Starting phenix.real_space_refine on Wed May 14 03:14:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vsp_43501/05_2025/8vsp_43501.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vsp_43501/05_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_43501/05_2025/8vsp_43501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vsp_43501/05_2025/8vsp_43501.map" model { file = "/net/cci-nas-00/data/ceres_data/8vsp_43501/05_2025/8vsp_43501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vsp_43501/05_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-5687/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: 5.54, 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: 2.75 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: 1.25 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: 3.42 Time building geometry restraints manager: 3.24 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: 0.07 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.100 Process input model: 25.610 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.310 ------------------------------------------------------------------------------- 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 : 1.271 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: 0.2504 time to fit residues: 117.3842 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 : 1.163 ------------------------------------------------------------------------------- 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 = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.114408 restraints weight = 16490.596| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.29 r_work: 0.3249 rms_B_bonded: 2.85 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 : 1.284 Fit side-chains REVERT: A 14 ASN cc_start: 0.8478 (m-40) cc_final: 0.8251 (m-40) REVERT: A 42 LYS cc_start: 0.7933 (tttt) cc_final: 0.7646 (tttt) REVERT: A 63 THR cc_start: 0.7695 (m) cc_final: 0.7334 (p) REVERT: A 135 SER cc_start: 0.8118 (p) cc_final: 0.7860 (t) REVERT: A 158 SER cc_start: 0.7915 (t) cc_final: 0.7379 (p) REVERT: A 164 ASP cc_start: 0.8236 (m-30) cc_final: 0.7962 (m-30) REVERT: B 14 MET cc_start: 0.8514 (mtp) cc_final: 0.8310 (mtm) REVERT: B 23 ARG cc_start: 0.7610 (ttt90) cc_final: 0.7305 (tpt170) REVERT: C 53 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.7279 (t80) REVERT: C 73 GLN cc_start: 0.8521 (tp40) cc_final: 0.8248 (tp40) REVERT: C 107 MET cc_start: 0.7372 (mmm) cc_final: 0.6925 (mmt) REVERT: C 115 MET cc_start: 0.6677 (mtp) cc_final: 0.6351 (mtp) REVERT: D 14 ASN cc_start: 0.8376 (m-40) cc_final: 0.8132 (m-40) REVERT: D 105 ASN cc_start: 0.8659 (t0) cc_final: 0.8249 (m-40) REVERT: D 118 VAL cc_start: 0.8693 (t) cc_final: 0.8446 (m) REVERT: D 154 THR cc_start: 0.8913 (m) cc_final: 0.8706 (m) REVERT: E 14 MET cc_start: 0.8616 (mtp) cc_final: 0.8362 (mtm) REVERT: E 23 ARG cc_start: 0.7478 (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: 0.7792 (p) cc_final: 0.7517 (t) REVERT: E 163 MET cc_start: 0.2735 (mtm) cc_final: 0.1892 (ptt) REVERT: G 14 ASN cc_start: 0.8377 (m-40) cc_final: 0.8112 (m-40) REVERT: G 43 GLU cc_start: 0.7634 (tp30) cc_final: 0.7425 (tp30) REVERT: G 82 THR cc_start: 0.8254 (p) cc_final: 0.8046 (p) REVERT: G 144 ASP cc_start: 0.8474 (p0) cc_final: 0.8218 (p0) REVERT: G 176 LEU cc_start: 0.7647 (tt) cc_final: 0.7303 (tp) REVERT: G 179 HIS cc_start: 0.8460 (t70) cc_final: 0.8158 (t70) REVERT: H 22 GLU cc_start: 0.6594 (mt-10) cc_final: 0.6300 (mt-10) REVERT: H 23 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6939 (tpt170) REVERT: H 163 MET cc_start: 0.3201 (mtm) cc_final: 0.2657 (ptt) REVERT: I 72 TYR cc_start: 0.8755 (t80) cc_final: 0.8484 (t80) outliers start: 36 outliers final: 18 residues processed: 306 average time/residue: 0.2291 time to fit residues: 98.8746 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 : 1.165 ------------------------------------------------------------------------------- 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 = 0.139072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.113522 restraints weight = 16844.977| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.27 r_work: 0.3226 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11661 Z= 0.167 Angle : 0.524 6.574 15906 Z= 0.275 Chirality : 0.044 0.137 1806 Planarity : 0.005 0.056 2055 Dihedral : 4.008 16.637 1653 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.72 % Allowed : 12.67 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (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 0.014 0.002 PHE G 