Starting phenix.real_space_refine on Fri Jan 17 21:07:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vsp_43501/01_2025/8vsp_43501.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vsp_43501/01_2025/8vsp_43501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vsp_43501/01_2025/8vsp_43501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vsp_43501/01_2025/8vsp_43501.map" model { file = "/net/cci-nas-00/data/ceres_data/8vsp_43501/01_2025/8vsp_43501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vsp_43501/01_2025/8vsp_43501.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 7239 2.51 5 N 1950 2.21 5 O 2157 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 11388 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1609 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1625 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 195} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 2, 'ARG:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 548 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 5, 'TRANS': 64} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: E, H, F, I, D, G Time building chain proxies: 5.52, per 1000 atoms: 0.48 Number of scatterers: 11388 At special positions: 0 Unit cell: (108.231, 104.456, 139.694, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 2157 8.00 N 1950 7.00 C 7239 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 79 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 173 " distance=2.03 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: 2.65 Conformation dependent library (CDL) restraints added in 1.5 seconds 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2778 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 18 sheets defined 36.2% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 57 through 79 removed outlier: 3.963A pdb=" N ALA A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 221 removed outlier: 3.646A pdb=" N ARG A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 64 removed outlier: 4.198A pdb=" N TYR B 60 " --> pdb=" O PRO B 56 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B 64 " --> pdb=" O TYR B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 73 Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 78 through 89 removed outlier: 3.617A pdb=" N GLN B 84 " --> pdb=" O ARG B 80 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU B 85 " --> pdb=" O HIS B 81 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 225 removed outlier: 3.874A pdb=" N GLY B 216 " --> pdb=" O PHE B 212 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 96 removed outlier: 3.517A pdb=" N ILE C 55 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY C 76 " --> pdb=" O TYR C 72 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG C 77 " --> pdb=" O GLN C 73 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS C 96 " --> pdb=" O ASN C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 52 Processing helix chain 'D' and resid 57 through 79 removed outlier: 3.963A pdb=" N ALA D 61 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS D 77 " --> pdb=" O ASN D 73 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 221 removed outlier: 3.646A pdb=" N ARG D 220 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER D 221 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 64 removed outlier: 4.199A pdb=" N TYR E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN E 64 " --> pdb=" O TYR E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 73 Processing helix chain 'E' and resid 73 through 78 Processing helix chain 'E' and resid 78 through 89 removed outlier: 3.618A pdb=" N GLN E 84 " --> pdb=" O ARG E 80 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU E 85 " --> pdb=" O HIS E 81 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG E 88 " --> pdb=" O GLN E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 225 removed outlier: 3.874A pdb=" N GLY E 216 " --> pdb=" O PHE E 212 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU E 217 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE E 218 " --> pdb=" O GLY E 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 96 removed outlier: 3.517A pdb=" N ILE F 55 " --> pdb=" O THR F 51 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG F 77 " --> pdb=" O GLN F 73 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS F 96 " --> pdb=" O ASN F 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 52 Processing helix chain 'G' and resid 57 through 79 removed outlier: 3.964A pdb=" N ALA G 61 " --> pdb=" O ASP G 57 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS G 77 " --> pdb=" O ASN G 73 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 221 removed outlier: 3.645A pdb=" N ARG G 220 " --> pdb=" O ILE G 216 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER G 221 " --> pdb=" O ARG G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 64 removed outlier: 4.198A pdb=" N TYR H 60 " --> pdb=" O PRO H 56 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN H 64 " --> pdb=" O TYR H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 73 Processing helix chain 'H' and resid 73 through 78 Processing helix chain 'H' and resid 78 through 89 removed outlier: 3.617A pdb=" N GLN H 84 " --> pdb=" O ARG H 80 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU H 85 " --> pdb=" O HIS H 81 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG H 88 " --> pdb=" O GLN H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 225 removed outlier: 3.874A pdb=" N GLY H 216 " --> pdb=" O PHE H 212 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU H 217 " --> pdb=" O LEU H 213 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE H 218 " --> pdb=" O GLY H 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 96 removed outlier: 3.517A pdb=" N ILE I 55 " --> pdb=" O THR I 51 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY I 76 " --> pdb=" O TYR I 72 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG I 77 " --> pdb=" O GLN I 73 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS I 96 " --> pdb=" O ASN I 92 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 46 removed outlier: 6.791A pdb=" N HIS A 27 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N TYR A 36 " --> pdb=" O TYR A 25 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N TYR A 25 " --> pdb=" O TYR A 36 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ASP A 38 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N GLY A 23 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER A 22 " --> pdb=" O TYR A 16 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR A 16 " --> pdb=" O SER A 22 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN A 24 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASN A 14 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR A 26 " --> pdb=" O GLY A 12 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLY A 12 " --> pdb=" O THR A 26 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ALA B 13 " --> pdb=" O TYR A 11 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL