cc_start: 0.8778 (OUTLIER) cc_final: 0.8347 (t70) REVERT: F 63 TYR cc_start: 0.7961 (t80) cc_final: 0.7655 (t80) REVERT: F 73 ILE cc_start: 0.6455 (OUTLIER) cc_final: 0.6229 (mp) REVERT: F 118 MET cc_start: 0.9589 (tpp) cc_final: 0.9367 (tpp) REVERT: F 142 LEU cc_start: 0.8752 (mm) cc_final: 0.8305 (tt) REVERT: F 146 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8899 (mt) outliers start: 75 outliers final: 54 residues processed: 245 average time/residue: 0.1081 time to fit residues: 44.7554 Evaluate side-chains 231 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 164 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 43 HIS Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 320 HIS 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 146 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 121 ILE 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 51 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 140 MET 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 330 THR Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 142 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 73 ILE 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 320 HIS Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain F residue 43 HIS Chi-restraints excluded: chain F residue 73 ILE 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 146 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 320 HIS 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 37 optimal weight: 0.2980 chunk 79 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.081833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.056568 restraints weight = 61024.264| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.10 r_work: 0.2751 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18606 Z= 0.174 Angle : 0.651 10.429 25137 Z= 0.335 Chirality : 0.043 0.175 2919 Planarity : 0.004 0.055 3115 Dihedral : 15.326 132.220 2895 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 4.38 % Allowed : 19.05 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.18), residues: 2303 helix: 1.25 (0.14), residues: 1288 sheet: -1.69 (0.34), residues: 259 loop : -3.13 (0.19), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 186 TYR 0.012 0.001 TYR G 291 PHE 0.016 0.001 PHE F 148 TRP 0.010 0.001 TRP E 184 HIS 0.003 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (18606) covalent geometry : angle 0.65068 / 0.33 (25137) hydrogen bonds : bond 0.03346 / 2.23 ( 1094) hydrogen bonds : angle 3.82794 / 2.63 ( 3177) *********************** 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 258 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 177 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 73 ILE cc_start: 0.6701 (OUTLIER) cc_final: 0.6452 (mp) REVERT: G 140 MET cc_start: 0.7143 (mtt) cc_final: 0.6785 (mtm) REVERT: G 142 LEU cc_start: 0.8576 (tt) cc_final: 0.8169 (mm) REVERT: G 146 LEU cc_start: 0.8906 (tt) cc_final: 0.8336 (mt) REVERT: G 162 ASP cc_start: 0.8653 (p0) cc_final: 0.8446 (p0) REVERT: A 43 HIS cc_start: 0.8690 (OUTLIER) cc_final: 0.8476 (t70) REVERT: A 63 TYR cc_start: 0.7749 (t80) cc_final: 0.7340 (t80) REVERT: A 111 ASP cc_start: 0.7848 (t0) cc_final: 0.7454 (t0) REVERT: A 146 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8706 (mt) REVERT: B 43 HIS cc_start: 0.8735 (OUTLIER) cc_final: 0.8322 (t70) REVERT: B 73 ILE cc_start: 0.6714 (OUTLIER) cc_final: 0.6474 (mp) REVERT: B 140 MET cc_start: 0.8043 (pmm) cc_final: 0.7653 (pmm) REVERT: B 146 LEU cc_start: 0.8926 (tt) cc_final: 0.8394 (mt) REVERT: C 73 ILE cc_start: 0.6493 (OUTLIER) cc_final: 0.6261 (mp) REVERT: C 142 LEU cc_start: 0.8813 (mm) cc_final: 0.8245 (tt) REVERT: C 146 LEU cc_start: 0.8930 (tt) cc_final: 0.8343 (mt) REVERT: C 256 GLU cc_start: 0.9498 (tp30) cc_final: 0.9223 (mm-30) REVERT: D 43 HIS cc_start: 0.8720 (OUTLIER) cc_final: 0.8348 (t70) REVERT: D 140 MET cc_start: 0.7871 (pmm) cc_final: 0.7665 (pmm) REVERT: D 142 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8203 (mm) REVERT: D 146 LEU cc_start: 0.8950 (tt) cc_final: 0.8398 (mt) REVERT: D 162 ASP cc_start: 0.8640 (p0) cc_final: 0.8431 (p0) REVERT: E 43 HIS cc_start: 0.8690 (OUTLIER) cc_final: 0.8254 (t70) REVERT: E 73 ILE cc_start: 