Starting phenix.real_space_refine on Tue Jun 10 04:20:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vsp_43501/06_2025/8vsp_43501.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vsp_43501/06_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_43501/06_2025/8vsp_43501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vsp_43501/06_2025/8vsp_43501.map" model { file = "/net/cci-nas-00/data/ceres_data/8vsp_43501/06_2025/8vsp_43501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vsp_43501/06_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-5710/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: 5.53, per 1000 atoms: 0.49 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=9, 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 Simple disulfide: pdb=" SG CYS D 109 " - pdb=" SG CYS D 165 " distance=2.03 Simple disulfide: pdb=" SG CYS G 109 " - pdb=" SG CYS G 165 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 79 " distance=2.03 Simple disulfide: pdb=" SG CYS H 15 " - pdb=" SG CYS H 79 " distance=2.03 Simple disulfide: pdb=" SG CYS E 117 " - pdb=" SG CYS E 173 " distance=2.03 Simple disulfide: pdb=" SG CYS H 117 " - pdb=" SG CYS H 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: 2.49 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: 1.47 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: 3.46 Time building geometry restraints manager: 3.00 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: 6411 11.68 - 23.36: 378 23.36 - 35.04: 123 35.04 - 46.73: 54 46.73 - 58.41: 6 Dihedral angle restraints: 6972 sinusoidal: 2673 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 6969 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: 2.07 - 2.63: 100 2.63 - 3.20: 9748 3.20 - 3.77: 16586 3.77 - 4.33: 23682 4.33 - 4.90: 38907 Nonbonded interactions: 89023 Sorted by model distance: nonbonded pdb=" OD1 ASP E 152 " pdb=" OG1 THR E 154 " model vdw 2.066 3.040 nonbonded pdb=" OD1 ASP B 152 " pdb=" OG1 THR B 154 " model vdw 2.066 3.040 nonbonded pdb=" OD1 ASP H 152 " pdb=" OG1 THR H 154 " model vdw 2.067 3.040 nonbonded pdb=" CE1 TYR C 50 " pdb=" CE1 TYR F 50 " model vdw 2.198 3.640 nonbonded pdb=" CE1 TYR F 50 " pdb=" CE1 TYR I 50 " model vdw 2.203 3.640 ... (remaining 89018 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: 0.08 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: 0.870 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.130 Process input model: 26.610 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.640 ------------------------------------------------------------------------------- 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 11661 Z= 0.211 Angle : 0.530 5.148 15906 Z= 0.314 Chirality : 0.045 0.238 1806 Planarity : 0.005 0.060 2055 Dihedral : 9.478 58.408 4167 Min Nonbonded Distance : 2.066 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 Details of bonding type rmsd hydrogen bonds : bond 0.24806 ( 627) hydrogen bonds : angle 7.18389 ( 1773) SS BOND : bond 0.00153 ( 9) SS BOND : angle 0.74174 ( 18) covalent geometry : bond 0.00391 (11652) covalent geometry : angle 0.52944 (15888) *********************** 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 : 1.122 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: 0.2577 time to fit residues: 120.8460 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 : 1.183 ------------------------------------------------------------------------------- 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: 0.0980 chunk 112 optimal weight: 1.9990 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: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.139950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.114407 restraints weight = 16490.596| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.29 r_work: 0.3249 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11661 Z= 0.156 Angle : 0.535 6.683 15906 Z= 0.285 Chirality : 0.044 0.151 1806 Planarity : 0.005 0.057 2055 Dihedral : 4.561 46.913 1656 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.06 % Allowed : 9.86 % Favored : 87.07 % 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: 1.57 (0.22), residues: 1440 helix: 2.38 (0.22), residues: 516 sheet: 0.87 (0.25), residues: 402 loop : -0.13 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 131 HIS 0.004 0.001 HIS G 7 PHE 0.016 0.002 PHE D 54 TYR 0.019 0.001 TYR B 60 ARG 0.005 0.001 ARG H 94 Details of bonding type rmsd hydrogen bonds : bond 0.05207 ( 627) hydrogen bonds : angle 4.63875 ( 1773) SS BOND : bond 0.00211 ( 9) SS BOND : angle 0.63588 ( 18) covalent geometry : bond 0.00349 (11652) covalent geometry : angle 0.53444 (15888) *********************** 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 326 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 290 time to evaluate : 1.204 Fit side-chains REVERT: A 14 ASN cc_start: 0.8477 (m-40) cc_final: 0.8251 (m-40) REVERT: A 42 LYS cc_start: 0.7927 (tttt) cc_final: 0.7639 (tttt) REVERT: A 63 THR cc_start: 0.7695 (m) cc_final: 0.7334 (p) REVERT: A 135 SER cc_start: 0.8116 (p) cc_final: 0.7858 (t) REVERT: A 158 SER cc_start: 0.7913 (t) cc_final: 0.7377 (p) REVERT: A 164 ASP cc_start: 0.8238 (m-30) cc_final: 0.7965 (m-30) REVERT: B 14 MET cc_start: 0.8513 (mtp) cc_final: 0.8307 (mtm) REVERT: B 23 ARG cc_start: 0.7609 (ttt90) cc_final: 