A 13 " --> pdb=" O PHE B 11 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE B 11 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU A 15 " --> pdb=" O TYR B 9 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TYR B 9 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG B 23 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA B 38 " --> pdb=" O TYR B 30 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TYR B 32 " --> pdb=" O GLU B 36 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLU B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 95 removed outlier: 5.108A pdb=" N ILE A 106 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU A 155 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE A 108 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU A 153 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LEU A 110 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N SER A 151 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP A 112 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LYS A 149 " --> pdb=" O ASP A 112 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 95 removed outlier: 5.108A pdb=" N ILE A 106 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU A 155 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE A 108 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU A 153 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LEU A 110 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N SER A 151 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP A 112 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LYS A 149 " --> pdb=" O ASP A 112 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 130 removed outlier: 4.846A pdb=" N TRP A 123 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 98 through 102 removed outlier: 5.975A pdb=" N PHE B 155 " --> pdb=" O ASP B 121 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN B 156 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU B 147 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU B 158 " --> pdb=" O THR B 145 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 128 through 133 Processing sheet with id=AA7, first strand: chain 'D' and resid 43 through 46 removed outlier: 6.791A pdb=" N HIS D 27 " --> pdb=" O GLN D 34 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N TYR D 36 " --> pdb=" O TYR D 25 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N TYR D 25 " --> pdb=" O TYR D 36 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ASP D 38 " --> pdb=" O GLY D 23 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N GLY D 23 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER D 22 " --> pdb=" O TYR D 16 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR D 16 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN D 24 " --> pdb=" O ASN D 14 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASN D 14 " --> pdb=" O GLN D 24 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR D 26 " --> pdb=" O GLY D 12 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLY D 12 " --> pdb=" O THR D 26 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ALA E 13 " --> pdb=" O TYR D 11 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL D 13 " --> pdb=" O PHE E 11 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE E 11 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LEU D 15 " --> pdb=" O TYR E 9 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TYR E 9 " --> pdb=" O LEU D 15 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG E 23 " --> pdb=" O THR E 18 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA E 38 " --> pdb=" O TYR E 30 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR E 32 " --> pdb=" O GLU E 36 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N GLU E 36 " --> pdb=" O TYR E 32 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 90 through 95 removed outlier: 5.108A pdb=" N ILE D 106 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU D 155 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE D 108 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU D 153 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LEU D 110 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N SER D 151 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP D 112 " --> pdb=" O LYS D 149 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LYS D 149 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 90 through 95 removed outlier: 5.108A pdb=" N ILE D 106 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU D 155 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE D 108 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU D 153 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LEU D 110 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N SER D 151 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP D 112 " --> pdb=" O LYS D 149 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LYS D 149 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 128 through 130 removed outlier: 4.847A pdb=" N TRP D 123 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 98 through 102 removed outlier: 5.976A pdb=" N PHE E 155 " --> pdb=" O ASP E 121 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN E 156 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU E 147 " --> pdb=" O GLN E 156 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU E 158 " --> pdb=" O THR E 145 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 133 Processing sheet with id=AB4, first strand: chain 'G' and resid 43 through 46 removed outlier: 6.790A pdb=" N HIS G 27 " --> pdb=" O GLN G 34 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N TYR G 36 " --> pdb=" O TYR G 25 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N TYR G 25 " --> pdb=" O TYR G 36 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ASP G 38 " --> pdb=" O GLY G 23 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N GLY G 23 " --> pdb=" O ASP G 38 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER G 22 " --> pdb=" O TYR G 16 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TYR G 16 " --> pdb=" O SER G 22 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN G 24 " --> pdb=" O ASN G 14 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASN G 14 " --> pdb=" O GLN G 24 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR G 26 " --> pdb=" O GLY G 12 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLY G 12 " --> pdb=" O THR G 26 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ALA H 13 " --> pdb=" O TYR G 11 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL G 13 " --> pdb=" O PHE H 11 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE H 11 " --> pdb=" O VAL G 13 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU G 15 " --> pdb=" O TYR H 9 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TYR H 9 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG H 23 " --> pdb=" O THR H 18 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA H 38 " --> pdb=" O TYR H 30 