54 TYR 0.012 0.001 TYR B 60 ARG 0.005 0.001 ARG E 94 Details of bonding type rmsd hydrogen bonds : bond 0.04524 ( 627) hydrogen bonds : angle 4.29823 ( 1773) SS BOND : bond 0.00263 ( 9) SS BOND : angle 0.60635 ( 18) covalent geometry : bond 0.00389 (11652) covalent geometry : angle 0.52395 (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 310 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 278 time to evaluate : 1.455 Fit side-chains revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7972 (tttt) cc_final: 0.7697 (tttt) REVERT: A 51 LEU cc_start: 0.8053 (mt) cc_final: 0.7843 (mp) REVERT: A 63 THR cc_start: 0.7773 (m) cc_final: 0.7411 (p) REVERT: A 68 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.7113 (mp) REVERT: A 132 GLU cc_start: 0.7411 (tt0) cc_final: 0.7026 (tm-30) REVERT: A 135 SER cc_start: 0.8082 (p) cc_final: 0.7828 (t) REVERT: A 158 SER cc_start: 0.7948 (t) cc_final: 0.7408 (p) REVERT: A 164 ASP cc_start: 0.8190 (m-30) cc_final: 0.7920 (m-30) REVERT: B 14 MET cc_start: 0.8464 (mtp) cc_final: 0.8262 (mtm) REVERT: B 23 ARG cc_start: 0.7598 (ttt90) cc_final: 0.7276 (tpt170) REVERT: B 149 ARG cc_start: 0.8688 (ttm-80) cc_final: 0.8433 (ttm-80) REVERT: B 163 MET cc_start: 0.2576 (ttm) cc_final: 0.1380 (ptt) REVERT: C 53 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7130 (t80) REVERT: C 73 GLN cc_start: 0.8558 (tp40) cc_final: 0.8262 (tp40) REVERT: C 107 MET cc_start: 0.7391 (mmm) cc_final: 0.7001 (mmt) REVERT: D 14 ASN cc_start: 0.8311 (m-40) cc_final: 0.8083 (m110) REVERT: D 105 ASN cc_start: 0.8653 (t0) cc_final: 0.8166 (m-40) REVERT: D 118 VAL cc_start: 0.8738 (t) cc_final: 0.8441 (m) REVERT: D 154 THR cc_start: 0.8945 (m) cc_final: 0.8726 (m) REVERT: D 176 LEU cc_start: 0.7952 (tt) cc_final: 0.7727 (tp) REVERT: E 14 MET cc_start: 0.8622 (mtp) cc_final: 0.8342 (mtm) REVERT: E 23 ARG cc_start: 0.7522 (ttt90) cc_final: 0.7259 (tpt170) REVERT: E 39 ARG cc_start: 0.8433 (ttp-170) cc_final: 0.8211 (ttp-170) REVERT: E 70 ARG cc_start: 0.7709 (ttt180) cc_final: 0.7474 (ttt-90) REVERT: E 163 MET cc_start: 0.2799 (mtm) cc_final: 0.1811 (ptt) REVERT: G 14 ASN cc_start: 0.8306 (m-40) cc_final: 0.8022 (m-40) REVERT: G 63 THR cc_start: 0.7707 (t) cc_final: 0.7456 (p) REVERT: G 113 ASN cc_start: 0.8339 (t0) cc_final: 0.7869 (t0) REVERT: G 144 ASP cc_start: 0.8529 (p0) cc_final: 0.8266 (p0) REVERT: G 176 LEU cc_start: 0.7726 (tt) cc_final: 0.7386 (tp) REVERT: G 179 HIS cc_start: 0.8462 (t70) cc_final: 0.8209 (t70) REVERT: H 22 GLU cc_start: 0.6532 (mt-10) cc_final: 0.6320 (mt-10) REVERT: H 23 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6305 (ttt-90) REVERT: H 86 GLU cc_start: 0.7357 (mm-30) cc_final: 0.6807 (mm-30) REVERT: H 163 MET cc_start: 0.3107 (mtm) cc_final: 0.2513 (ptt) outliers start: 32 outliers final: 25 residues processed: 289 average time/residue: 0.2381 time to fit residues: 95.8410 Evaluate side-chains 296 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 268 time to evaluate : 1.182 ------------------------------------------------------------------------------- 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: 0.0980 chunk 52 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 116 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 143 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 ASN G 120 ASN H 64 GLN ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.137078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.111697 restraints weight = 16706.853| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.27 r_work: 0.3234 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11661 Z= 0.151 Angle : 0.498 5.797 15906 Z= 0.262 Chirality : 0.043 0.131 1806 Planarity : 0.005 0.054 2055 Dihedral : 3.941 14.284 1653 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.98 % Allowed : 13.78 % 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: 1.87 (0.22), residues: 1440 helix: 3.04 (0.22), residues: 498 sheet: 0.93 (0.25), residues: 402 loop : -0.24 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 180 HIS 0.005 0.001 HIS G 27 PHE 0.019 0.002 PHE G 54 TYR 0.010 0.001 TYR G 152 ARG 0.006 0.001 ARG E 94 Details of bonding type rmsd hydrogen bonds : bond 0.04017 ( 627) hydrogen bonds : angle 4.08283 ( 1773) SS BOND : bond 0.00242 ( 9) SS BOND : angle 0.51781 ( 18) covalent geometry : bond 0.00352 (11652) covalent geometry : angle 0.49833 (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 313 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 278 time to evaluate : 1.213 Fit side-chains revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7951 (tttt) cc_final: 0.7710 (tttt) REVERT: A 63 THR cc_start: 0.7745 (m) cc_final: 0.7413 (p) REVERT: A 68 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.7090 (mp) REVERT: A 132 GLU cc_start: 0.7404 (tt0) cc_final: 0.7008 (tm-30) REVERT: A 135 SER cc_start: 0.8149 (p) cc_final: 0.7887 (t) REVERT: A 158 SER cc_start: 0.7964 (t) cc_final: 0.7419 (p) REVERT: A 164 ASP cc_start: 0.8225 (m-30) cc_final: 0.7932 (m-30) REVERT: B 23 ARG cc_start: 0.7510 (ttt90) cc_final: 0.7106 (tpt170) REVERT: B 137 GLU cc_start: 0.6086 (tt0) cc_final: 0.5832 (tm-30) REVERT: B 149 ARG cc_start: 0.8707 (ttm-80) cc_final: 0.8405 (ttm-80) REVERT: C 53 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.7008 (t80) REVERT: C 73 GLN cc_start: 0.8533 (tp40) cc_final: 0.8264 (tp40) REVERT: C 107 MET cc_start: 0.7361 (mmm) cc_final: 0.6997 (mmt) REVERT: D 26 THR cc_start: 0.8707 (p) cc_final: 0.8407 (m) REVERT: D 87 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8404 (mm-30) REVERT: D 105 ASN cc_start: 0.8624 (t0) cc_final: 0.8298 (m-40) REVERT: D 118 VAL cc_start: 0.8745 (t) cc_final: 0.8464 (m) REVERT: D 154 THR cc_start: 0.8950 (m) cc_final: 0.8728 (m) REVERT: E 10 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8577 (pt0) REVERT: E 14 MET cc_start: 0.8603 (mtp) cc_final: 0.8352 (mtm) REVERT: E 23 ARG cc_start: 0.7453 (ttt90) cc_final: 0.7211 (tpt170) REVERT: E 39 ARG cc_start: 0.8448 (ttp-170) cc_final: 0.8245 (ttp-110) REVERT: E 69 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7716 (mm-30) REVERT: E 137 GLU cc_start: 0.5967 (tt0) cc_final: 0.5752 (tm-30) REVERT: E 163 MET cc_start: 0.2934 (mtm) cc_final: 0.1816 (ptt) REVERT: G 14 ASN cc_start: 0.8263 (m-40) cc_final: 0.7991 (m-40) REVERT: G 63 THR cc_start: 0.7665 (t) cc_final: 0.7431 (p) REVERT: G 113 ASN cc_start: 0.8354 (t0) cc_final: 0.7857 (t0) REVERT: G 144 ASP cc_start: 0.8519 (p0) cc_final: 0.8229 (p0) REVERT: G 176 LEU cc_start: 0.7781 (tt) cc_final: 0.7474 (tp) REVERT: G 179 HIS cc_start: 0.8422 (t70) cc_final: 0.8164 (t70) REVERT: H 23 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.6316 (ttt-90) REVERT: H 86 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6757 (mm-30) REVERT: H 163 MET cc_start: 0.3059 (mtm) cc_final: 0.2563 (ptt) outliers start: 35 outliers final: 24 residues processed: 290 average time/residue: 0.2396 time to fit residues: 96.7686 Evaluate side-chains 300 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 272 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 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 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 107 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: 0.8980 chunk 4 optimal weight: 0.0060 chunk 17 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 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: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 ASN 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 = 0.3745 r_free = 0.3745 target = 0.139321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.113951 restraints weight = 16541.860| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.26 r_work: 0.3238 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2742 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= 0.136 Angle : 0.489 6.727 15906 Z= 0.256 Chirality : 0.042 0.129 1806 Planarity : 0.005 0.054 2055 Dihedral : 3.845 14.413 1653 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.98 % Allowed : 13.95 % Favored : 83.08 % 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: 1.95 (0.23), residues: 1440 helix: 3.11 (0.22), residues: 501 sheet: 0.99 (0.25), residues: 402 loop : -0.24 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 180 HIS 0.003 0.001 HIS G 7 PHE 0.026 0.002 PHE G 54 TYR 0.012 0.001 TYR B 60 ARG 0.006 0.000 ARG E 94 Details of bonding type rmsd hydrogen bonds : bond 0.03777 ( 627) hydrogen bonds : angle 3.91467 ( 1773) SS BOND : bond 0.00210 ( 9) SS BOND : angle 0.42596 ( 18) covalent geometry : bond 0.00314 (11652) covalent geometry : angle 0.48883 (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 315 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 280 time to evaluate : 1.163 Fit side-chains revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7968 (tttt) cc_final: 0.7734 (tttt) REVERT: A 63 THR cc_start: 0.7768 (m) cc_final: 0.7421 (p) REVERT: A 68 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7082 (mp) REVERT: A 132 GLU cc_start: 0.7438 (tt0) cc_final: 0.7050 (tm-30) REVERT: A 135 SER cc_start: 0.8155 (p) cc_final: 0.7888 (t) REVERT: A 158 SER cc_start: 0.7740 (t) cc_final: 0.7170 (p) REVERT: B 23 ARG cc_start: 0.7515 (ttt90) cc_final: 0.7071 (tpt170) REVERT: B 137 GLU cc_start: 0.6120 (tt0) cc_final: 0.5866 (tm-30) REVERT: B 149 ARG cc_start: 0.8681 (ttm-80) cc_final: 0.8370 (ttm-80) REVERT: C 73 GLN cc_start: 0.8512 (tp40) cc_final: 0.8259 (tp40) REVERT: C 107 MET cc_start: 0.7374 (mmm) cc_final: 0.7003 (mmt) REVERT: D 26 THR cc_start: 0.8661 (p) cc_final: 0.8400 (m) REVERT: D 87 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8201 (mm-30) REVERT: D 118 VAL cc_start: 0.8747 (t) cc_final: 0.8446 (m) REVERT: D 154 THR cc_start: 0.8940 (m) cc_final: 0.8725 (m) REVERT: D 176 LEU cc_start: 0.7919 (tp) cc_final: 0.7716 (tp) REVERT: E 14 MET cc_start: 0.8597 (mtp) cc_final: 0.8344 (mtm) REVERT: E 23 ARG cc_start: 0.7439 (ttt90) cc_final: 0.7215 (tpt170) REVERT: E 163 MET cc_start: 0.2950 (mtm) cc_final: 0.1823 (ptt) REVERT: F 77 ARG cc_start: 0.8638 (mmm-85) cc_final: 0.8342 (mtp180) REVERT: G 14 ASN cc_start: 0.8234 (m-40) cc_final: 0.7972 (m-40) REVERT: G 63 THR cc_start: 0.7638 (t) cc_final: 0.7427 (p) REVERT: G 113 ASN cc_start: 0.8355 (t0) cc_final: 0.7853 (t0) REVERT: G 144 ASP cc_start: 0.8522 (p0) cc_final: 0.8241 (p0) REVERT: G 176 LEU cc_start: 0.7805 (tt) cc_final: 0.7459 (tp) REVERT: G 179 HIS cc_start: 0.8401 (t70) cc_final: 0.8161 (t70) REVERT: H 23 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.6356 (ttt-90) REVERT: H 86 GLU cc_start: 0.7277 (mm-30) cc_final: 0.6735 (mm-30) REVERT: H 163 MET cc_start: 0.3097 (mtm) cc_final: 0.2610 (ptt) outliers start: 35 outliers final: 29 residues processed: 293 average time/residue: 0.2448 time to fit residues: 99.2278 Evaluate side-chains 304 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 273 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 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 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 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: 1.9990 chunk 14 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 139 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN ** 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 = 0.3738 r_free = 0.3738 target = 0.138693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.112431 restraints weight = 16590.324| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.28 r_work: 0.3214 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 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 0.041 11661 Z= 0.177 Angle : 0.518 5.839 15906 Z= 0.272 Chirality : 0.044 0.128 1806 Planarity : 0.005 0.054 2055 Dihedral : 3.951 15.310 1653 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.91 % Allowed : 13.78 % Favored : 82.31 % 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: 1.90 (0.22), residues: 1440 helix: 3.05 (0.22), residues: 501 sheet: 0.94 (0.25), residues: 402 loop : -0.23 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 131 HIS 0.003 0.001 HIS H 177 PHE 0.021 0.002 PHE D 54 TYR 0.011 0.001 TYR B 60 ARG 0.008 0.001 ARG E 48 Details of bonding type rmsd hydrogen bonds : bond 0.03974 ( 627) hydrogen bonds : angle 3.96932 ( 1773) SS BOND : bond 0.00305 ( 9) SS BOND : angle 0.47895 ( 18) covalent geometry : bond 0.00421 (11652) covalent geometry : angle 0.51759 (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 324 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 278 time to evaluate : 1.208 Fit side-chains revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7970 (tttt) cc_final: 0.7707 (tttt) REVERT: A 68 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.7124 (mp) REVERT: A 132 GLU cc_start: 0.7455 (tt0) cc_final: 0.7065 (tm-30) REVERT: A 135 SER cc_start: 0.8120 (p) cc_final: 0.7854 (t) REVERT: A 158 SER cc_start: 0.7986 (t) cc_final: 0.7433 (p) REVERT: B 23 ARG cc_start: 0.7541 (ttt90) cc_final: 0.7212 (tpt-90) REVERT: B 82 ASN cc_start: 0.8377 (m-40) cc_final: 0.7666 (m-40) REVERT: B 137 GLU cc_start: 0.6179 (tt0) cc_final: 0.5976 (tm-30) REVERT: B 149 ARG cc_start: 0.8694 (ttm-80) cc_final: 0.8386 (ttm-80) REVERT: C 73 GLN cc_start: 0.8528 (tp40) cc_final: 0.8279 (tp40) REVERT: C 107 MET cc_start: 0.7386 (mmm) cc_final: 0.7112 (mmt) REVERT: C 115 MET cc_start: 0.6819 (mtp) cc_final: 0.6552 (mtp) REVERT: D 26 THR cc_start: 0.8684 (p) cc_final: 0.8422 (m) REVERT: D 87 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8289 (mm-30) REVERT: D 118 VAL cc_start: 0.8742 (t) cc_final: 0.8436 (m) REVERT: D 154 THR cc_start: 0.8949 (m) cc_final: 0.8734 (m) REVERT: D 176 LEU