0.6839 (OUTLIER) cc_final: 0.6612 (mp) REVERT: E 142 LEU cc_start: 0.8790 (mm) cc_final: 0.8560 (tt) REVERT: E 193 GLU cc_start: 0.9309 (tt0) cc_final: 0.8948 (tp30) REVERT: E 260 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8698 (tm-30) REVERT: F 43 HIS cc_start: 0.8757 (OUTLIER) cc_final: 0.8358 (t70) REVERT: F 63 TYR cc_start: 0.7920 (t80) cc_final: 0.7599 (t80) REVERT: F 73 ILE cc_start: 0.6537 (OUTLIER) cc_final: 0.6302 (mp) REVERT: F 118 MET cc_start: 0.9607 (tpp) cc_final: 0.9383 (tpp) REVERT: F 136 GLU cc_start: 0.8896 (pp20) cc_final: 0.8675 (pp20) REVERT: F 140 MET cc_start: 0.7067 (mtt) cc_final: 0.6687 (mtm) REVERT: F 142 LEU cc_start: 0.8723 (mm) cc_final: 0.8363 (tt) outliers start: 81 outliers final: 57 residues processed: 252 average time/residue: 0.1101 time to fit residues: 46.9799 Evaluate side-chains 232 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 163 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 43 HIS Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 226 VAL 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 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 146 LEU Chi-restraints excluded: chain A residue 164 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 73 ILE Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 98 ILE 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 131 VAL 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 51 THR Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 140 MET 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 330 THR Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 142 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 73 ILE 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 73 ILE 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 131 VAL 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 320 HIS 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 95 optimal weight: 0.5980 chunk 101 optimal weight: 7.9990 chunk 223 optimal weight: 0.6980 chunk 225 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 161 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 198 optimal weight: 50.0000 chunk 113 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.082925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.060276 restraints weight = 59819.730| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.05 r_work: 0.2814 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18606 Z= 0.117 Angle : 0.637 13.474 25137 Z= 0.323 Chirality : 0.042 0.163 2919 Planarity : 0.004 0.054 3115 Dihedral : 15.033 131.521 2893 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.35 % Allowed : 19.81 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.18), residues: 2303 helix: 1.31 (0.14), residues: 1295 sheet: -1.69 (0.34), residues: 259 loop : -3.06 (0.19), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 186 TYR 0.011 0.001 TYR G 291 PHE 0.021 0.001 PHE D 138 TRP 0.012 0.001 TRP E 302 HIS 0.001 0.000 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (18606) covalent geometry : angle 0.63706 / 0.32 (25137) hydrogen bonds : bond 0.03171 / 2.11 ( 1094) hydrogen bonds : angle 3.74654 / 2.58 ( 3177) *********************** 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 239 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 177 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 73 ILE cc_start: 0.6618 (OUTLIER) cc_final: 0.6381 (mp) REVERT: G 138 PHE cc_start: 0.7907 (m-80) cc_final: 0.7702 (m-80) REVERT: G 140 MET cc_start: 0.7046 (mtt) cc_final: 0.6695 (mtm) REVERT: G 162 ASP cc_start: 0.8662 (p0) cc_final: 0.8447 (p0) REVERT: G 256 GLU cc_start: 0.9497 (tp30) cc_final: 0.9262 (mm-30) REVERT: A 43 HIS cc_start: 0.8680 (OUTLIER) cc_final: 0.8475 (t70) REVERT: A 63 TYR cc_start: 0.7777 (t80) cc_final: 0.7378 (t80) REVERT: A 111 ASP cc_start: 0.7820 (t0) cc_final: 0.7448 (t0) REVERT: A 146 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8723 (mt) REVERT: A 158 MET cc_start: 0.9299 (ttp) cc_final: 0.8889 (tpp) REVERT: B 43 HIS cc_start: 0.8706 (OUTLIER) cc_final: 0.8230 (t70) REVERT: B 73 ILE cc_start: 0.6743 (OUTLIER) cc_final: 0.6504 (mp) REVERT: B 140 MET cc_start: 0.7919 (pmm) cc_final: 0.7649 (pmm) REVERT: B 162 ASP cc_start: 