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR H 32 " --> pdb=" O GLU H 36 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLU H 36 " --> pdb=" O TYR H 32 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 90 through 95 removed outlier: 5.109A pdb=" N ILE G 106 " --> pdb=" O LEU G 155 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU G 155 " --> pdb=" O ILE G 106 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE G 108 " --> pdb=" O LEU G 153 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU G 153 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LEU G 110 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N SER G 151 " --> pdb=" O LEU G 110 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ASP G 112 " --> pdb=" O LYS G 149 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LYS G 149 " --> pdb=" O ASP G 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 90 through 95 removed outlier: 5.109A pdb=" N ILE G 106 " --> pdb=" O LEU G 155 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU G 155 " --> pdb=" O ILE G 106 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE G 108 " --> pdb=" O LEU G 153 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU G 153 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LEU G 110 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N SER G 151 " --> pdb=" O LEU G 110 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ASP G 112 " --> pdb=" O LYS G 149 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LYS G 149 " --> pdb=" O ASP G 112 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 128 through 130 removed outlier: 4.846A pdb=" N TRP G 123 " --> pdb=" O VAL G 130 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 98 through 102 removed outlier: 5.976A pdb=" N PHE H 155 " --> pdb=" O ASP H 121 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN H 156 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU H 147 " --> pdb=" O GLN H 156 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU H 158 " --> pdb=" O THR H 145 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 128 through 133 651 hydrogen bonds defined for protein. 1773 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: 3.04 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3744 1.34 - 1.46: 2599 1.46 - 1.58: 5246 1.58 - 1.69: 0 1.69 - 1.81: 63 Bond restraints: 11652 Sorted by residual: bond pdb=" N VAL B 46 " pdb=" CA VAL B 46 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.19e-02 7.06e+03 7.92e+00 bond pdb=" N VAL E 46 " pdb=" CA VAL E 46 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.19e-02 7.06e+03 7.70e+00 bond pdb=" N VAL H 46 " pdb=" CA VAL H 46 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.19e-02 7.06e+03 7.68e+00 bond pdb=" N VAL H 44 " pdb=" CA VAL H 44 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.22e+00 bond pdb=" N VAL B 44 " pdb=" CA VAL B 44 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 6.99e+00 ... (remaining 11647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 15057 1.03 - 2.06: 617 2.06 - 3.09: 174 3.09 - 4.12: 28 4.12 - 5.15: 12 Bond angle restraints: 15888 Sorted by residual: angle pdb=" CA ASP E 152 " pdb=" C ASP E 152 " pdb=" O ASP E 152 " ideal model delta sigma weight residual 122.38 117.89 4.49 1.49e+00 4.50e-01 9.07e+00 angle pdb=" CA ASP B 152 " pdb=" C ASP B 152 " pdb=" O ASP B 152 " ideal model delta sigma weight residual 122.38 117.91 4.47 1.49e+00 4.50e-01 9.00e+00 angle pdb=" CA ASP H 152 " pdb=" C ASP H 152 " pdb=" O ASP H 152 " ideal model delta sigma weight residual 122.38 117.97 4.41 1.49e+00 4.50e-01 8.76e+00 angle pdb=" C ASN E 19 " pdb=" CA ASN E 19 " pdb=" CB ASN E 19 " ideal model delta sigma weight residual 116.34 112.30 4.04 1.40e+00 5.10e-01 8.33e+00 angle pdb=" C ASN B 19 " pdb=" CA ASN B 19 " pdb=" CB ASN B 19 " ideal model delta sigma weight residual 116.34 112.31 4.03 1.40e+00 5.10e-01 8.30e+00 ... (remaining 15883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.68: 6397 11.68 - 23.36: 374 23.36 - 35.04: 123 35.04 - 46.73: 54 46.73 - 58.41: 6 Dihedral angle restraints: 6954 sinusoidal: 2655 harmonic: 4299 Sorted by residual: dihedral pdb=" CA LEU A 140 " pdb=" CB LEU A 140 " pdb=" CG LEU A 140 " pdb=" CD1 LEU A 140 " ideal model delta sinusoidal sigma weight residual 60.00 118.41 -58.41 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LEU D 140 " pdb=" CB LEU D 140 " pdb=" CG LEU D 140 " pdb=" CD1 LEU D 140 " ideal model delta sinusoidal sigma weight residual 60.00 118.36 -58.36 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA LEU G 140 " pdb=" CB LEU G 140 " pdb=" CG LEU G 140 " pdb=" CD1 LEU G 140 " ideal model delta sinusoidal sigma weight residual 60.00 118.34 -58.34 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 6951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1399 0.048 - 0.095: 286 0.095 - 0.143: 115 0.143 - 0.190: 3 0.190 - 0.238: 3 Chirality restraints: 1806 Sorted by residual: chirality pdb=" CA VAL H 44 " pdb=" N VAL H 44 " pdb=" C VAL H 44 " pdb=" CB VAL H 44 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA VAL B 44 " pdb=" N VAL B 44 " pdb=" C VAL B 44 " pdb=" CB VAL B 44 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA VAL E 44 " pdb=" N VAL E 44 " pdb=" C VAL E 44 " pdb=" CB VAL E 44 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1803 not shown) Planarity restraints: 2055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY H 54 " -0.040 5.00e-02 4.00e+02 6.01e-02 5.78e+00 pdb=" N PRO H 55 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO H 55 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 55 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 54 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO B 55 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 55 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 55 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 54 " 0.040 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO E 55 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO E 55 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 55 " 0.033 5.00e-02 4.00e+02 ... (remaining 2052 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 96 2.60 - 3.18: 9306 3.18 - 3.75: 16700 3.75 - 4.33: 23688 4.33 - 4.90: 39251 Nonbonded interactions: 89041 Sorted by model distance: nonbonded pdb=" SG CYS E 15 " pdb=" SG CYS E 79 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS H 15 " pdb=" SG CYS H 79 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS G 109 " pdb=" SG CYS G 165 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS D 109 " pdb=" SG CYS D 165 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS E 117 " pdb=" SG CYS E 173 " model vdw 2.033 3.760 ... (remaining 89036 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 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 24.820 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 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 : 0.004 0.034 11652 Z= 0.258 Angle : 0.529 5.148 15888 Z= 0.314 Chirality : 0.045 0.238 1806 Planarity : 0.005 