0.7304 (tpt170) REVERT: C 53 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7283 (t80) REVERT: C 73 GLN cc_start: 0.8520 (tp40) cc_final: 0.8248 (tp40) REVERT: C 107 MET cc_start: 0.7375 (mmm) cc_final: 0.6929 (mmt) REVERT: C 115 MET cc_start: 0.6674 (mtp) cc_final: 0.6351 (mtp) REVERT: D 14 ASN cc_start: 0.8377 (m-40) cc_final: 0.8134 (m-40) REVERT: D 105 ASN cc_start: 0.8658 (t0) cc_final: 0.8249 (m-40) REVERT: D 118 VAL cc_start: 0.8692 (t) cc_final: 0.8446 (m) REVERT: D 154 THR cc_start: 0.8914 (m) cc_final: 0.8707 (m) REVERT: E 14 MET cc_start: 0.8613 (mtp) cc_final: 0.8358 (mtm) REVERT: E 23 ARG cc_start: 0.7480 (ttt90) cc_final: 0.7243 (tpt170) REVERT: E 39 ARG cc_start: 0.8397 (ttp-170) cc_final: 0.8178 (ttp-110) REVERT: E 77 THR cc_start: 0.7790 (p) cc_final: 0.7516 (t) REVERT: E 163 MET cc_start: 0.2732 (mtm) cc_final: 0.1892 (ptt) REVERT: G 14 ASN cc_start: 0.8376 (m-40) cc_final: 0.8110 (m-40) REVERT: G 43 GLU cc_start: 0.7639 (tp30) cc_final: 0.7430 (tp30) REVERT: G 82 THR cc_start: 0.8254 (p) cc_final: 0.8045 (p) REVERT: G 144 ASP cc_start: 0.8473 (p0) cc_final: 0.8217 (p0) REVERT: G 176 LEU cc_start: 0.7645 (tt) cc_final: 0.7300 (tp) REVERT: G 179 HIS cc_start: 0.8458 (t70) cc_final: 0.8158 (t70) REVERT: H 22 GLU cc_start: 0.6597 (mt-10) cc_final: 0.6304 (mt-10) REVERT: H 23 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6941 (tpt170) REVERT: H 163 MET cc_start: 0.3205 (mtm) cc_final: 0.2660 (ptt) REVERT: I 72 TYR cc_start: 0.8756 (t80) cc_final: 0.8486 (t80) outliers start: 36 outliers final: 18 residues processed: 306 average time/residue: 0.2349 time to fit residues: 101.3341 Evaluate side-chains 292 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 272 time to evaluate : 1.232 ------------------------------------------------------------------------------- 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 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 77 LYS 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 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 Chi-restraints excluded: chain I residue 113 LEU 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: 0.0570 chunk 38 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 39 optimal weight: 20.0000 chunk 70 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- 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 ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.139078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.113528 restraints weight = 16846.939| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.27 r_work: 0.3193 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11661 Z= 0.166 Angle : 0.524 6.539 15906 Z= 0.275 Chirality : 0.044 0.136 1806 Planarity : 0.005 0.056 2055 Dihedral : 4.009 16.696 1653 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.72 % Allowed : 12.76 % Favored : 84.52 % 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: 1.75 (0.22), residues: 1440 helix: 2.62 (0.22), residues: 516 sheet: 0.92 (0.25), residues: 402 loop : -0.10 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 180 HIS 0.005 0.001 HIS G 27 PHE 0.015 0.002 PHE G 54 TYR 0.013 0.001 TYR B 60 ARG 0.005 0.000 ARG E 94 Details of bonding type rmsd hydrogen bonds : bond 0.04526 ( 627) hydrogen bonds : angle 4.29869 ( 1773) SS BOND : bond 0.00263 ( 9) SS BOND : angle 0.60553 ( 18) covalent geometry : bond 0.00387 (11652) covalent geometry : angle 0.52398 (15888) *********************** 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 311 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 279 time to evaluate : 1.173 Fit side-chains revert: symmetry clash REVERT: A 14 ASN cc_start: 0.8480 (m-40) cc_final: 0.8279 (m110) REVERT: A 42 LYS cc_start: 0.7944 (tttt) cc_final: 0.7663 (tttt) REVERT: A 51 LEU cc_start: 0.8037 (mt) cc_final: 0.7828 (mp) REVERT: A 63 THR cc_start: 0.7751 (m) cc_final: 0.7388 (p) REVERT: A 68 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.7087 (mp) REVERT: A 132 GLU cc_start: 0.7409 (tt0) cc_final: 0.7019 (tm-30) REVERT: A 135 SER cc_start: 0.8056 (p) cc_final: 0.7801 (t) REVERT: A 158 SER cc_start: 0.7940 (t) cc_final: 0.7391 (p) REVERT: A 164 ASP cc_start: 0.8176 (m-30) cc_final: 0.7901 (m-30) REVERT: B 14 MET cc_start: 0.8462 (mtp) cc_final: 0.8245 (mtm) REVERT: B 23 ARG cc_start: 0.7597 (ttt90) cc_final: 0.7265 (tpt170) REVERT: B 149 ARG cc_start: 0.8679 (ttm-80) cc_final: 0.8420 (ttm-80) REVERT: B 163 MET cc_start: 0.2586 (ttm) cc_final: 0.1378 (ptt) REVERT: C 53 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.7156 (t80) REVERT: C 73 GLN cc_start: 0.8550 (tp40) cc_final: 0.8251 (tp40) REVERT: C 107 MET cc_start: 0.7395 (mmm) cc_final: 0.7002 (mmt) REVERT: D 14 ASN cc_start: 0.8314 (m-40) cc_final: 0.8075 (m110) REVERT: D 105 ASN cc_start: 0.8654 (t0) cc_final: 0.8158 (m-40) REVERT: D 118 VAL cc_start: 0.8733 (t) cc_final: 0.8428 (m) REVERT: D 154 THR cc_start: 0.8942 (m) cc_final: 0.8724 (m) REVERT: D 176 LEU cc_start: 0.7912 (tt) cc_final: 0.7687 (tp) REVERT: E 14 MET cc_start: 0.8628 (mtp) cc_final: 0.8335 (mtm) REVERT: E 23 ARG cc_start: 0.7540 (ttt90) cc_final: 0.7260 (tpt170) REVERT: E 39 ARG cc_start: 0.8432 (ttp-170) cc_final: 0.8208 (ttp-170) REVERT: E 70 ARG cc_start: 0.7720 (ttt180) cc_final: 0.7485 (ttt-90) REVERT: E 163 MET cc_start: 0.2808 (mtm) cc_final: 0.1819 (ptt) REVERT: G 14 ASN cc_start: 0.8305 (m-40) cc_final: 0.8008 (m-40) REVERT: G 63 THR cc_start: 0.7686 (t) cc_final: 0.7438 (p) REVERT: G 113 ASN cc_start: 0.8345 (t0) cc_final: 0.7867 (t0) REVERT: G 144 ASP cc_start: 0.8523 (p0) cc_final: 0.8257 (p0) REVERT: G 176 LEU cc_start: 0.7685 (tt) cc_final: 0.7346 (tp) REVERT: G 179 HIS cc_start: 0.8453 (t70) cc_final: 0.8207 (t70) REVERT: H 22 GLU cc_start: 0.6532 (mt-10) cc_final: 0.6313 (mt-10) REVERT: H 23 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6293 (ttt-90) REVERT: H 86 GLU cc_start: 0.7394 (mm-30) cc_final: 0.6846 (mm-30) REVERT: H 163 MET cc_start: 0.3116 (mtm) cc_final: 0.2521 (ptt) outliers start: 32 outliers final: 25 residues processed: 290 average time/residue: 0.2775 time to fit residues: 113.1096 Evaluate side-chains 297 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 269 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 68 LEU 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 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 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 154 THR 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 95 MET Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain I residue 113 LEU 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: 1.9990 chunk 122 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 chunk 116 optimal weight: 7.9990 chunk 14 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 chunk 143 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 GLN D 120 ASN ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3747 r_free = 0.3747 target = 0.139631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.114308 restraints weight = 16622.924| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.25 r_work: 0.3202 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11661 Z= 0.139 Angle : 0.491 5.775 15906 Z= 0.258 Chirality : 0.043 0.131 1806 Planarity : 0.005 0.054 2055 Dihedral : 3.900 14.179 1653 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.72 % Allowed : 14.03 % Favored : 83.25 % 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: 1.92 (0.23), residues: 1440 helix: 3.09 (0.22), residues: 498 sheet: 0.97 (0.25), residues: 402 loop : -0.23 (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 0.019 0.002 PHE G 54 TYR 0.010 0.001 TYR G 152 ARG 0.007 0.001 ARG E 94 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 627) hydrogen bonds : angle 4.03981 ( 1773) SS BOND : bond 0.00214 ( 9) SS BOND : angle 0.50781 ( 18) covalent geometry : bond 0.00321 (11652) covalent geometry : angle 0.49106 (15888) *********************** 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 311 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 279 time to evaluate : 1.201 Fit side-chains revert: symmetry clash REVERT: A 14 ASN cc_start: 0.8455 (m-40) cc_final: 0.8117 (m-40) REVERT: A 42 LYS cc_start: 0.7933 (tttt) cc_final: 0.7688 (tttt) REVERT: A 63 THR cc_start: 0.7704 (m) cc_final: 0.7358 (p) REVERT: A 68 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.7062 (mp) REVERT: A 132 GLU cc_start: 0.7430 (tt0) cc_final: 0.7027 (tm-30) REVERT: A 135 SER cc_start: 0.8110 (p) cc_final: 0.7859 (t) REVERT: A 158 SER cc_start: 0.7953 (t) cc_final: 0.7404 (p) REVERT: A 164 ASP cc_start: 0.8174 (m-30) cc_final: 0.7884 (m-30) REVERT: B 23 ARG cc_start: 0.7502 (ttt90) cc_final: 0.7089 (tpt170) REVERT: B 137 GLU cc_start: 0.6094 (tt0) cc_final: 0.5836 (tm-30) REVERT: B 149 ARG cc_start: 0.8692 (ttm-80) cc_final: 0.8385 (ttm-80) REVERT: C 53 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.6975 (t80) REVERT: C 73 GLN cc_start: 0.8514 (tp40) cc_final: 0.8244 (tp40) REVERT: C 107 MET cc_start: 0.7363 (mmm) cc_final: 0.6956 (mmt) REVERT: C 115 MET cc_start: 0.6897 (mtp) cc_final: 0.6681 (mtp) REVERT: D 26 THR cc_start: 0.8685 (p) cc_final: 0.8402 (m) REVERT: D 87 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8397 (mm-30) REVERT: D 118 VAL cc_start: 0.8735 (t) cc_final: 0.8438 (m) REVERT: D 154 THR cc_start: 0.8942 (m) cc_final: 0.8726 (m) REVERT: E 14 MET cc_start: 0.8605 (mtp) cc_final: 0.8345 (mtm) REVERT: E 23 ARG cc_start: 0.7485 (ttt90) cc_final: 0.7233 (tpt170) REVERT: E 39 ARG cc_start: 0.8438 (ttp-170) cc_final: 0.8235 (ttp-110) REVERT: E 69 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7711 (mm-30) REVERT: E 163 MET cc_start: 0.2941 (mtm) cc_final: 0.1826 (ptt) REVERT: G 14 ASN cc_start: 0.8243 (m-40) cc_final: 0.7962 (m-40) REVERT: G 63 THR cc_start: 0.7631 (t) cc_final: 0.7424 (p) REVERT: G 113 ASN cc_start: 0.8349 (t0) cc_final: 0.7840 (t0) REVERT: G 144 ASP cc_start: 0.8494 (p0) cc_final: 0.8203 (p0) REVERT: G 176 LEU cc_start: 0.7744 (tt) cc_final: 0.7397 (tp) REVERT: G 179 HIS cc_start: 0.8410 (t70) cc_final: 0.8193 (t70) REVERT: H 23 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.6308 (ttt-90) REVERT: H 86 GLU cc_start: 0.7326 (mm-30) cc_final: 0.6782 (mm-30) REVERT: H 163 MET cc_start: 0.3065 (mtm) cc_final: 0.2565 (ptt) outliers start: 32 outliers final: 23 residues processed: 289 average time/residue: 0.2560 time to fit residues: 104.3534 Evaluate side-chains 297 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 271 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain B residue 44 VAL 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 77 LYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 44 VAL 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 G residue 45 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 62 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 139 THR 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: 0.9990 chunk 13 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3728 r_free = 0.3728 target = 0.138219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.112732 restraints weight = 16523.533| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.27 r_work: 0.3218 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11661 Z= 0.200 Angle : 0.532 7.329 15906 Z= 0.279 Chirality : 0.044 0.128 1806 Planarity : 0.005 0.055 2055 Dihedral : 4.032 15.997 1653 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.32 % Allowed : 13.95 % Favored : 82.74 % 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: 1.77 (0.22), residues: 1440 helix: 2.93 (0.22), residues: 498 sheet: 0.89 (0.25), residues: 402 loop : -0.28 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 188 HIS 0.004 0.001 HIS G 27 PHE 0.027 0.002 PHE G 54 TYR 0.011 0.002 TYR D 11 ARG 0.007 0.001 ARG E 94 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 627) hydrogen bonds : angle 4.08431 ( 1773) SS BOND : bond 0.00327 ( 9) SS BOND : angle 0.53292 ( 18) covalent geometry : bond 0.00474 (11652) covalent geometry : angle 0.53184 (15888) *********************** 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 316 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 277 time to evaluate : 1.164 Fit side-chains revert: symmetry clash REVERT: A 14 ASN cc_start: 0.8470 (m-40) cc_final: 0.8136 (m-40) REVERT: A 42 LYS cc_start: 0.8014 (tttt) cc_final: 0.7744 (tttt) REVERT: A 68 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.7153 (mp) REVERT: A 132 GLU cc_start: 0.7446 (tt0) cc_final: 0.7066 (tm-30) REVERT: A 135 SER cc_start: 0.8174 (p) cc_final: 0.7908 (t) REVERT: A 158 SER cc_start: 0.7970 (t) cc_final: 0.7423 (p) REVERT: A 164 ASP cc_start: 0.8162 (m-30) cc_final: 0.7897 (m-30) REVERT: B 23 ARG cc_start: 0.7635 (ttt90) cc_final: 0.7329 (tpt-90) REVERT: B 82 ASN cc_start: 0.8364 (m-40) cc_final: 0.7670 (m-40) REVERT: B 137 GLU cc_start: 0.6164 (tt0) cc_final: 0.5962 (tm-30) REVERT: C 73 GLN cc_start: 0.8552 (tp40) cc_final: 0.8263 (tp40) REVERT: C 107 MET cc_start: 0.7375 (mmm) cc_final: 0.7092 (mmt) REVERT: D 26 THR cc_start: 0.8694 (p) cc_final: 0.8415 (m) REVERT: D 87 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8202 (mm-30) REVERT: D 118 VAL cc_start: 0.8755 (t) cc_final: 0.8444 (m) REVERT: D 154 THR cc_start: 0.8952 (m) cc_final: 0.8730 (m) REVERT: D 176 LEU cc_start: 0.7936 (tp) cc_final: 0.7720 (tp) REVERT: E 10 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8612 (pt0) REVERT: E 14 MET cc_start: 0.8595 (mtp) cc_final: 0.8327 (mtm) REVERT: E 23 ARG cc_start: 0.7450 (ttt90) cc_final: 0.7194 (tpt170) REVERT: E 30 TYR cc_start: 0.8551 (m-80) cc_final: 0.8273 (m-80) REVERT: E 39 ARG cc_start: 0.8443 (ttp-170) cc_final: 0.8241 (ttp-110) REVERT: F 77 ARG cc_start: 0.8664 (mmm-85) cc_final: 0.8329 (mtp180) REVERT: G 14 ASN cc_start: 0.8270 (m-40) cc_final: 0.8009 (m-40) REVERT: G 63 THR cc_start: 0.7698 (t) cc_final: 0.7480 (p) REVERT: G 113 ASN cc_start: 0.8372 (t0) cc_final: 0.7852 (t0) REVERT: G 144 ASP cc_start: 0.8523 (p0) cc_final: 0.8247 (p0) REVERT: G 176 LEU cc_start: 0.7821 (tt) cc_final: 0.7524 (tp) REVERT: G 179 HIS cc_start: 0.8414 (t70) cc_final: 0.8173 (t70) REVERT: H 23 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6364 (ttt-90) REVERT: H 86 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6727 (mm-30) REVERT: H 163 MET cc_start: 0.3044 (mtm) cc_final: 0.2599 (ptt) outliers start: 39 outliers final: 33 residues processed: 293 average time/residue: 0.2394 time to fit residues: 97.0936 Evaluate side-chains 307 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 271 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 68 LEU 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 E residue 176 GLU 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 75 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 139 THR Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain H residue 185 THR 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: 1.9990 chunk 49 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 138 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.138937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.113412 restraints weight = 16729.176| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.25 r_work: 0.3230 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11661 Z= 0.167 Angle : 0.509 5.784 15906 Z= 0.268 Chirality : 0.043 0.133 1806 Planarity : 0.005 0.054 2055 Dihedral : 3.955 14.836 1653 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.57 % Allowed : 14.20 % 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: 1.86 (0.22), residues: 1440 helix: 3.04 (0.22), residues: 498 sheet: 0.92 (0.25), residues: 402 loop : -0.26 (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 27 PHE 0.020 0.002 PHE D 54 TYR 0.010 0.001 TYR G 152 ARG 0.007 0.001 ARG E 94 Details of bonding type rmsd hydrogen bonds : bond 0.03928 ( 627) hydrogen bonds : angle 3.97110 ( 1773) SS BOND : bond 0.00272 ( 9) SS BOND : angle 0.48443 ( 18) covalent geometry : bond 0.00396 (11652) covalent geometry : angle 0.50896 (15888) *********************** 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 323 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 281 time to evaluate : 1.170 Fit side-chains revert: symmetry clash REVERT: A 14 ASN cc_start: 0.8443 (m-40) cc_final: 0.8147 (m-40) REVERT: A 42 LYS cc_start: 0.7993 (tttt) cc_final: 0.7729 (tttt) REVERT: A 68 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7136 (mp) REVERT: A 132 GLU cc_start: 0.7463 (tt0) cc_final: 0.7086 (tm-30) REVERT: A 135 SER cc_start: 0.8179 (p) cc_final: 0.7905 (t) REVERT: A 158 SER cc_start: 0.7984 (t) cc_final: 0.7431 (p) REVERT: A 164 ASP cc_start: 0.8189 (m-30) cc_final: 0.7894 (m-30) REVERT: B 23 ARG cc_start: 0.7507 (ttt90) cc_final: 0.7166 (tpt-90) REVERT: B 72 ARG cc_start: 0.8205 (ttm170) cc_final: 0.7956 (ttm170) REVERT: B 82 ASN cc_start: 0.8379 (m-40) cc_final: 0.7657 (m-40) REVERT: B 137 GLU cc_start: 0.6178 (tt0) cc_final: 0.5976 (tm-30) REVERT: B 149 ARG cc_start: 0.8695 (ttm-80) cc_final: 0.8387 (ttm-80) REVERT: C 73 GLN cc_start: 0.8521 (tp40) cc_final: 0.8268 (tp40) REVERT: C 107 MET cc_start: 0.7384 (mmm) cc_final: 0.7106 (mmt) REVERT: D 26 THR cc_start: 0.8682 (p) cc_final: 0.8412 (m) REVERT: D 87 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8287 (mm-30) REVERT: D 118 VAL cc_start: 0.8742 (t) cc_final: 0.8438 (m) REVERT: D 154 THR cc_start: 0.8944 (m) cc_final: 0.8726 (m) REVERT: D 176 LEU cc_start: 0.7864 (tp) cc_final: 0.7658 (tp) REVERT: E 10 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8593 (pt0) REVERT: E 14 MET cc_start: 0.8588 (mtp) cc_final: 0.8338 (mtm) REVERT: E 23 ARG cc_start: 0.7424 (ttt90) cc_final: 0.7148 (tpt170) REVERT: E 39 ARG cc_start: 0.8462 (ttp-170) cc_final: 0.8239 (ttp-110) REVERT: E 163 MET cc_start: 0.2894 (mtm) cc_final: 0.2150 (pmm) REVERT: F 77 ARG cc_start: 0.8652 (mmm-85) cc_final: 0.8332 (mtp180) REVERT: G 14 ASN cc_start: 0.8227 (m-40) cc_final: 0.7963 (m-40) REVERT: G 63 THR cc_start: 0.7671 (t) cc_final: 0.7449 (p) REVERT: G 113 ASN cc_start: 0.8382 (t0) cc_final: 0.7856 (t0) REVERT: G 144 ASP cc_start: 0.8494 (p0) cc_final: 0.8227 (p0) REVERT: G 176 LEU cc_start: 0.7840 (tt) cc_final: 0.7525 (tp) REVERT: G 179 HIS cc_start: 0.8389 (t70) cc_final: 0.8160 (t70) REVERT: H 23 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6296 (ttt-90) REVERT: H 86 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6711 (mm-30) REVERT: H 163 MET cc_start: 0.3038 (mtm) cc_final: 0.2633 (ptt) outliers start: 42 outliers final: 31 residues processed: 299 average time/residue: 0.2614 time to fit residues: 109.7821 Evaluate side-chains 312 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 278 time to evaluate : 1.148 ------------------------------------------------------------------------------- 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 68 LEU Chi-restraints excluded: chain A residue 75 LEU 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 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 160 MET Chi-restraints excluded: chain E residue 176 GLU 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 75 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 139 THR Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain H residue 185 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 5.9990 chunk 65 optimal weight: 0.0040 chunk 73 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.139168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.113733 restraints weight = 16787.442| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.24 r_work: 0.3203 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11661 Z= 0.161 Angle : 0.510 5.901 15906 Z= 0.267 Chirality : 0.043 0.175 1806 Planarity : 0.005 0.054 2055 Dihedral : 3.916 14.953 1653 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.74 % Allowed : 14.37 % Favored : 81.89 % 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: 1.91 (0.22), residues: 1440 helix: 3.05 (0.22), residues: 504 sheet: 0.94 (0.25), residues: 402 loop : -0.23 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 180 HIS 0.003 0.001 HIS H 174 PHE 0.021 0.002 PHE D 54 TYR 0.009 0.001 TYR G 152 ARG 0.008 0.001 ARG E 94 Details of bonding type rmsd hydrogen bonds : bond 0.03857 ( 627) hydrogen bonds : angle 3.94784 ( 1773) SS BOND : bond 0.00271 ( 9) SS BOND : angle 0.49908 ( 18) covalent geometry : bond 0.00382 (11652) covalent geometry : angle 0.50972 (15888) *********************** 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 325 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 281 time to evaluate : 1.184 Fit side-chains revert: symmetry clash REVERT: A 14 ASN cc_start: 0.8459 (m-40) cc_final: 0.8151 (m-40) REVERT: A 42 LYS cc_start: 0.7989 (tttt) cc_final: 0.7733 (tttt) REVERT: A 68 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7142 (mp) REVERT: A 132 GLU cc_start: 0.7426 (tt0) cc_final: 0.7032 (tm-30) REVERT: A 135 SER cc_start: 0.8154 (p) cc_final: 0.7882 (t) REVERT: A 158 SER cc_start: 0.7973 (t) cc_final: 0.7417 (p) REVERT: A 164 ASP cc_start: 0.8137 (m-30) cc_final: 0.7818 (m-30) REVERT: B 23 ARG cc_start: 0.7515 (ttt90) cc_final: 0.7189 (tpt-90) REVERT: B 72 ARG cc_start: 0.8178 (ttm170) cc_final: 0.7947 (ttm170) REVERT: B 82 ASN cc_start: 0.8380 (m-40) cc_final: 0.7653 (m-40) REVERT: B 137 GLU cc_start: 0.6222 (tt0) cc_final: 0.6020 (tm-30) REVERT: C 107 MET cc_start: 0.7433 (mmm) cc_final: 0.7164 (mmt) REVERT: D 26 THR cc_start: 0.8679 (p) cc_final: 0.8404 (m) REVERT: D 87 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8291 (mm-30) REVERT: D 118 VAL cc_start: 0.8741 (t) cc_final: 0.8417 (m) REVERT: D 154 THR cc_start: 0.8939 (m) cc_final: 0.8729 (m) REVERT: D 176 LEU cc_start: 0.7819 (tp) cc_final: 0.7614 (tp) REVERT: E 10 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8570 (pt0) REVERT: E 14 MET cc_start: 0.8576 (mtp) cc_final: 0.8329 (mtm) REVERT: E 39 ARG cc_start: 0.8441 (ttp-170) cc_final: 0.8214 (ttp-110) REVERT: E 163 MET cc_start: 0.2649 (mtm) cc_final: 0.2145 (ptt) REVERT: F 77 ARG cc_start: 0.8664 (mmm-85) cc_final: 0.8344 (mtp180) REVERT: G 14 ASN cc_start: 0.8258 (m-40) cc_final: 0.7974 (m-40) REVERT: G 25 TYR cc_start: 0.9046 (t80) cc_final: 0.8360 (t80) REVERT: G 113 ASN cc_start: 0.8397 (t0) cc_final: 0.7865 (t0) REVERT: G 144 ASP cc_start: 0.8496 (p0) cc_final: 0.8220 (p0) REVERT: G 176 LEU cc_start: 0.7894 (tt) cc_final: 0.7567 (tp) REVERT: G 179 HIS cc_start: 0.8378 (t70) cc_final: 0.8161 (t70) REVERT: H 23 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6232 (ttt-90) REVERT: H 86 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6743 (mm-30) REVERT: H 163 MET cc_start: 0.3028 (mtm) cc_final: 0.2635 (ptt) outliers start: 44 outliers final: 33 residues processed: 299 average time/residue: 0.2397 time to fit residues: 99.3028 Evaluate side-chains 319 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 283 time to evaluate : 1.092 ------------------------------------------------------------------------------- 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 68 LEU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain B residue 176 GLU 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 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 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 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 H residue 185 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 16 optimal weight: 0.5980 chunk 139 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 11 optimal weight: 0.0070 chunk 96 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 52 optimal weight: 0.0370 chunk 112 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 ASN ** E 156 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 = 0.3755 r_free = 0.3755 target = 0.140221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.114878 restraints weight = 16686.087| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.24 r_work: 0.3251 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11661 Z= 0.113 Angle : 0.481 5.876 15906 Z= 0.251 Chirality : 0.042 0.135 1806 Planarity : 0.005 0.053 2055 Dihedral : 3.764 14.221 1653 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.23 % Allowed : 14.80 % Favored : 81.97 % 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: 2.09 (0.23), residues: 1440 helix: 3.28 (0.22), residues: 501 sheet: 1.08 (0.26), residues: 399 loop : -0.23 (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 D 179 PHE 0.023 0.001 PHE G 54 TYR 0.008 0.001 TYR G 152 ARG 0.008 0.001 ARG H 94 Details of bonding type rmsd hydrogen bonds : bond 0.03442 ( 627) hydrogen bonds : angle 3.77344 ( 1773) SS BOND : bond 0.00185 ( 9) SS BOND : angle 0.42812 ( 18) covalent geometry : bond 0.00257 (11652) covalent geometry : angle 0.48057 (15888) *********************** 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 323 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 285 time to evaluate : 2.216 Fit side-chains revert: symmetry clash REVERT: A 14 ASN cc_start: 0.8412 (m-40) cc_final: 0.8093 (m-40) REVERT: A 42 LYS cc_start: 0.8017 (tttt) cc_final: 0.7764 (tttt) REVERT: A 63 THR cc_start: 0.7698 (m) cc_final: 0.7463 (p) REVERT: A 68 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7116 (mp) REVERT: A 132 GLU cc_start: 0.7465 (tt0) cc_final: 0.7088 (tm-30) REVERT: A 158 SER cc_start: 0.7758 (t) cc_final: 0.7187 (p) REVERT: B 23 ARG cc_start: 0.7547 (ttt90) cc_final: 0.7146 (tpt170) REVERT: B 82 ASN cc_start: 0.8399 (m-40) cc_final: 0.7680 (m-40) REVERT: B 149 ARG cc_start: 0.8653 (ttm-80) cc_final: 0.8337 (ttm-80) REVERT: C 73 GLN cc_start: 0.8495 (tp40) cc_final: 0.8271 (tp40) REVERT: C 107 MET cc_start: 0.7386 (mmm) cc_final: 0.7127 (mmt) REVERT: D 26 THR cc_start: 0.8648 (p) cc_final: 0.8393 (m) REVERT: D 87 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8349 (mm-30) REVERT: D 118 VAL cc_start: 0.8747 (t) cc_final: 0.8449 (m) REVERT: D 154 THR cc_start: 0.8929 (m) cc_final: 0.8726 (m) REVERT: D 176 LEU cc_start: 0.7852 (tp) cc_final: 0.7634 (tp) REVERT: E 10 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8706 (pt0) REVERT: E 23 ARG cc_start: 0.7512 (tpt170) cc_final: 0.7272 (tpt170) REVERT: E 137 GLU cc_start: 0.6064 (tt0) cc_final: 0.5839 (tm-30) REVERT: E 163 MET cc_start: 0.2581 (mtm) cc_final: 0.2232 (ptt) REVERT: G 14 ASN cc_start: 0.8215 (m-40) cc_final: 0.7940 (m-40) REVERT: G 25 TYR cc_start: 0.9023 (t80) cc_final: 0.8337 (t80) REVERT: G 87 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8509 (mm-30) REVERT: G 113 ASN cc_start: 0.8380 (t0) cc_final: 0.7860 (t0) REVERT: G 