0.8549 (p0) cc_final: 0.8341 (p0) REVERT: C 73 ILE cc_start: 0.6499 (OUTLIER) cc_final: 0.6244 (mp) REVERT: C 136 GLU cc_start: 0.8796 (pp20) cc_final: 0.8557 (pp20) REVERT: C 142 LEU cc_start: 0.8796 (mm) cc_final: 0.8255 (tt) REVERT: C 146 LEU cc_start: 0.8906 (tt) cc_final: 0.8315 (mt) REVERT: C 256 GLU cc_start: 0.9483 (tp30) cc_final: 0.9223 (mm-30) REVERT: D 43 HIS cc_start: 0.8705 (OUTLIER) cc_final: 0.8391 (t70) REVERT: D 140 MET cc_start: 0.7656 (pmm) cc_final: 0.7431 (pmm) REVERT: D 142 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8227 (mm) REVERT: D 146 LEU cc_start: 0.8925 (tt) cc_final: 0.8377 (mt) REVERT: E 43 HIS cc_start: 0.8655 (OUTLIER) cc_final: 0.8237 (t70) REVERT: E 73 ILE cc_start: 0.6760 (OUTLIER) cc_final: 0.6541 (mp) REVERT: E 142 LEU cc_start: 0.8778 (mm) cc_final: 0.8573 (tt) REVERT: E 193 GLU cc_start: 0.9293 (tt0) cc_final: 0.9012 (tp30) REVERT: E 260 GLU cc_start: 0.9030 (tm-30) cc_final: 0.8628 (tm-30) REVERT: F 43 HIS cc_start: 0.8715 (OUTLIER) cc_final: 0.8285 (t70) REVERT: F 63 TYR cc_start: 0.7953 (t80) cc_final: 0.7644 (t80) REVERT: F 73 ILE cc_start: 0.6463 (OUTLIER) cc_final: 0.6243 (mp) REVERT: F 118 MET cc_start: 0.9589 (tpp) cc_final: 0.9350 (tpp) REVERT: F 136 GLU cc_start: 0.8807 (pp20) cc_final: 0.8583 (pp20) REVERT: F 140 MET cc_start: 0.7061 (mtt) cc_final: 0.6514 (mtm) REVERT: F 142 LEU cc_start: 0.8727 (mm) cc_final: 0.8492 (tt) REVERT: F 260 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8722 (tm-30) outliers start: 62 outliers final: 40 residues processed: 234 average time/residue: 0.1044 time to fit residues: 41.3215 Evaluate side-chains 215 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 163 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 43 HIS Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 226 VAL 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 70 LEU 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 226 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 73 ILE 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 73 ILE Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 140 MET 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 330 THR Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 320 HIS Chi-restraints excluded: chain E residue 43 HIS Chi-restraints excluded: chain E residue 73 ILE 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 F residue 43 HIS Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 82 CYS 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 320 HIS 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 86 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 223 optimal weight: 0.6980 chunk 217 optimal weight: 0.7980 chunk 151 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 227 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 179 optimal weight: 0.9990 chunk 155 optimal weight: 0.5980 chunk 146 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 234 ASN D 234 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.083698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.060824 restraints weight = 59230.092| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.06 r_work: 0.2834 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18606 Z= 0.112 Angle : 0.641 12.568 25137 Z= 0.324 Chirality : 0.043 0.160 2919 Planarity : 0.004 0.053 3115 Dihedral : 14.747 131.661 2893 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.81 % Allowed : 20.18 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.18), residues: 2303 helix: 1.37 (0.14), residues: 1295 sheet: -1.71 (0.33), residues: 259 loop : -3.01 (0.19), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 244 TYR 0.011 0.001 TYR F 291 PHE 0.016 0.001 PHE F 148 TRP 0.012 0.001 TRP G 302 HIS 0.004 0.001 HIS D 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (18606) covalent geometry : angle 0.64082 / 0.32 (25137) hydrogen bonds : bond 0.03098 / 2.05 ( 1094) hydrogen bonds : angle 3.72402 / 2.56 ( 3177) ********************** 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 230 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 178 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 73 ILE cc_start: 0.6473 (OUTLIER) cc_final: 0.6220 (mp) REVERT: G 136 GLU