Starting phenix.real_space_refine on Sat Aug 23 09:57:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vsp_43501/08_2025/8vsp_43501.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vsp_43501/08_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_43501/08_2025/8vsp_43501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vsp_43501/08_2025/8vsp_43501.map" model { file = "/net/cci-nas-00/data/ceres_data/8vsp_43501/08_2025/8vsp_43501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vsp_43501/08_2025/8vsp_43501.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 2, 'PHE:plan': 1, '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, 'HIS:plan': 2, 'ARG:plan': 1} 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: D, G, E, H, F, I Time building chain proxies: 2.40, per 1000 atoms: 0.21 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: 1.05 Conformation dependent library (CDL) restraints added in 429.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.43 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: 1.89 Time building geometry restraints manager: 1.37 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } 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: 1.000 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.630 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.270 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG E 39 TYR 0.008 0.001 TYR G 25 PHE 0.013 0.001 PHE D 148 TRP 0.004 0.001 TRP B 61 HIS 0.003 0.001 HIS H 177 Details of bonding type rmsd covalent geometry : bond 0.00391 (11652) covalent geometry : angle 0.52944 (15888) SS BOND : bond 0.00153 ( 9) SS BOND : angle 0.74174 ( 18) hydrogen bonds : bond 0.24806 ( 627) hydrogen bonds : angle 7.18389 ( 1773) *********************** 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 : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.8494 (m110) cc_final: 0.8223 (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: 0.7645 (ptm) REVERT: D 14 ASN cc_start: 0.8447 (m110) cc_final: 0.8097 (m-40) REVERT: D 28 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8212 (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: 0.8023 (m) REVERT: D 81 SER cc_start: 0.8207 (t) cc_final: 0.7742 (p) REVERT: D 82 THR cc_start: 0.8392 (p) cc_final: 0.7896 (p) REVERT: D 87 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8210 (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: 0.8170 (m) REVERT: D 177 LEU cc_start: 0.8152 (mt) cc_final: 0.7891 (mm) REVERT: E 14 MET cc_start: 0.8766 (mtp) cc_final: 0.8497 (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: 0.8101 (m-40) REVERT: G 82 THR cc_start: 0.8365 (p) cc_final: 0.8155 (p) REVERT: G 106 ILE cc_start: 0.8322 (mt) cc_final: 0.8101 (mt) REVERT: G 125 SER cc_start: 0.8025 (t) cc_final: 0.7421 (p) REVERT: G 144 ASP cc_start: 0.8433 (p0) cc_final: 0.8116 (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: 0.7634 (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: 0.5392 (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: 0.2580 (ptt) REVERT: I 72 TYR cc_start: 0.8638 (t80) cc_final: 0.8398 (t80) REVERT: I 73 GLN cc_start: 0.8465 (tp40) cc_final: 0.8257 (mm-40) outliers start: 6 outliers final: 1 residues processed: 338 average time/residue: 0.1220 time to fit residues: 57.2773 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 : 0.339 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.0570 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 0.3980 chunk 55 optimal weight: 0.