cc_start: 0.7858 (tp) cc_final: 0.7641 (tp) REVERT: E 10 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8396 (pt0) REVERT: E 14 MET cc_start: 0.8600 (mtp) cc_final: 0.8350 (mtm) REVERT: E 30 TYR cc_start: 0.8540 (m-80) cc_final: 0.8273 (m-80) REVERT: F 77 ARG cc_start: 0.8656 (mmm-85) cc_final: 0.8349 (mtp180) REVERT: G 14 ASN cc_start: 0.8250 (m-40) cc_final: 0.7982 (m-40) REVERT: G 63 THR cc_start: 0.7681 (t) cc_final: 0.7456 (p) REVERT: G 113 ASN cc_start: 0.8383 (t0) cc_final: 0.7859 (t0) REVERT: G 144 ASP cc_start: 0.8536 (p0) cc_final: 0.8268 (p0) REVERT: G 176 LEU cc_start: 0.7837 (tt) cc_final: 0.7526 (tp) REVERT: G 179 HIS cc_start: 0.8399 (t70) cc_final: 0.8170 (t70) REVERT: H 23 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.6285 (ttt-90) REVERT: H 86 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6724 (mm-30) REVERT: H 163 MET cc_start: 0.3040 (mtm) cc_final: 0.2596 (ptt) outliers start: 46 outliers final: 35 residues processed: 298 average time/residue: 0.2436 time to fit residues: 100.2334 Evaluate side-chains 312 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 274 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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 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 95 MET 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 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: 0.0170 chunk 65 optimal weight: 0.1980 chunk 73 optimal weight: 0.3980 chunk 130 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 108 optimal weight: 0.0020 chunk 13 optimal weight: 2.9990 overall best weight: 0.2226 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 ASN ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN H 64 GLN I 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.140837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.115665 restraints weight = 16787.794| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.27 r_work: 0.3236 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11661 Z= 0.095 Angle : 0.464 5.717 15906 Z= 0.243 Chirality : 0.042 0.174 1806 Planarity : 0.005 0.054 2055 Dihedral : 3.653 13.315 1653 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.55 % Allowed : 15.65 % 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: 2.27 (0.23), residues: 1440 helix: 3.43 (0.22), residues: 504 sheet: 1.17 (0.26), residues: 399 loop : -0.14 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 180 HIS 0.002 0.001 HIS E 174 PHE 0.018 0.001 PHE D 54 TYR 0.007 0.001 TYR G 152 ARG 0.006 0.000 ARG E 94 Details of bonding type rmsd hydrogen bonds : bond 0.03238 ( 627) hydrogen bonds : angle 3.70461 ( 1773) SS BOND : bond 0.00155 ( 9) SS BOND : angle 0.43417 ( 18) covalent geometry : bond 0.00207 (11652) covalent geometry : angle 0.46442 (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 318 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 288 time to evaluate : 1.356 Fit side-chains revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7994 (tttt) cc_final: 0.7759 (tttt) REVERT: A 68 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6963 (mp) REVERT: A 132 GLU cc_start: 0.7468 (tt0) cc_final: 0.7055 (tm-30) REVERT: A 135 SER cc_start: 0.8142 (p) cc_final: 0.7862 (t) REVERT: B 23 ARG cc_start: 0.7541 (ttt90) cc_final: 0.7156 (tpt170) REVERT: B 82 ASN cc_start: 0.8371 (m-40) cc_final: 0.7688 (m-40) REVERT: B 149 ARG cc_start: 0.8633 (ttm-80) cc_final: 0.8322 (ttm-80) REVERT: C 73 GLN cc_start: 0.8498 (tp40) cc_final: 0.8270 (tp40) REVERT: C 107 MET cc_start: 0.7336 (mmm) cc_final: 0.7031 (mmt) REVERT: C 115 MET cc_start: 0.6772 (mtp) cc_final: 0.6531 (mtp) REVERT: D 26 THR cc_start: 0.8571 (p) cc_final: 0.8358 (m) REVERT: D 87 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8238 (mm-30) REVERT: D 105 ASN cc_start: 0.8576 (t0) cc_final: 0.8266 (m-40) REVERT: D 118 VAL cc_start: 0.8736 (t) cc_final: 0.8449 (m) REVERT: D 176 LEU cc_start: 0.7805 (tp) cc_final: 0.7599 (tp) REVERT: E 10 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8506 (pt0) REVERT: E 137 GLU cc_start: 0.6015 (tt0) cc_final: 0.5747 (tm-30) REVERT: E 163 MET cc_start: 0.2770 (mtm) cc_final: 0.2265 (ptp) REVERT: G 14 ASN cc_start: 0.8156 (m-40) cc_final: 0.7906 (m-40) REVERT: G 25 TYR cc_start: 0.8969 (t80) cc_final: 0.8308 (t80) REVERT: G 113 ASN cc_start: 0.8373 (t0) cc_final: 0.7862 (t0) REVERT: G 144 ASP cc_start: 0.8451 (p0) cc_final: 0.8141 (p0) REVERT: G 176 LEU cc_start: 0.7757 (tt) cc_final: 0.7405 (tp) REVERT: G 179 HIS cc_start: 0.8353 (t70) cc_final: 0.8135 (t70) REVERT: H 