0.060 2055 Dihedral : 9.478 58.408 4167 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.51 % Allowed : 4.08 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.23), residues: 1440 helix: 1.17 (0.22), residues: 504 sheet: 0.70 (0.26), residues: 402 loop : -0.26 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 61 HIS 0.003 0.001 HIS H 177 PHE 0.013 0.001 PHE D 148 TYR 0.008 0.001 TYR G 25 ARG 0.002 0.000 ARG E 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 332 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.8494 (m110) cc_final: 0.8224 (m110) REVERT: A 43 GLU cc_start: 0.7263 (tp30) cc_final: 0.6944 (tp30) REVERT: A 44 THR cc_start: 0.8565 (m) cc_final: 0.7872 (t) REVERT: A 158 SER cc_start: 0.7735 (t) cc_final: 0.7181 (p) REVERT: A 164 ASP cc_start: 0.8166 (m-30) cc_final: 0.7897 (m-30) REVERT: B 14 MET cc_start: 0.8724 (mtp) cc_final: 0.8514 (mtm) REVERT: C 73 GLN cc_start: 0.8495 (tp40) cc_final: 0.8266 (tp40) REVERT: C 107 MET cc_start: 0.6894 (mmm) cc_final: 0.6427 (mmt) REVERT: C 109 MET cc_start: 0.7907 (ptm) cc_final: 0.7644 (ptm) REVERT: D 14 ASN cc_start: 0.8447 (m110) cc_final: 0.8100 (m-40) REVERT: D 28 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8213 (mt-10) REVERT: D 42 LYS cc_start: 0.8029 (tttt) cc_final: 0.7825 (tttt) REVERT: D 63 THR cc_start: 0.8263 (m) cc_final: 0.8021 (m) REVERT: D 81 SER cc_start: 0.8207 (t) cc_final: 0.7743 (p) REVERT: D 82 THR cc_start: 0.8392 (p) cc_final: 0.7898 (p) REVERT: D 87 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8208 (mm-30) REVERT: D 105 ASN cc_start: 0.8706 (t0) cc_final: 0.8312 (m-40) REVERT: D 118 VAL cc_start: 0.8567 (t) cc_final: 0.8171 (m) REVERT: D 177 LEU cc_start: 0.8152 (mt) cc_final: 0.7890 (mm) REVERT: E 14 MET cc_start: 0.8766 (mtp) cc_final: 0.8494 (mtm) REVERT: E 83 TYR cc_start: 0.8419 (t80) cc_final: 0.7969 (t80) REVERT: E 163 MET cc_start: 0.2647 (mtm) cc_final: 0.1831 (ptt) REVERT: E 176 GLU cc_start: 0.7182 (pt0) cc_final: 0.6971 (pt0) REVERT: E 185 THR cc_start: 0.8391 (m) cc_final: 0.8178 (t) REVERT: G 14 ASN cc_start: 0.8379 (m110) cc_final: 0.8100 (m-40) REVERT: G 82 THR cc_start: 0.8365 (p) cc_final: 0.8154 (p) REVERT: G 106 ILE cc_start: 0.8322 (mt) cc_final: 0.8100 (mt) REVERT: G 125 SER cc_start: 0.8025 (t) cc_final: 0.7422 (p) REVERT: G 144 ASP cc_start: 0.8433 (p0) cc_final: 0.8111 (p0) REVERT: G 176 LEU cc_start: 0.7717 (tt) cc_final: 0.7332 (tp) REVERT: G 179 HIS cc_start: 0.8252 (t70) cc_final: 0.7694 (t70) REVERT: H 6 ASP cc_start: 0.8559 (t0) cc_final: 0.8257 (t0) REVERT: H 22 GLU cc_start: 0.5616 (mt-10) cc_final: 0.5395 (mt-10) REVERT: H 30 TYR cc_start: 0.8657 (m-80) cc_final: 0.8381 (m-80) REVERT: H 93 ARG cc_start: 0.8529 (ttt180) cc_final: 0.8274 (ttt-90) REVERT: H 163 MET cc_start: 0.3111 (mtm) cc_final: 0.2582 (ptt) REVERT: I 72 TYR cc_start: 0.8638 (t80) cc_final: 0.8399 (t80) REVERT: I 73 GLN cc_start: 0.8465 (tp40) cc_final: 0.8256 (mm-40) outliers start: 6 outliers final: 1 residues processed: 338 average time/residue: 0.2612 time to fit residues: 121.6775 Evaluate side-chains 297 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 296 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 91 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 3.9990 chunk 109 optimal weight: 0.4980 chunk 60 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 103 GLN A 120 ASN B 64 GLN C 64 GLN C 75 GLN ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN D 86 ASN D 103 GLN D 120 ASN D 179 HIS ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 GLN G 14 ASN G 103 GLN G 120 ASN H 64 GLN ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 75 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.139831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.114279 restraints weight = 16539.809| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.28 r_work: 0.3182 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11652 Z= 0.258 Angle : 0.553 6.545 15888 Z= 0.296 Chirality : 0.044 0.130 1806 Planarity : 0.005 0.057 2055 Dihedral : 4.628 47.813 1656 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.98 % Allowed : 10.12 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.22), residues: 1440 helix: 2.37 (0.22), residues: 516 sheet: 0.90 (0.25), residues: 402 loop : -0.14 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 131 HIS 0.004 0.001 HIS G 7 PHE 0.016 0.002 PHE D 54 TYR 0.017 0.001 TYR B 60 ARG 0.005 0.001 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 284 time to evaluate : 1.210 Fit side-chains REVERT: A 14 ASN cc_start: 0.8478 (m-40) cc_final: 0.8209 (m-40) REVERT: A 42 LYS cc_start: 0.7842 (tttt) cc_final: 0.7559 (tttt) REVERT: A 43 GLU cc_start: 0.7447 (tp30) cc_final: 0.7120 (tp30) REVERT: A 44 THR cc_start: 0.8555 (m) cc_final: 0.7643 (t) REVERT: A 135 SER cc_start: 0.8000 (p) cc_final: 0.7736 (t) REVERT: A 158 SER cc_start: 0.7879 (t) cc_final: 0.7302 (p) REVERT: A 164 ASP cc_start: 0.8147 (m-30) cc_final: 0.7853 (m-30) REVERT: B 14 MET cc_start: 0.8518 (mtp) cc_final: 0.8242 (mtm) REVERT: B 23 ARG cc_start: 0.7566 (ttt90) cc_final: 0.7259 (tpt170) REVERT: C 53 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7416 (t80) REVERT: C 73 GLN cc_start: 0.8511 (tp40) cc_final: 0.8180 (tp40) REVERT: C 107 MET cc_start: 0.7339 (mmm) cc_final: 0.6890 (mmt) REVERT: C 115 MET cc_start: 0.6867 (mtp) cc_final: 0.6491 (mtp) REVERT: D 14 ASN cc_start: 0.8374 (m-40) cc_final: 0.8098 (m-40) REVERT: D 28 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8184 (mt-10) REVERT: D 118 VAL cc_start: 0.8659 (t) cc_final: 0.8366 (m) REVERT: D 177 LEU cc_start: 0.8071 (mt) cc_final: 0.7833 (mm) REVERT: E 14 MET cc_start: 0.8615 (mtp) cc_final: 0.8348 (mtm) REVERT: E 23 ARG cc_start: 0.7499 (ttt90) cc_final: 0.7215 (tpt170) REVERT: E 39 ARG cc_start: 0.8394 (ttp-170) cc_final: 0.8093 (ttp-110) REVERT: E 163 MET cc_start: 0.2803 (mtm) cc_final: 0.1946 (ptt) REVERT: G 14 ASN cc_start: 0.8348 (m-40) cc_final: 0.8048 (m-40) REVERT: G 43 GLU cc_start: 0.7655 (tp30) cc_final: 0.7448 (tp30) REVERT: G 82 THR cc_start: 0.8137 (p) cc_final: 0.7924 (p) REVERT: G 144 ASP cc_start: 0.8534 (p0) cc_final: 0.8283 (p0) REVERT: G 176 LEU cc_start: 0.7511 (tt) cc_final: 0.7192 (tp) REVERT: G 179 HIS cc_start: 0.8386 (t70) cc_final: 0.8089 (t70) REVERT: H 23 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6111 (ttt-90) REVERT: H 163 MET cc_start: 0.3234 (mtm) cc_final: 0.2685 (ptt) REVERT: I 72 TYR cc_start: 0.8755 (t80) cc_final: 0.8484 (t80) outliers start: 35 outliers final: 17 residues processed: 299 average time/residue: 0.2499 time to fit residues: 104.0402 Evaluate side-chains 286 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 267 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain F residue 53 PHE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain I residue 53 PHE Chi-restraints excluded: chain I residue 111 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 113 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 39 optimal weight: 20.0000 chunk 70 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 