144 ASP cc_start: 0.8484 (p0) cc_final: 0.8187 (p0) REVERT: G 176 LEU cc_start: 0.7956 (tt) cc_final: 0.7564 (tp) REVERT: G 179 HIS cc_start: 0.8371 (t70) cc_final: 0.8147 (t70) REVERT: H 23 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6201 (ttt-90) REVERT: H 86 GLU cc_start: 0.7317 (mm-30) cc_final: 0.6782 (mm-30) REVERT: H 163 MET cc_start: 0.3129 (mtm) cc_final: 0.2630 (ptt) outliers start: 38 outliers final: 28 residues processed: 299 average time/residue: 0.3083 time to fit residues: 127.9459 Evaluate side-chains 309 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 278 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 68 LEU 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 61 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 81 LEU Chi-restraints excluded: chain F residue 111 THR 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 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 160 MET Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain I residue 49 LEU 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 107 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 91 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 127 optimal weight: 0.3980 chunk 135 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.139537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.114199 restraints weight = 16758.900| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.24 r_work: 0.3237 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11661 Z= 0.152 Angle : 0.510 6.180 15906 Z= 0.266 Chirality : 0.043 0.147 1806 Planarity : 0.005 0.053 2055 Dihedral : 3.851 14.839 1653 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.23 % Allowed : 14.97 % Favored : 81.80 % 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: 2.06 (0.23), residues: 1440 helix: 3.24 (0.22), residues: 504 sheet: 1.04 (0.26), residues: 402 loop : -0.23 (0.28), residues: 534 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 0.002 PHE D 54 TYR 0.009 0.001 TYR D 152 ARG 0.009 0.001 ARG E 94 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 627) hydrogen bonds : angle 3.85309 ( 1773) SS BOND : bond 0.00266 ( 9) SS BOND : angle 0.38449 ( 18) covalent geometry : bond 0.00361 (11652) covalent geometry : angle 0.51024 (15888) *********************** 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 324 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 286 time to evaluate : 1.485 Fit side-chains revert: symmetry clash REVERT: A 14 ASN cc_start: 0.8448 (m-40) cc_final: 0.8175 (m-40) REVERT: A 42 LYS cc_start: 0.8003 (tttt) cc_final: 0.7742 (tttt) REVERT: A 68 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7117 (mp) REVERT: A 132 GLU cc_start: 0.7462 (tt0) cc_final: 0.7072 (tm-30) REVERT: A 135 SER cc_start: 0.8100 (p) cc_final: 0.7854 (t) REVERT: A 158 SER cc_start: 0.7778 (t) cc_final: 0.7183 (p) REVERT: B 23 ARG cc_start: 0.7577 (ttt90) cc_final: 0.7148 (tpt170) REVERT: B 72 ARG cc_start: 0.8264 (ttm170) cc_final: 0.7975 (ttm170) REVERT: B 82 ASN cc_start: 0.8393 (m-40) cc_final: 0.7625 (m-40) REVERT: B 149 ARG cc_start: 0.8693 (ttm-80) cc_final: 0.8359 (ttm-80) REVERT: C 73 GLN cc_start: 0.8510 (tp40) cc_final: 0.8273 (tp40) REVERT: C 107 MET cc_start: 0.7397 (mmm) cc_final: 0.7143 (mmt) REVERT: D 26 THR cc_start: 0.8678 (p) cc_final: 0.8437 (m) REVERT: D 87 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8372 (mm-30) REVERT: D 118 VAL cc_start: 0.8742 (t) cc_final: 0.8420 (m) REVERT: D 154 THR cc_start: 0.8939 (m) cc_final: 0.8733 (m) REVERT: E 10 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8396 (pt0) REVERT: E 137 GLU cc_start: 0.6059 (tt0) cc_final: 0.5844 (tm-30) REVERT: E 163 MET cc_start: 0.2577 (mtm) cc_final: 0.2259 (ptt) REVERT: G 14 ASN cc_start: 0.8259 (m-40) cc_final: 0.7959 (m-40) REVERT: G 25 TYR cc_start: 0.9051 (t80) cc_final: 0.8211 (t80) REVERT: G 87 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8508 (mm-30) REVERT: G 113 ASN cc_start: 0.8394 (t0) cc_final: 0.7875 (t0) REVERT: G 144 ASP cc_start: 0.8537 (p0) cc_final: 0.8242 (p0) REVERT: G 176 LEU cc_start: 0.7959 (tt) cc_final: 0.7594 (tp) REVERT: G 179 HIS cc_start: 0.8416 (t70) cc_final: 0.8178 (t70) REVERT: H 14 MET cc_start: 0.8332 (mtp) cc_final: 0.8001 (mtm) REVERT: H 23 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6257 (ttt-90) REVERT: H 86 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6715 (mm-30) REVERT: H 163 MET cc_start: 0.3140 (mtm) cc_final: 0.2659 (ptt) outliers start: 38 outliers final: 30 residues processed: 299 average time/residue: 0.3138 time to fit residues: 128.7749 Evaluate side-chains 314 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 281 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 68 LEU 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 61 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 115 MET 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 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 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 H residue 185 THR Chi-restraints excluded: chain I residue 49 LEU 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 107 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 41 optimal weight: 0.0030 chunk 124 optimal weight: 0.9980 chunk 82 optimal weight: 0.1980 chunk 93 optimal weight: 