23 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6250 (ttt-90) REVERT: H 86 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6723 (mm-30) REVERT: H 163 MET cc_start: 0.3047 (mtm) cc_final: 0.2532 (ptt) REVERT: I 67 THR cc_start: 0.8503 (t) cc_final: 0.8301 (p) outliers start: 30 outliers final: 19 residues processed: 300 average time/residue: 0.2466 time to fit residues: 102.3040 Evaluate side-chains 309 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 287 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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 75 LEU 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 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 59 LEU 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 160 MET Chi-restraints excluded: chain H residue 185 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 16 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 85 optimal weight: 0.0870 chunk 32 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 101 optimal weight: 0.0040 chunk 5 optimal weight: 0.9990 overall best weight: 0.4770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 ASN D 120 ASN G 120 ASN H 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.140037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.114620 restraints weight = 16695.575| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.24 r_work: 0.3249 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3153 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= 0.124 Angle : 0.490 7.245 15906 Z= 0.255 Chirality : 0.043 0.164 1806 Planarity : 0.005 0.053 2055 Dihedral : 3.714 13.885 1653 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.47 % Allowed : 15.73 % 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: 2.26 (0.23), residues: 1440 helix: 3.41 (0.22), residues: 501 sheet: 1.19 (0.26), residues: 402 loop : -0.14 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 180 HIS 0.006 0.001 HIS G 70 PHE 0.020 0.002 PHE A 54 TYR 0.010 0.001 TYR D 152 ARG 0.009 0.001 ARG E 94 Details of bonding type rmsd hydrogen bonds : bond 0.03426 ( 627) hydrogen bonds : angle 3.72895 ( 1773) SS BOND : bond 0.00207 ( 9) SS BOND : angle 0.33362 ( 18) covalent geometry : bond 0.00289 (11652) covalent geometry : angle 0.49063 (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 313 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 284 time to evaluate : 1.214 Fit side-chains revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8002 (tttt) cc_final: 0.7757 (tttt) REVERT: A 68 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.7080 (mp) REVERT: A 132 GLU cc_start: 0.7467 (tt0) cc_final: 0.7079 (tm-30) REVERT: A 135 SER cc_start: 0.8168 (p) cc_final: 0.7905 (t) REVERT: B 23 ARG cc_start: 0.7583 (ttt90) cc_final: 0.7152 (tpt170) REVERT: B 25 ARG cc_start: 0.8233 (mtp180) cc_final: 0.8029 (ttt180) REVERT: B 48 ARG cc_start: 0.7700 (mtt-85) cc_final: 0.7480 (ttm170) REVERT: B 149 ARG cc_start: 0.8647 (ttm-80) cc_final: 0.8330 (ttm-80) REVERT: C 73 GLN cc_start: 0.8509 (tp40) cc_final: 0.8263 (tp40) REVERT: C 115 MET cc_start: 0.6789 (mtp) cc_final: 0.6553 (mtp) REVERT: D 26 THR cc_start: 0.8682 (p) cc_final: 0.8404 (m) REVERT: D 87 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8316 (mm-30) REVERT: D 118 VAL cc_start: 0.8741 (t) cc_final: 0.8457 (m) REVERT: D 176 LEU cc_start: 0.7868 (tp) cc_final: 0.7650 (tp) REVERT: E 10 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8558 (pt0) REVERT: E 23 ARG cc_start: 0.7579 (tpt170) cc_final: 0.7343 (tpt170) REVERT: E 30 TYR cc_start: 0.8429 (m-80) cc_final: 0.8132 (m-80) REVERT: E 137 GLU cc_start: 0.6066 (tt0) cc_final: 0.5815 (tm-30) REVERT: E 163 MET cc_start: 0.2701 (mtm) cc_final: 0.2358 (ptt) REVERT: G 14 ASN cc_start: 0.8193 (m-40) cc_final: 0.7954 (m-40) REVERT: G 25 TYR cc_start: 0.9006 (t80) cc_final: 0.8337 (t80) REVERT: G 113 ASN cc_start: 0.8376 (t0) cc_final: 0.7860 (t0) REVERT: G 144 ASP cc_start: 0.8498 (p0) cc_final: 0.8203 (p0) REVERT: G 176 LEU cc_start: 0.7920 (tt) cc_final: 0.7528 (tp) REVERT: G 179 HIS cc_start: 0.8417 (t70) cc_final: 0.8181 (t70) REVERT: H 23 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6136 (ttt-90) REVERT: H 30 TYR cc_start: 0.8583 (m-80) cc_final: 0.8333 (m-80) REVERT: H 86 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6691 (mm-30) REVERT: H 163 MET cc_start: 0.3075 (mtm) cc_final: 0.2531 (ptt) outliers start: 29 outliers final: 23 residues processed: 298 average time/residue: 0.2612 time to fit residues: 106.8254 Evaluate side-chains 308 