ASN D 120 ASN E 174 HIS ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN H 64 GLN H 174 HIS ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.137230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.111718 restraints weight = 16925.626| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.27 r_work: 0.3174 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 11652 Z= 0.382 Angle : 0.584 6.505 15888 Z= 0.308 Chirality : 0.046 0.145 1806 Planarity : 0.005 0.056 2055 Dihedral : 4.281 16.593 1653 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.23 % Allowed : 12.76 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.22), residues: 1440 helix: 2.28 (0.22), residues: 516 sheet: 0.83 (0.25), residues: 402 loop : -0.20 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP G 123 HIS 0.008 0.001 HIS G 27 PHE 0.016 0.002 PHE H 122 TYR 0.015 0.002 TYR B 60 ARG 0.006 0.001 ARG E 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 275 time to evaluate : 1.427 Fit side-chains REVERT: A 42 LYS cc_start: 0.7893 (tttt) cc_final: 0.7628 (tttt) REVERT: A 43 GLU cc_start: 0.7522 (tp30) cc_final: 0.7147 (tp30) REVERT: A 44 THR cc_start: 0.8582 (m) cc_final: 0.7790 (t) REVERT: A 132 GLU cc_start: 0.7391 (tt0) cc_final: 0.7032 (tm-30) REVERT: A 158 SER cc_start: 0.7944 (t) cc_final: 0.7371 (p) REVERT: A 164 ASP cc_start: 0.8094 (m-30) cc_final: 0.7822 (m-30) REVERT: B 14 MET cc_start: 0.8502 (mtp) cc_final: 0.8238 (mtm) REVERT: B 23 ARG cc_start: 0.7619 (ttt90) cc_final: 0.7209 (tpt170) REVERT: B 163 MET cc_start: 0.2701 (ttm) cc_final: 0.1478 (ptt) REVERT: C 53 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.7151 (t80) REVERT: C 73 GLN cc_start: 0.8582 (tp40) cc_final: 0.8270 (tp40) REVERT: C 107 MET cc_start: 0.7403 (mmm) cc_final: 0.7056 (mmt) REVERT: D 28 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8158 (mt-10) REVERT: D 105 ASN cc_start: 0.8622 (t0) cc_final: 0.8246 (m-40) REVERT: D 118 VAL cc_start: 0.8729 (t) cc_final: 0.8410 (m) REVERT: D 177 LEU cc_start: 0.8131 (mt) cc_final: 0.7883 (mm) REVERT: E 14 MET cc_start: 0.8603 (mtp) cc_final: 0.8350 (mtm) REVERT: E 23 ARG cc_start: 0.7504 (ttt90) cc_final: 0.7207 (tpt170) REVERT: E 39 ARG cc_start: 0.8456 (ttp-170) cc_final: 0.8245 (ttp-110) REVERT: E 70 ARG cc_start: 0.7744 (ttt180) cc_final: 0.7521 (ttt-90) REVERT: E 163 MET cc_start: 0.2902 (mtm) cc_final: 0.1960 (ptt) REVERT: G 14 ASN cc_start: 0.8343 (m-40) cc_final: 0.8050 (m-40) REVERT: G 63 THR cc_start: 0.7768 (t) cc_final: 0.7494 (p) REVERT: G 82 THR cc_start: 0.8206 (p) cc_final: 0.7989 (p) REVERT: G 144 ASP cc_start: 0.8536 (p0) cc_final: 0.8260 (p0) REVERT: G 176 LEU cc_start: 0.7716 (tt) cc_final: 0.7408 (tp) REVERT: G 179 HIS cc_start: 0.8385 (t70) cc_final: 0.8138 (t70) REVERT: H 23 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6274 (ttt-90) REVERT: H 46 VAL cc_start: 0.8242 (t) cc_final: 0.7778 (p) REVERT: H 86 GLU cc_start: 0.7388 (mm-30) cc_final: 0.6854 (mm-30) REVERT: H 163 MET cc_start: 0.3151 (mtm) cc_final: 0.2642 (ptt) outliers start: 38 outliers final: 27 residues processed: 287 average time/residue: 0.2577 time to fit residues: 102.8949 Evaluate side-chains 297 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 268 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain F residue 53 PHE Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 87 LEU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain I residue 53 PHE Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 111 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 139 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 ASN G 120 ASN H 64 GLN ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.136741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.111253 restraints weight = 16662.233| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.23 r_work: 0.3210 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11652 Z= 0.277 Angle : 0.524 5.989 15888 Z= 0.277 Chirality : 0.044 0.131 1806 Planarity : 0.005 0.054 2055 Dihedral : 4.138 15.082 1653 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.32 % Allowed : 13.86 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.22), residues: 1440 helix: 2.69 (0.22), residues: 498 sheet: 0.82 (0.25), residues: 402 loop : -0.30 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 180 HIS 0.004 0.001 HIS G 27 PHE 0.015 0.002 PHE D 54 TYR 0.011 0.001 TYR G 152 ARG 0.006 0.001 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 277 time to evaluate : 1.268 Fit side-chains REVERT: A 42 LYS cc_start: 0.7906 (tttt) cc_final: 0.7623 (tttt) REVERT: A 43 GLU cc_start: 0.7506 (tp30) cc_final: 0.7256 (tp30) REVERT: A 44 THR cc_start: 0.8591 (m) cc_final: 0.7450 (t) REVERT: A 132 GLU cc_start: 0.7465 (tt0) cc_final: 0.7074 (tm-30) REVERT: A 158 SER cc_start: 0.7959 (t) cc_final: 0.7402 (p) REVERT: A 164 ASP cc_start: 0.8170 (m-30) cc_final: 0.7910 (m-30) REVERT: B 14 MET cc_start: 0.8473 (mtp) cc_final: 0.8244 (mtm) REVERT: B 23 ARG cc_start: 0.7647 (ttt90) cc_final: 0.7237 (tpt170) REVERT: B 137 GLU cc_start: 0.6020 (tt0) cc_final: 0.5807 (tm-30) REVERT: C 53 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.6994 (t80) REVERT: C 73 GLN cc_start: 0.8561 (tp40) cc_final: 0.8278 (tp40) REVERT: C 107 MET cc_start: 0.7423 (mmm) cc_final: 0.7111 (mmt) REVERT: D 26 THR cc_start: 0.8693 (p) cc_final: 0.8401 (m) REVERT: D 28 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8169 (mt-10) REVERT: D 105 ASN cc_start: 0.8586 (t0) cc_final: 0.8253 (m-40) REVERT: D 118 VAL cc_start: 0.8735 (t) cc_final: 0.8433 (m) REVERT: D 177 LEU cc_start: 0.8107 (mt) cc_final: 0.7886 (mm) REVERT: E 10 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8603 (pt0) REVERT: E 14 MET cc_start: 0.8559 (mtp) cc_final: 0.8343 (mtm) REVERT: E 23 ARG cc_start: 0.7450 (ttt90) cc_final: 0.7171 (tpt170) REVERT: E 39 ARG cc_start: 0.8421 (ttp-170) cc_final: 0.8217 (ttp-110) REVERT: E 69 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7743 (mm-30) REVERT: E 70 ARG cc_start: 0.7682 (ttt180) cc_final: 0.7442 (ttt-90) REVERT: G 14 ASN cc_start: 0.8261 (m-40) cc_final: 0.7981 (m-40) REVERT: G 63 THR cc_start: 0.7692 (t) cc_final: 0.7469 (p) REVERT: G 144 ASP cc_start: 0.8531 (p0) cc_final: 0.8258 (p0) REVERT: G 176 LEU cc_start: 0.7752 (tt) cc_final: 0.7442 (tp) REVERT: G 179 HIS cc_start: 0.8355 (t70) cc_final: 0.8111 (t70) REVERT: H 23 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.6288 (ttt-90) REVERT: H 86 GLU cc_start: 0.7331 (mm-30) cc_final: 0.6803 (mm-30) REVERT: H 163 MET cc_start: 0.3140 (mtm) cc_final: 0.2664 (ptt) outliers start: 39 outliers final: 29 residues processed: 290 average time/residue: 0.2887 time to fit residues: 114.9136 Evaluate side-chains 302 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 270 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain F residue 53 PHE Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain I residue 53 PHE Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 111 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 130 