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 = 0.140163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.114602 restraints weight = 16636.812| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.27 r_work: 0.3202 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11661 Z= 0.149 Angle : 0.531 6.574 15906 Z= 0.285 Chirality : 0.044 0.125 1806 Planarity : 0.005 0.057 2055 Dihedral : 4.521 47.420 1656 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.72 % Allowed : 10.12 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.22), residues: 1440 helix: 2.45 (0.22), residues: 516 sheet: 0.89 (0.25), residues: 402 loop : -0.12 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 48 TYR 0.018 0.001 TYR B 60 PHE 0.015 0.002 PHE D 54 TRP 0.007 0.001 TRP E 131 HIS 0.004 0.001 HIS G 7 Details of bonding type rmsd covalent geometry : bond 0.00330 (11652) covalent geometry : angle 0.53117 (15888) SS BOND : bond 0.00189 ( 9) SS BOND : angle 0.57959 ( 18) hydrogen bonds : bond 0.05256 ( 627) hydrogen bonds : angle 4.66223 ( 1773) *********************** 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 322 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 290 time to evaluate : 0.439 Fit side-chains REVERT: A 14 ASN cc_start: 0.8471 (m-40) cc_final: 0.8215 (m-40) REVERT: A 42 LYS cc_start: 0.7888 (tttt) cc_final: 0.7608 (tttt) REVERT: A 43 GLU cc_start: 0.7599 (tp30) cc_final: 0.7286 (tp30) REVERT: A 44 THR cc_start: 0.8563 (m) cc_final: 0.7645 (t) REVERT: A 63 THR cc_start: 0.7637 (m) cc_final: 0.7278 (p) REVERT: A 135 SER cc_start: 0.8058 (p) cc_final: 0.7792 (t) REVERT: A 158 SER cc_start: 0.7893 (t) cc_final: 0.7339 (p) REVERT: A 164 ASP cc_start: 0.8168 (m-30) cc_final: 0.7890 (m-30) REVERT: B 14 MET cc_start: 0.8520 (mtp) cc_final: 0.8279 (mtm) REVERT: B 23 ARG cc_start: 0.7636 (ttt90) cc_final: 0.7307 (tpt170) REVERT: C 53 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.7334 (t80) REVERT: C 73 GLN cc_start: 0.8520 (tp40) cc_final: 0.8214 (tp40) REVERT: C 107 MET cc_start: 0.7372 (mmm) cc_final: 0.6917 (mmt) REVERT: C 115 MET cc_start: 0.6712 (mtp) cc_final: 0.6353 (mtp) REVERT: D 14 ASN cc_start: 0.8374 (m-40) cc_final: 0.8097 (m-40) REVERT: D 28 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8232 (mt-10) REVERT: D 81 SER cc_start: 0.8267 (t) cc_final: 0.8035 (p) REVERT: D 96 LYS cc_start: 0.8601 (tttp) cc_final: 0.8377 (tttp) REVERT: D 105 ASN cc_start: 0.8649 (t0) cc_final: 0.8143 (m-40) REVERT: D 118 VAL cc_start: 0.8670 (t) cc_final: 0.8401 (m) REVERT: D 177 LEU cc_start: 0.8078 (mt) cc_final: 0.7863 (mm) REVERT: E 14 MET cc_start: 0.8602 (mtp) cc_final: 0.8336 (mtm) REVERT: E 23 ARG cc_start: 0.7501 (ttt90) cc_final: 0.7236 (tpt170) REVERT: E 39 ARG cc_start: 0.8404 (ttp-170) cc_final: 0.8176 (ttp-110) REVERT: E 77 THR cc_start: 0.7751 (p) cc_final: 0.7463 (t) REVERT: E 163 MET cc_start: 0.2774 (mtm) cc_final: 0.1923 (ptt) REVERT: G 14 ASN cc_start: 0.8374 (m-40) cc_final: 0.8075 (m-40) REVERT: G 43 GLU cc_start: 0.7661 (tp30) cc_final: 0.7448 (tp30) REVERT: G 82 THR cc_start: 0.8180 (p) cc_final: 0.7971 (p) REVERT: G 144 ASP cc_start: 0.8457 (p0) cc_final: 0.8186 (p0) REVERT: G 176 LEU cc_start: 0.7561 (tt) cc_final: 0.7217 (tp) REVERT: G 179 HIS cc_start: 0.8425 (t70) cc_final: 0.8137 (t70) REVERT: H 22 GLU cc_start: 0.6272 (mt-10) cc_final: 0.6009 (mt-10) REVERT: H 45 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7178 (mt-10) REVERT: H 163 MET cc_start: 0.3230 (mtm) cc_final: 0.2679 (ptt) REVERT: I 72 TYR cc_start: 0.8741 (t80) cc_final: 0.8467 (t80) outliers start: 32 outliers final: 16 residues processed: 306 average time/residue: 0.1128 time to fit residues: 48.5628 Evaluate side-chains 291 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 274 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 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 91 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain I residue 53 PHE Chi-restraints excluded: chain I residue 111 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 29 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 113 optimal weight: 0.0070 chunk 109 