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 282 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 75 LEU 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 77 LYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain 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 160 MET Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain I residue 64 GLN 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: 0.5980 chunk 88 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 chunk 117 optimal weight: 0.3980 chunk 80 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.139768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.114143 restraints weight = 16718.039| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.24 r_work: 0.3236 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3164 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= 0.147 Angle : 0.504 6.922 15906 Z= 0.262 Chirality : 0.043 0.148 1806 Planarity : 0.005 0.053 2055 Dihedral : 3.789 14.432 1653 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.72 % Allowed : 15.48 % 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: 2.16 (0.23), residues: 1440 helix: 3.34 (0.22), residues: 501 sheet: 1.16 (0.25), residues: 399 loop : -0.22 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 180 HIS 0.006 0.001 HIS G 70 PHE 0.019 0.002 PHE D 54 TYR 0.010 0.001 TYR D 152 ARG 0.009 0.001 ARG E 94 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 627) hydrogen bonds : angle 3.80122 ( 1773) SS BOND : bond 0.00256 ( 9) SS BOND : angle 0.38461 ( 18) covalent geometry : bond 0.00349 (11652) covalent geometry : angle 0.50454 (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 316 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 284 time to evaluate : 1.209 Fit side-chains revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7985 (tttt) cc_final: 0.7736 (tttt) REVERT: A 68 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7114 (mp) REVERT: A 132 GLU cc_start: 0.7487 (tt0) cc_final: 0.7090 (tm-30) REVERT: A 135 SER cc_start: 0.8183 (p) cc_final: 0.7917 (t) REVERT: A 158 SER cc_start: 0.7766 (t) cc_final: 0.7172 (p) REVERT: B 23 ARG cc_start: 0.7775 (ttt90) cc_final: 0.7457 (tpt170) REVERT: C 73 GLN cc_start: 0.8523 (tp40) cc_final: 0.8268 (tp40) REVERT: C 115 MET cc_start: 0.6738 (mtp) cc_final: 0.6489 (mtp) REVERT: D 26 THR cc_start: 0.8675 (p) cc_final: 0.8413 (m) REVERT: D 87 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8316 (mm-30) REVERT: D 118 VAL cc_start: 0.8749 (t) cc_final: 0.8434 (m) REVERT: E 10 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8397 (pt0) REVERT: E 137 GLU cc_start: 0.6082 (tt0) cc_final: 0.5817 (tm-30) REVERT: E 163 MET cc_start: 0.2681 (mtm) cc_final: 0.2381 (ptt) REVERT: G 14 ASN cc_start: 0.8212 (m-40) cc_final: 0.7935 (m-40) REVERT: G 25 TYR cc_start: 0.9032 (t80) cc_final: 0.8216 (t80) REVERT: G 113 ASN cc_start: 0.8398 (t0) cc_final: 0.7872 (t0) REVERT: G 144 ASP cc_start: 0.8526 (p0) cc_final: 0.8262 (p0) REVERT: G 176 LEU cc_start: 0.7923 (tt) cc_final: 0.7582 (tp) REVERT: G 179 HIS cc_start: 0.8418 (t70) cc_final: 0.8174 (t70) REVERT: H 23 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6858 (tpt170) REVERT: H 30 TYR cc_start: 0.8582 (m-80) cc_final: 0.8353 (m-80) REVERT: H 86 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6740 (mm-30) REVERT: H 163 MET cc_start: 0.3178 (mtm) cc_final: 0.2680 (ptt) outliers start: 32 outliers final: 28 residues processed: 297 average time/residue: 0.2527 time to fit residues: 103.4172 Evaluate side-chains 312 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 281 time to evaluate : 1.322 ------------------------------------------------------------------------------- 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 75 LEU 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 77 LYS 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 75 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 64 GLN 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: 0.9990 chunk 92 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 41 optimal weight: 0.0020 chunk 124 optimal weight: 0.8980 chunk 82 optimal weight: 0.0970 chunk 93 optimal weight: 0.5980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 ASN 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 = 0.3757 r_free = 0.3757 target = 0.140601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.115181 restraints weight = 16646.150| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.24 r_work: 0.3251 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3284 