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 121 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN H 64 GLN ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.138563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.113246 restraints weight = 16535.640| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.23 r_work: 0.3226 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11652 Z= 0.277 Angle : 0.523 6.964 15888 Z= 0.275 Chirality : 0.044 0.129 1806 Planarity : 0.005 0.054 2055 Dihedral : 4.094 15.155 1653 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.40 % Allowed : 14.37 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.22), residues: 1440 helix: 2.82 (0.22), residues: 498 sheet: 0.82 (0.25), residues: 402 loop : -0.29 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 188 HIS 0.003 0.001 HIS H 177 PHE 0.017 0.002 PHE D 54 TYR 0.010 0.001 TYR G 152 ARG 0.006 0.001 ARG E 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 277 time to evaluate : 1.340 Fit side-chains REVERT: A 42 LYS cc_start: 0.7888 (tttt) cc_final: 0.7631 (tttt) REVERT: A 43 GLU cc_start: 0.7466 (tp30) cc_final: 0.7153 (tp30) REVERT: A 44 THR cc_start: 0.8602 (m) cc_final: 0.7725 (t) REVERT: A 132 GLU cc_start: 0.7485 (tt0) cc_final: 0.7099 (tm-30) REVERT: A 158 SER cc_start: 0.7957 (t) cc_final: 0.7405 (p) REVERT: A 164 ASP cc_start: 0.8162 (m-30) cc_final: 0.7898 (m-30) REVERT: B 14 MET cc_start: 0.8446 (mtp) cc_final: 0.8236 (mtm) REVERT: B 23 ARG cc_start: 0.7639 (ttt90) cc_final: 0.7305 (tpt-90) REVERT: B 82 ASN cc_start: 0.8381 (m-40) cc_final: 0.7711 (m-40) REVERT: B 137 GLU cc_start: 0.6171 (tt0) cc_final: 0.5949 (tm-30) REVERT: B 149 ARG cc_start: 0.8740 (ttm-80) cc_final: 0.8430 (ttm-80) REVERT: C 73 GLN cc_start: 0.8531 (tp40) cc_final: 0.8273 (tp40) REVERT: C 107 MET cc_start: 0.7395 (mmm) cc_final: 0.7128 (mmt) REVERT: D 26 THR cc_start: 0.8701 (p) cc_final: 0.8421 (m) REVERT: D 28 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8163 (mt-10) REVERT: D 118 VAL cc_start: 0.8743 (t) cc_final: 0.8439 (m) REVERT: D 177 LEU cc_start: 0.8112 (mt) cc_final: 0.7871 (mm) REVERT: E 10 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8634 (pt0) REVERT: E 14 MET cc_start: 0.8554 (mtp) cc_final: 0.8345 (mtm) REVERT: E 23 ARG cc_start: 0.7447 (ttt90) cc_final: 0.7128 (tpt170) REVERT: E 39 ARG cc_start: 0.8420 (ttp-170) cc_final: 0.8217 (ttp-110) REVERT: E 163 MET cc_start: 0.2782 (mtm) cc_final: 0.2019 (ptt) REVERT: F 115 MET cc_start: 0.6828 (mtp) cc_final: 0.6521 (mtp) REVERT: G 14 ASN cc_start: 0.8243 (m-40) cc_final: 0.7976 (m-40) REVERT: G 63 THR cc_start: 0.7682 (t) cc_final: 0.7462 (p) REVERT: G 144 ASP cc_start: 0.8543 (p0) cc_final: 0.8276 (p0) REVERT: G 176 LEU cc_start: 0.7768 (tt) cc_final: 0.7451 (tp) REVERT: G 179 HIS cc_start: 0.8357 (t70) cc_final: 0.8107 (t70) REVERT: H 23 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6276 (ttt-90) REVERT: H 86 GLU cc_start: 0.7296 (mm-30) cc_final: 0.6777 (mm-30) REVERT: H 163 MET cc_start: 0.3000 (mtm) cc_final: 0.2663 (ptt) outliers start: 40 outliers final: 33 residues processed: 292 average time/residue: 0.2690 time to fit residues: 107.8479 Evaluate side-chains 306 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 271 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 53 PHE Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 111 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 6 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 139 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN H 64 GLN I 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.138887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.113515 restraints weight = 16693.045| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.25 r_work: 0.3223 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11652 Z= 0.256 Angle : 0.513 5.774 15888 Z= 0.271 Chirality : 0.043 0.128 1806 Planarity : 0.005 0.053 2055 Dihedral : 4.044 14.773 1653 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.74 % Allowed : 14.97 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.22), residues: 1440 helix: 2.94 (0.22), residues: 498 sheet: 0.85 (0.25), residues: 402 loop : -0.28 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 180 HIS 0.003 0.001 HIS G 7 PHE 0.020 0.002 PHE D 54 TYR 0.010 0.001 TYR G 152 ARG 0.007 0.001 ARG E 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 277 time to evaluate : 1.351 Fit side-chains REVERT: A 42 LYS cc_start: 0.7862 (tttt) cc_final: 0.7612 (tttt) REVERT: A 43 GLU cc_start: 0.7444 (tp30) cc_final: 0.7149 (tp30) REVERT: A 44 THR cc_start: 0.8603 (m) cc_final: 0.7756 (t) REVERT: A 132 GLU cc_start: 0.7510 (tt0) cc_final: 0.7121 (tm-30) REVERT: A 158 SER cc_start: 0.7972 (t) cc_final: 0.7422 (p) REVERT: A 164 ASP cc_start: 0.8190 (m-30) cc_final: 0.7901 (m-30) REVERT: B 23 ARG cc_start: 0.7606 (ttt90) cc_final: 0.7295 (tpt-90) REVERT: B 39 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8202 (ttp-170) REVERT: B 82 ASN cc_start: 0.8399 (m-40) cc_final: 0.7664 (m-40) REVERT: B 137 GLU cc_start: 0.6174 (tt0) cc_final: 0.5958 (tm-30) REVERT: B 149 ARG cc_start: 0.8716 (ttm-80) cc_final: 0.8388 (ttm-80) REVERT: C 73 GLN cc_start: 0.8522 (tp40) cc_final: 0.8290 (tp40) REVERT: C 107 MET cc_start: 0.7413 (mmm) cc_final: 0.7145 (mmt) REVERT: D 26 THR cc_start: 0.8691 (p) cc_final: 0.8418 (m) REVERT: D 28 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8159 (mt-10) REVERT: D 118 VAL cc_start: 0.8737 (t) cc_final: 0.8440 (m) REVERT: D 177 LEU cc_start: 0.8121 (mt) cc_final: 0.7857 (mm) REVERT: E 10 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8628 (pt0) REVERT: E 23 ARG cc_start: 0.7404 (ttt90) cc_final: 0.7122 (tpt170) REVERT: E 39 ARG cc_start: 0.8443 (ttp-170) cc_final: 0.8202 (ttp-110) REVERT: E 163 MET cc_start: 0.2735 (mtm) cc_final: 0.2303 (ptt) REVERT: F 77 ARG cc_start: 0.8658 (mmm-85) cc_final: 0.8312 (mtp180) REVERT: G 14 ASN cc_start: 0.8217 (m-40) cc_final: 0.7958 (m-40) REVERT: G 25 TYR cc_start: 0.9035 (t80) cc_final: 0.8396 (t80) REVERT: G 144 ASP cc_start: 0.8525 (p0) cc_final: 0.8256 (p0) REVERT: G 176 LEU cc_start: 0.7772 (tt) cc_final: 0.7435 (tp) REVERT: G 179 HIS cc_start: 0.8349 (t70) cc_final: 0.8101 (t70) REVERT: H 23 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6216 (ttt-90) REVERT: H 86 GLU cc_start: 0.7277 (mm-30) cc_final: 0.6751 (mm-30) REVERT: H 156 GLN cc_start: 0.8466 (mt0) cc_final: 0.8229 (tt0) REVERT: H 163 MET cc_start: 0.3040 (mtm) cc_final: 0.2696 (ptt) outliers start: 44 outliers final: 32 residues processed: 293 average time/residue: 0.2740 time to fit residues: 111.1359 Evaluate side-chains 311 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 276 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain I residue 53 PHE Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 111 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.5980 chunk 65 optimal weight: 0.0770 chunk 73 optimal weight: 0.0050 chunk 130 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.4554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN H 64 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.138588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.113082 restraints weight = 16729.792| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.26 r_work: 0.3235 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11652 Z= 0.191 Angle : 0.495 5.809 15888 Z= 0.259 Chirality : 0.042 0.157 1806 Planarity : 0.005 0.053 2055 Dihedral : 3.909 14.715 1653 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.74 % Allowed : 15.65 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.23), residues: 1440 helix: 3.20 (0.22), residues: 501 sheet: 0.96 (0.25), residues: 402 loop : -0.22 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 180 HIS 0.003 0.001 HIS H 177 PHE 0.020 0.001 PHE D 54 TYR 0.016 0.001 TYR B 60 ARG 0.007 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 279 time to evaluate : 1.154 Fit side-chains REVERT: A 42 LYS cc_start: 0.7864 (tttt) cc_final: 0.7600 (tttt) REVERT: A 43 GLU cc_start: 0.7428 (tp30) cc_final: 0.7153 (tp30) REVERT: A 44 THR cc_start: 0.8576 (m) cc_final: 0.7776 (t) REVERT: A 63 THR cc_start: 0.7736 (m) cc_final: 0.7474 (p) REVERT: A 132 GLU cc_start: 0.7492 (tt0) cc_final: 0.7115 (tm-30) REVERT: A 158 SER cc_start: 0.7976 (t) cc_final: 0.7419 (p) REVERT: B 23 ARG cc_start: 0.7528 (ttt90) cc_final: 0.7061 (tpt170) REVERT: B 82 ASN cc_start: 0.8412 (m-40) cc_final: 0.7679 (m-40) REVERT: B 137 GLU cc_start: 0.6183 (tt0) cc_final: 0.5972 (tm-30) REVERT: B 149 ARG cc_start: 0.8685 (ttm-80) cc_final: 0.8349 (ttm-80) REVERT: C 73 GLN cc_start: 0.8521 (tp40) cc_final: 0.8292 (tp40) REVERT: C 107 MET cc_start: 0.7422 (mmm) cc_final: 0.7151 (mmt) REVERT: D 26 THR cc_start: 0.8657 (p) cc_final: 0.8394 (m) REVERT: D 28 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8160 (mt-10) REVERT: D 71 ASN cc_start: 0.8111 (m-40) cc_final: 0.7900 (m-40) REVERT: D 118 VAL cc_start: 0.8733 (t) cc_final: 0.8448 (m) REVERT: D 177 LEU cc_start: 0.8128 (mt) cc_final: 0.7917 (mm) REVERT: E 10 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8569 (pt0) REVERT: E 23 ARG cc_start: 0.7366 (ttt90) cc_final: 0.7135 (tpt170) REVERT: E 163 MET cc_start: 0.2681 (mtm) cc_final: 0.2341 (ptt) REVERT: F 77 ARG cc_start: 0.8673 (mmm-85) cc_final: 0.8325 (mtp180) REVERT: F 115 MET cc_start: 0.6493 (mtp) cc_final: 0.6098 (mtp) REVERT: G 14 ASN cc_start: 0.8221 (m-40) cc_final: 0.7965 (m-40) REVERT: G 25 TYR cc_start: 0.9019 (t80) cc_final: 0.8378 (t80) REVERT: G 87 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8477 (mm-30) REVERT: G 144 ASP cc_start: 0.8523 (p0) cc_final: 0.8222 (p0) REVERT: G 176 LEU cc_start: 0.7796 (tt) cc_final: 0.7445 (tp) REVERT: G 179 HIS cc_start: 0.8365 (t70) cc_final: 0.8126 (t70) REVERT: H 14 MET cc_start: 0.8373 (mtp) cc_final: 0.8087 (mtt) REVERT: H 23 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.6195 (ttt-90) REVERT: H 57 ASP cc_start: 0.8297 (m-30) cc_final: 0.7710 (m-30) REVERT: H 86 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6740 (mm-30) REVERT: H 163 MET cc_start: 0.3021 (mtm) cc_final: 0.2680 (ptt) outliers start: 44 outliers final: 34 residues processed: 297 average time/residue: 0.2541 time to fit residues: 104.9661 Evaluate side-chains 310 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 274 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain I residue 53 PHE Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 111 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 16 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN H 64 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.138798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.113170 restraints weight = 16676.408| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.24 r_work: 0.3214 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11652 Z= 0.273 Angle : 0.528 8.769 15888 Z= 0.275 Chirality : 0.043 0.156 1806 Planarity : 0.005 0.052 2055 Dihedral : 3.991 15.330 1653 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.32 % Allowed : 16.16 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.22), residues: 1440 helix: 3.09 (0.22), residues: 498 sheet: 0.87 (0.25), residues: 402 loop : -0.27 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 180 HIS 0.004 0.001 HIS H 177 PHE 0.018 0.002 PHE D 54 TYR 0.014 0.001 TYR B 60 ARG 0.008 0.001 ARG E 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 278 time to evaluate : 1.322 Fit side-chains REVERT: A 42 LYS cc_start: 0.7885 (tttt) cc_final: 0.7603 (tttt) REVERT: A 43 GLU cc_start: 0.7443 (tp30) cc_final: 0.7136 (tp30) REVERT: A 44 THR cc_start: 0.8619 (m) cc_final: 0.7893 (t) REVERT: A 132 GLU cc_start: 0.7500 (tt0) cc_final: 0.7126 (tm-30) REVERT: A 158 SER cc_start: 0.7990 (t) cc_final: 0.7441 (p) REVERT: B 23 ARG cc_start: 0.7536 (ttt90) cc_final: 0.7204 (tpt-90) REVERT: B 82 ASN cc_start: 0.8397 (m-40) cc_final: 0.7627 (m-40) REVERT: B 137 GLU cc_start: 0.6222 (tt0) cc_final: 0.6010 (tm-30) REVERT: D 26 THR cc_start: 0.8688 (p) cc_final: 0.8444 (m) REVERT: D 28 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8154 (mt-10) REVERT: D 118 VAL cc_start: 0.8735 (t) cc_final: 0.8421 (m) REVERT: D 177 LEU cc_start: 0.8141 (mt) cc_final: 0.7854 (mm) REVERT: E 10 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8409 (pt0) REVERT: E 23 ARG cc_start: 0.7409 (ttt90) cc_final: 0.7031 (tpt170) REVERT: E 137 GLU cc_start: 0.6155 (tt0) cc_final: 0.5905 (tm-30) REVERT: E 163 MET cc_start: 0.2696 (mtm) cc_final: 0.2384 (ptt) REVERT: F 77 ARG cc_start: 0.8674 (mmm-85) cc_final: 0.8328 (mtp180) REVERT: G 14 ASN cc_start: 0.8242 (m-40) cc_final: 0.7980 (m-40) REVERT: G 25 TYR cc_start: 0.9046 (t80) cc_final: 0.8324 (t80) REVERT: G 144 ASP cc_start: 0.8506 (p0) cc_final: 0.8225 (p0) REVERT: G 179 HIS cc_start: 0.8365 (t70) cc_final: 0.8124 (t70) REVERT: H 14 MET cc_start: 0.8373 (mtp) cc_final: 0.8098 (mtt) REVERT: H 23 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6297 (ttt-90) REVERT: H 86 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6726 (mm-30) REVERT: H 163 MET cc_start: 0.3063 (mtm) cc_final: 0.2719 (ptt) outliers start: 39 outliers final: 32 residues processed: 294 average time/residue: 0.2626 time to fit residues: 106.1440 Evaluate side-chains 311 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 277 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain I residue 53 PHE Chi-restraints excluded: chain I residue 95 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 91 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 127 optimal weight: 0.5980 chunk 135 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN H 64 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.138304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.112732 restraints weight = 16724.925| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.28 r_work: 0.3224 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11652 Z= 0.246 Angle : 0.520 8.381 15888 Z= 0.270 Chirality : 0.043 0.147 1806 Planarity : 0.005 0.053 2055 Dihedral : 3.948 15.206 1653 