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 111 optimal weight: 0.5980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN C 92 ASN D 120 ASN E 156 GLN E 174 HIS 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.140318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.114803 restraints weight = 16775.242| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.30 r_work: 0.3227 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2365 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= 0.132 Angle : 0.500 6.579 15906 Z= 0.262 Chirality : 0.043 0.152 1806 Planarity : 0.005 0.055 2055 Dihedral : 3.881 17.107 1653 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.72 % Allowed : 12.41 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.23), residues: 1440 helix: 2.82 (0.22), residues: 516 sheet: 1.00 (0.25), residues: 402 loop : -0.08 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 70 TYR 0.011 0.001 TYR B 60 PHE 0.016 0.002 PHE G 54 TRP 0.006 0.001 TRP D 180 HIS 0.004 0.001 HIS G 7 Details of bonding type rmsd covalent geometry : bond 0.00296 (11652) covalent geometry : angle 0.50022 (15888) SS BOND : bond 0.00207 ( 9) SS BOND : angle 0.57609 ( 18) hydrogen bonds : bond 0.04206 ( 627) hydrogen bonds : angle 4.18569 ( 1773) *********************** 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 312 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 280 time to evaluate : 0.442 Fit side-chains REVERT: A 42 LYS cc_start: 0.7892 (tttt) cc_final: 0.7627 (tttt) REVERT: A 43 GLU cc_start: 0.7453 (tp30) cc_final: 0.7191 (tp30) REVERT: A 44 THR cc_start: 0.8577 (m) cc_final: 0.7747 (t) REVERT: A 51 LEU cc_start: 0.8053 (mt) cc_final: 0.7846 (mp) REVERT: A 63 THR cc_start: 0.7671 (m) cc_final: 0.7405 (p) REVERT: A 68 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.7071 (mp) REVERT: A 132 GLU cc_start: 0.7398 (tt0) cc_final: 0.6989 (tm-30) REVERT: A 135 SER cc_start: 0.8039 (p) cc_final: 0.7799 (t) REVERT: A 158 SER cc_start: 0.7712 (t) cc_final: 0.7154 (p) REVERT: A 164 ASP cc_start: 0.8221 (m-30) cc_final: 0.7923 (m-30) REVERT: B 23 ARG cc_start: 0.7491 (ttt90) cc_final: 0.7156 (tpt170) REVERT: B 149 ARG cc_start: 0.8656 (ttm-80) cc_final: 0.8401 (ttm-80) REVERT: B 163 MET cc_start: 0.2378 (ttm) cc_final: 0.1223 (ptt) REVERT: C 53 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7158 (t80) REVERT: C 73 GLN cc_start: 0.8559 (tp40) cc_final: 0.8273 (tp40) REVERT: C 107 MET cc_start: 0.7366 (mmm) cc_final: 0.6928 (mmt) REVERT: D 14 ASN cc_start: 0.8322 (m-40) cc_final: 0.8101 (m-40) REVERT: D 28 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8220 (mt-10) REVERT: D 81 SER cc_start: 0.8324 (t) cc_final: 0.8074 (p) REVERT: D 96 LYS cc_start: 0.8665 (tttp) cc_final: 0.8324 (tttt) REVERT: D 105 ASN cc_start: 0.8635 (t0) cc_final: 0.8161 (m-40) REVERT: D 113 ASN cc_start: 0.8509 (t0) cc_final: 0.8295 (t0) REVERT: D 118 VAL cc_start: 0.8721 (t) cc_final: 0.8439 (m) REVERT: E 14 MET cc_start: 0.8590 (mtp) cc_final: 0.8375 (mtm) REVERT: E 23 ARG cc_start: 0.7492 (ttt90) cc_final: 0.7265 (tpt170) REVERT: E 77 THR cc_start: 0.7782 (p) cc_final: 0.7516 (t) REVERT: E 156 GLN cc_start: 0.8233 (mt0) cc_final: 0.7937 (mt0) REVERT: E 163 MET cc_start: 0.2717 (mtm) cc_final: 0.1772 (ptt) REVERT: G 14 ASN cc_start: 0.8285 (m-40) cc_final: 0.8004 (m-40) REVERT: G 63 THR cc_start: 0.7655 (t) cc_final: 0.7420 (p) REVERT: G 113 ASN cc_start: 0.8314 (t0) cc_final: 0.7848 (t0) REVERT: G 144 ASP cc_start: 0.8514 (p0) cc_final: 0.8256 (p0) REVERT: G 176 LEU cc_start: 0.7653 (tt) cc_final: 0.7291 (tp) REVERT: G 179 HIS cc_start: 0.8439 (t70) cc_final: 0.8193 (t70) REVERT: H 45 GLU cc_start: 0.7287 (mt-10) cc_final: 0.7083 (mt-10) REVERT: H 86 GLU cc_start: 0.7350 (mm-30) cc_final: 0.6798 (mm-30) REVERT: H 163 MET cc_start: 0.3073 (mtm) cc_final: 0.2496 (ptt) outliers start: 32 