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= 0.115 Angle : 0.488 7.450 15906 Z= 0.254 Chirality : 0.042 0.135 1806 Planarity : 0.005 0.053 2055 Dihedral : 3.716 13.941 1653 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.55 % Allowed : 15.99 % Favored : 81.46 % 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: 2.24 (0.23), residues: 1440 helix: 3.44 (0.22), residues: 501 sheet: 1.20 (0.26), residues: 396 loop : -0.21 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 180 HIS 0.006 0.001 HIS G 70 PHE 0.018 0.001 PHE D 54 TYR 0.010 0.001 TYR D 152 ARG 0.009 0.001 ARG E 94 Details of bonding type rmsd hydrogen bonds : bond 0.03319 ( 627) hydrogen bonds : angle 3.71916 ( 1773) SS BOND : bond 0.00190 ( 9) SS BOND : angle 0.33372 ( 18) covalent geometry : bond 0.00266 (11652) covalent geometry : angle 0.48827 (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 308 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 278 time to evaluate : 1.218 Fit side-chains revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7977 (tttt) cc_final: 0.7740 (tttt) REVERT: A 68 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.7100 (mp) REVERT: A 132 GLU cc_start: 0.7508 (tt0) cc_final: 0.7089 (tm-30) REVERT: A 135 SER cc_start: 0.8199 (p) cc_final: 0.7931 (t) REVERT: B 23 ARG cc_start: 0.7747 (ttt90) cc_final: 0.7394 (tpt170) REVERT: C 73 GLN cc_start: 0.8518 (tp40) cc_final: 0.8260 (tp40) REVERT: C 115 MET cc_start: 0.6785 (mtp) cc_final: 0.6536 (mtp) REVERT: D 26 THR cc_start: 0.8669 (p) cc_final: 0.8399 (m) REVERT: D 87 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8325 (mm-30) REVERT: D 118 VAL cc_start: 0.8741 (t) cc_final: 0.8442 (m) REVERT: E 10 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8558 (pt0) REVERT: E 137 GLU cc_start: 0.6063 (tt0) cc_final: 0.5796 (tm-30) REVERT: E 163 MET cc_start: 0.2675 (mtm) cc_final: 0.2445 (ptt) REVERT: G 14 ASN cc_start: 0.8222 (m-40) cc_final: 0.7959 (m-40) REVERT: G 25 TYR cc_start: 0.9013 (t80) cc_final: 0.8305 (t80) REVERT: G 113 ASN cc_start: 0.8390 (t0) cc_final: 0.7854 (t0) REVERT: G 144 ASP cc_start: 0.8470 (p0) cc_final: 0.8169 (p0) REVERT: G 176 LEU cc_start: 0.7921 (tt) cc_final: 0.7525 (tp) REVERT: G 179 HIS cc_start: 0.8415 (t70) cc_final: 0.8172 (t70) REVERT: H 23 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6898 (tpt170) REVERT: H 30 TYR cc_start: 0.8566 (m-80) cc_final: 0.8323 (m-80) REVERT: H 86 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6778 (mm-30) REVERT: H 163 MET cc_start: 0.2778 (mtm) cc_final: 0.2523 (ptt) outliers start: 30 outliers final: 24 residues processed: 293 average time/residue: 0.2572 time to fit residues: 103.1535 Evaluate side-chains 306 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 279 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 75 LEU 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 77 LYS 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 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 160 MET Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 64 GLN 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: 0.8980 chunk 13 optimal weight: 1.9990 chunk 104 optimal weight: 0.0050 chunk 65 optimal weight: 0.0970 chunk 95 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN H 64 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.140591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.115101 restraints weight = 16568.657| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.23 r_work: 0.3246 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3261 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= 0.142 Angle : 0.505 7.226 15906 Z= 0.262 Chirality : 0.043 0.131 1806 Planarity : 0.005 0.053 2055 Dihedral : 3.787 15.104 1653 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.72 % Allowed : 15.56 % Favored : 81.72 % 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: 2.15 (0.23), residues: 1440 helix: 3.35 (0.22), residues: 501 sheet: 1.12 (0.25), residues: 399 loop : -0.23 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 180 HIS 0.006 0.001 HIS G 70 PHE 0.015 0.002 PHE D 54 TYR 0.010 0.001 TYR D 152 ARG 0.010 0.001 ARG E 94 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 627) hydrogen bonds : angle 3.77700 ( 1773) SS BOND : bond 0.00266 ( 9) SS BOND : angle 0.37903 ( 18) covalent geometry : bond 0.00336 (11652) covalent geometry : angle 0.50518 (15888) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6387.14 seconds wall clock time: 111 minutes 3.69 seconds (6663.69 seconds total)