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.32 % Allowed : 16.58 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.22), residues: 1440 helix: 3.12 (0.22), residues: 498 sheet: 0.89 (0.25), residues: 402 loop : -0.27 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 180 HIS 0.003 0.001 HIS H 177 PHE 0.019 0.002 PHE D 54 TYR 0.010 0.001 TYR G 152 ARG 0.009 0.001 ARG E 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 276 time to evaluate : 1.245 Fit side-chains REVERT: A 42 LYS cc_start: 0.7906 (tttt) cc_final: 0.7627 (tttt) REVERT: A 43 GLU cc_start: 0.7428 (tp30) cc_final: 0.7130 (tp30) REVERT: A 44 THR cc_start: 0.8618 (m) cc_final: 0.7893 (t) REVERT: A 132 GLU cc_start: 0.7534 (tt0) cc_final: 0.7146 (tm-30) REVERT: A 158 SER cc_start: 0.7980 (t) cc_final: 0.7423 (p) REVERT: B 23 ARG cc_start: 0.7536 (ttt90) cc_final: 0.7222 (tpt-90) REVERT: B 82 ASN cc_start: 0.8403 (m-40) cc_final: 0.7655 (m-40) REVERT: B 137 GLU cc_start: 0.6216 (tt0) cc_final: 0.6015 (tm-30) REVERT: B 149 ARG cc_start: 0.8804 (ttm110) cc_final: 0.8470 (ttm170) REVERT: D 26 THR cc_start: 0.8688 (p) cc_final: 0.8442 (m) REVERT: D 28 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8183 (mt-10) REVERT: D 118 VAL cc_start: 0.8744 (t) cc_final: 0.8430 (m) REVERT: D 177 LEU cc_start: 0.8157 (mt) cc_final: 0.7885 (mm) REVERT: E 10 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8397 (pt0) REVERT: E 137 GLU cc_start: 0.6160 (tt0) cc_final: 0.5919 (tm-30) REVERT: E 163 MET cc_start: 0.2727 (mtm) cc_final: 0.2447 (ptt) REVERT: F 77 ARG cc_start: 0.8685 (mmm-85) cc_final: 0.8322 (mtp180) REVERT: F 115 MET cc_start: 0.6567 (mtp) cc_final: 0.6337 (mtp) REVERT: G 14 ASN cc_start: 0.8237 (m-40) cc_final: 0.7981 (m-40) REVERT: G 25 TYR cc_start: 0.9038 (t80) cc_final: 0.8311 (t80) REVERT: G 144 ASP cc_start: 0.8494 (p0) cc_final: 0.8215 (p0) REVERT: G 179 HIS cc_start: 0.8352 (t70) cc_final: 0.8113 (t70) REVERT: H 14 MET cc_start: 0.8380 (mtp) cc_final: 0.8104 (mtt) REVERT: H 23 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6256 (ttt-90) REVERT: H 86 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6709 (mm-30) REVERT: H 163 MET cc_start: 0.3033 (mtm) cc_final: 0.2710 (ptt) outliers start: 39 outliers final: 36 residues processed: 292 average time/residue: 0.2574 time to fit residues: 104.9170 Evaluate side-chains 312 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 274 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain I residue 53 PHE Chi-restraints excluded: chain I residue 95 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 30 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 92 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 93 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN H 64 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.139505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.114024 restraints weight = 16612.394| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.24 r_work: 0.3230 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11652 Z= 0.226 Angle : 0.510 7.564 15888 Z= 0.265 Chirality : 0.043 0.140 1806 Planarity : 0.005 0.052 2055 Dihedral : 3.905 15.020 1653 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.15 % Allowed : 16.67 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.22), residues: 1440 helix: 3.16 (0.22), residues: 501 sheet: 0.93 (0.25), residues: 402 loop : -0.25 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 180 HIS 0.003 0.001 HIS H 177 PHE 0.019 0.002 PHE D 54 TYR 0.009 0.001 TYR G 152 ARG 0.009 0.001 ARG E 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 275 time to evaluate : 1.334 Fit side-chains REVERT: A 42 LYS cc_start: 0.7884 (tttt) cc_final: 0.7607 (tttt) REVERT: A 43 GLU cc_start: 0.7404 (tp30) cc_final: 0.7115 (tp30) REVERT: A 44 THR cc_start: 0.8619 (m) cc_final: 0.7893 (t) REVERT: A 63 THR cc_start: 0.7794 (m) cc_final: 0.7499 (p) REVERT: A 132 GLU cc_start: 0.7523 (tt0) cc_final: 0.7133 (tm-30) REVERT: A 158 SER cc_start: 0.7979 (t) cc_final: 0.7428 (p) REVERT: B 23 ARG cc_start: 0.7540 (ttt90) cc_final: 0.7225 (tpt-90) REVERT: B 82 ASN cc_start: 0.8395 (m-40) cc_final: 0.7631 (m-40) REVERT: B 149 ARG cc_start: 0.8814 (ttm110) cc_final: 0.8415 (ttm170) REVERT: D 26 THR cc_start: 0.8688 (p) cc_final: 0.8440 (m) REVERT: D 28 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8186 (mt-10) REVERT: D 87 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8439 (mm-30) REVERT: D 118 VAL cc_start: 0.8765 (t) cc_final: 0.8440 (m) REVERT: D 177 LEU cc_start: 0.8168 (mt) cc_final: 0.7939 (mm) REVERT: E 10 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8377 (pt0) REVERT: E 163 MET cc_start: 0.2686 (mtm) cc_final: 0.2485 (ptt) REVERT: F 77 ARG cc_start: 0.8677 (mmm-85) cc_final: 0.8321 (mtp180) REVERT: F 115 MET cc_start: 0.6538 (mtp) cc_final: 0.6322 (mtp) REVERT: G 14 ASN cc_start: 0.8241 (m-40) cc_final: 0.7984 (m-40) REVERT: G 25 TYR cc_start: 0.9037 (t80) cc_final: 0.8309 (t80) REVERT: G 144 ASP cc_start: 0.8494 (p0) cc_final: 0.8213 (p0) REVERT: G 179 HIS cc_start: 0.8361 (t70) cc_final: 0.8133 (t70) REVERT: H 14 MET cc_start: 0.8356 (mtp) cc_final: 0.8085 (mtt) REVERT: H 23 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.6248 (ttt-90) REVERT: H 57 ASP cc_start: 0.8313 (m-30) cc_final: 0.7752 (m-30) REVERT: H 86 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6754 (mm-30) REVERT: H 138 GLU cc_start: 0.8061 (tp30) cc_final: 0.7838 (tp30) REVERT: H 163 MET cc_start: 0.3014 (mtm) cc_final: 0.2716 (ptt) outliers start: 37 outliers final: 33 residues processed: 290 average time/residue: 0.2627 time to fit residues: 105.0405 Evaluate side-chains 308 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 273 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain I residue 53 PHE Chi-restraints excluded: chain I residue 95 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 7 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 104 optimal weight: 0.0060 chunk 65 optimal weight: 0.0010 chunk 95 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 overall best weight: 0.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN H 64 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.139679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.114371 restraints weight = 16614.446| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.23 r_work: 0.3251 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11652 Z= 0.178 Angle : 0.491 6.757 15888 Z= 0.255 Chirality : 0.042 0.127 1806 Planarity : 0.005 0.052 2055 Dihedral : 3.817 15.271 1653 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.72 % Allowed : 17.35 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.23), residues: 1440 helix: 3.31 (0.22), residues: 501 sheet: 1.01 (0.25), residues: 399 loop : -0.21 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 180 HIS 0.003 0.001 HIS E 174 PHE 0.013 0.001 PHE D 54 TYR 0.008 0.001 TYR G 152 ARG 0.009 0.001 ARG E 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6530.29 seconds wall clock time: 118 minutes 30.76 seconds (7110.76 seconds total)