0.5980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 ASN 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 = 0.3754 r_free = 0.3754 target = 0.140162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.114789 restraints weight = 16606.465| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.24 r_work: 0.3245 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11661 Z= 0.130 Angle : 0.500 7.637 15906 Z= 0.259 Chirality : 0.042 0.140 1806 Planarity : 0.005 0.053 2055 Dihedral : 3.794 14.374 1653 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.89 % Allowed : 15.90 % Favored : 81.21 % 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: 2.14 (0.23), residues: 1440 helix: 3.33 (0.22), residues: 504 sheet: 1.13 (0.26), residues: 399 loop : -0.24 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 180 HIS 0.002 0.001 HIS G 7 PHE 0.017 0.001 PHE D 54 TYR 0.009 0.001 TYR D 152 ARG 0.009 0.001 ARG E 94 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 627) hydrogen bonds : angle 3.78798 ( 1773) SS BOND : bond 0.00214 ( 9) SS BOND : angle 0.37134 ( 18) covalent geometry : bond 0.00303 (11652) covalent geometry : angle 0.50037 (15888) ********************** 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 315 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 281 time to evaluate : 1.404 Fit side-chains revert: symmetry clash REVERT: A 14 ASN cc_start: 0.8417 (m-40) cc_final: 0.8124 (m-40) REVERT: A 42 LYS cc_start: 0.7996 (tttt) cc_final: 0.7751 (tttt) REVERT: A 68 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.7125 (mp) REVERT: A 132 GLU cc_start: 0.7479 (tt0) cc_final: 0.7098 (tm-30) REVERT: A 135 SER cc_start: 0.8100 (p) cc_final: 0.7857 (t) REVERT: A 158 SER cc_start: 0.7762 (t) cc_final: 0.7177 (p) REVERT: B 23 ARG cc_start: 0.7570 (ttt90) cc_final: 0.7118 (tpt170) REVERT: B 72 ARG cc_start: 0.8183 (ttm170) cc_final: 0.7982 (ttm170) REVERT: B 82 ASN cc_start: 0.8381 (m-40) cc_final: 0.7634 (m-40) REVERT: C 73 GLN cc_start: 0.8510 (tp40) cc_final: 0.8273 (tp40) REVERT: C 77 ARG cc_start: 0.8717 (mmm-85) cc_final: 0.8331 (mtm180) REVERT: C 107 MET cc_start: 0.7397 (mmm) cc_final: 0.7143 (mmt) REVERT: D 26 THR cc_start: 0.8673 (p) cc_final: 0.8401 (m) REVERT: D 87 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8359 (mm-30) REVERT: D 118 VAL cc_start: 0.8746 (t) cc_final: 0.8433 (m) REVERT: E 10 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8693 (pt0) REVERT: E 137 GLU cc_start: 0.6013 (tt0) cc_final: 0.5799 (tm-30) REVERT: E 163 MET cc_start: 0.2609 (mtm) cc_final: 0.2364 (ptt) REVERT: G 14 ASN cc_start: 0.8220 (m-40) cc_final: 0.7961 (m-40) REVERT: G 25 TYR cc_start: 0.9033 (t80) cc_final: 0.8289 (t80) REVERT: G 87 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8498 (mm-30) REVERT: G 113 ASN cc_start: 0.8448 (t0) cc_final: 0.7939 (t0) REVERT: G 144 ASP cc_start: 0.8509 (p0) cc_final: 0.8200 (p0) REVERT: G 176 LEU cc_start: 0.7925 (tt) cc_final: 0.7536 (tp) REVERT: G 179 HIS cc_start: 0.8398 (t70) cc_final: 0.8163 (t70) REVERT: H 14 MET cc_start: 0.8318 (mtp) cc_final: 0.7995 (mtm) REVERT: H 23 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6183 (ttt-90) REVERT: H 30 TYR cc_start: 0.8572 (m-80) cc_final: 0.8349 (m-80) REVERT: H 86 GLU cc_start: 0.7318 (mm-30) cc_final: 0.6792 (mm-30) REVERT: H 163 MET cc_start: 0.3095 (mtm) cc_final: 0.2638 (ptt) outliers start: 34 outliers final: 29 residues processed: 292 average time/residue: 0.3050 time to fit residues: 123.1563 Evaluate side-chains 310 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 278 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 68 LEU 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 61 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 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 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 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain I residue 49 LEU 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 107 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 65 optimal weight: 0.0570 chunk 95 optimal weight: 0.0170 chunk 85 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3747 r_free = 0.3747 target = 0.139609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.114160 restraints weight = 16613.099| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.24 r_work: 0.3239 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11661 Z= 0.145 Angle : 0.514 7.444 15906 Z= 0.266 Chirality : 0.043 0.141 1806 Planarity : 0.005 0.053 2055 Dihedral : 3.834 15.378 1653 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.98 % Allowed : 15.82 % Favored : 81.21 % 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: 2.07 (0.23), residues: 1440 helix: 3.32 (0.22), residues: 501 sheet: 1.07 (0.26), residues: 399 loop : -0.30 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 180 HIS 0.003 0.001 HIS H 177 PHE 0.018 0.002 PHE A 54 TYR 0.009 0.001 TYR G 152 ARG 0.009 0.001 ARG E 94 Details of bonding type rmsd hydrogen bonds : bond 0.03572 ( 627) hydrogen bonds : angle 3.82859 ( 1773) SS BOND : bond 0.00247 ( 9) SS BOND : angle 0.36827 ( 18) covalent geometry : bond 0.00343 (11652) covalent geometry : angle 0.51386 (15888) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7006.00 seconds wall clock time: 123 minutes 36.38 seconds (7416.38 seconds total)