cc_start: 0.8771 (pp20) cc_final: 0.8551 (pp20) REVERT: G 140 MET cc_start: 0.6832 (mtt) cc_final: 0.6566 (mtp) REVERT: G 158 MET cc_start: 0.9133 (mtp) cc_final: 0.8931 (ttm) REVERT: G 162 ASP cc_start: 0.8617 (p0) cc_final: 0.8414 (p0) REVERT: G 256 GLU cc_start: 0.9497 (tp30) cc_final: 0.9270 (mm-30) REVERT: A 43 HIS cc_start: 0.8632 (OUTLIER) cc_final: 0.8422 (t70) REVERT: A 63 TYR cc_start: 0.7759 (t80) cc_final: 0.7361 (t80) REVERT: A 111 ASP cc_start: 0.7749 (t0) cc_final: 0.7348 (t0) REVERT: A 146 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8702 (mt) REVERT: A 154 LEU cc_start: 0.9555 (tt) cc_final: 0.9061 (pp) REVERT: A 260 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8793 (tm-30) REVERT: B 43 HIS cc_start: 0.8620 (OUTLIER) cc_final: 0.8162 (t70) REVERT: B 73 ILE cc_start: 0.6609 (OUTLIER) cc_final: 0.6356 (mp) REVERT: B 140 MET cc_start: 0.7679 (pmm) cc_final: 0.7456 (pmm) REVERT: C 73 ILE cc_start: 0.6317 (OUTLIER) cc_final: 0.6071 (mp) REVERT: C 136 GLU cc_start: 0.8746 (pp20) cc_final: 0.8497 (pp20) REVERT: C 256 GLU cc_start: 0.9473 (tp30) cc_final: 0.9226 (mm-30) REVERT: E 43 HIS cc_start: 0.8601 (OUTLIER) cc_final: 0.8129 (t70) REVERT: E 73 ILE cc_start: 0.6578 (OUTLIER) cc_final: 0.6340 (mp) REVERT: E 142 LEU cc_start: 0.8788 (mm) cc_final: 0.8573 (tt) REVERT: E 193 GLU cc_start: 0.9272 (tt0) cc_final: 0.9044 (tp30) REVERT: E 260 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8583 (tm-30) REVERT: F 43 HIS cc_start: 0.8700 (OUTLIER) cc_final: 0.8307 (t70) REVERT: F 63 TYR cc_start: 0.7944 (t80) cc_final: 0.7632 (t80) REVERT: F 73 ILE cc_start: 0.6286 (OUTLIER) cc_final: 0.6034 (mp) REVERT: F 136 GLU cc_start: 0.8791 (pp20) cc_final: 0.8565 (pp20) REVERT: F 142 LEU cc_start: 0.8706 (mm) cc_final: 0.8488 (tt) outliers start: 52 outliers final: 38 residues processed: 228 average time/residue: 0.1068 time to fit residues: 41.2871 Evaluate side-chains 207 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 159 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 43 HIS Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 82 CYS Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 226 VAL 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 146 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain B residue 98 ILE 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 73 ILE Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 140 MET 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 330 THR Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 128 VAL 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 73 ILE Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain F residue 43 HIS Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 82 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 99 optimal weight: 70.0000 chunk 44 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 176 optimal weight: 2.9990 chunk 120 optimal weight: 0.0980 chunk 31 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 171 optimal weight: 6.9990 chunk 220 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 320 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.083986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.061482 restraints weight = 59812.467| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.07 r_work: 0.2882 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18606 Z= 0.112 Angle : 0.642 12.854 25137 Z= 0.324 Chirality : 0.042 0.161 2919 Planarity : 0.004 0.053 3115 Dihedral : 14.540 131.947 2893 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.71 % Allowed : 20.51 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.18), residues: 2303 helix: 1.46 (0.14), residues: 1295 sheet: -1.68 (0.33), residues: 259 loop : -2.95 (0.20), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 244 TYR 0.012 0.001 TYR B 291 PHE 0.022 0.001 PHE G 138 TRP 0.012 0.001 TRP C 302 HIS 0.004 0.001 HIS D 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (18606) covalent geometry : angle 0.64222 / 0.32 (25137) hydrogen bonds : bond 0.03042 / 2.01 ( 1094) hydrogen bonds : angle 3.67818 / 2.53 ( 3177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3827.86 seconds wall clock time: 66 minutes 50.84 seconds (4010.84 seconds total)