outliers final: 22 residues processed: 292 average time/residue: 0.1183 time to fit residues: 48.0720 Evaluate side-chains 298 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 274 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 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 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 91 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain I residue 53 PHE Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 111 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 118 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN D 120 ASN E 156 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.137144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.111758 restraints weight = 16775.864| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.26 r_work: 0.3188 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 11661 Z= 0.275 Angle : 0.581 6.487 15906 Z= 0.307 Chirality : 0.046 0.139 1806 Planarity : 0.005 0.053 2055 Dihedral : 4.250 17.410 1653 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.47 % Allowed : 14.71 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.22), residues: 1440 helix: 2.68 (0.22), residues: 495 sheet: 0.77 (0.25), residues: 402 loop : -0.34 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 94 TYR 0.016 0.002 TYR D 11 PHE 0.019 0.003 PHE G 54 TRP 0.010 0.002 TRP G 123 HIS 0.006 0.001 HIS G 27 Details of bonding type rmsd covalent geometry : bond 0.00656 (11652) covalent geometry : angle 0.58103 (15888) SS BOND : bond 0.00462 ( 9) SS BOND : angle 0.69216 ( 18) hydrogen bonds : bond 0.04788 ( 627) hydrogen bonds : angle 4.33137 ( 1773) *********************** 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 319 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 290 time to evaluate : 0.471 Fit side-chains REVERT: A 42 LYS cc_start: 0.7906 (tttt) cc_final: 0.7644 (tttt) REVERT: A 43 GLU cc_start: 0.7524 (tp30) cc_final: 0.7175 (tp30) REVERT: A 44 THR cc_start: 0.8595 (m) cc_final: 0.7835 (t) REVERT: A 68 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.7150 (mp) REVERT: A 132 GLU cc_start: 0.7404 (tt0) cc_final: 0.7024 (tm-30) REVERT: A 135 SER cc_start: 0.8087 (p) cc_final: 0.7827 (t) REVERT: A 158 SER cc_start: 0.7976 (t) cc_final: 0.7419 (p) REVERT: A 164 ASP cc_start: 0.8174 (m-30) cc_final: 0.7941 (m-30) REVERT: B 23 ARG cc_start: 0.7641 (ttt90) cc_final: 0.7195 (tpt170) REVERT: B 137 GLU cc_start: 0.6058 (tt0) cc_final: 0.5803 (tm-30) REVERT: B 163 MET cc_start: 0.2510 (ttm) cc_final: 0.1636 (ptt) REVERT: C 53 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7071 (t80) REVERT: C 73 GLN cc_start: 0.8580 (tp40) cc_final: 0.8277 (tp40) REVERT: C 107 MET cc_start: 0.7408 (mmm) cc_final: 0.7076 (mmt) REVERT: D 28 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8199 (mt-10) REVERT: D 51 LEU cc_start: 0.8206 (mt) cc_final: 0.7858 (mp) REVERT: D 105 ASN cc_start: 0.8587 (t0) cc_final: 0.8261 (m-40) REVERT: D 118 VAL cc_start: 0.8748 (t) cc_final: 0.8437 (m) REVERT: E 10 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8636 (pt0) REVERT: E 14 MET cc_start: 0.8615 (mtp) cc_final: 0.8323 (mtm) REVERT: E 23 ARG cc_start: 0.7432 (ttt90) cc_final: 0.7100 (tpt170) REVERT: E 30 TYR cc_start: 0.8541 (m-80) cc_final: 0.8293 (m-80) REVERT: E 48 ARG cc_start: 0.7709 (mtt-85) cc_final: 0.7468 (mtp85) REVERT: E 69 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7790 (mm-30) REVERT: E 88 ARG cc_start: 0.7269 (mtp180) cc_final: 0.7066 (mtp180) REVERT: E 163 MET cc_start: 0.3057 (mtm) cc_final: 0.1885 (ptt) REVERT: G 14 ASN cc_start: 0.8333 (m-40) cc_final: 0.8061 (m-40) REVERT: G 63 THR cc_start: 0.7789 (t) cc_final: 0.7523 (p) REVERT: G 144 ASP cc_start: 0.8573 (p0) cc_final: 0.8298 (p0) REVERT: G 176 LEU cc_start: 0.7777 (tt) cc_final: 0.7504 (tp) REVERT: G 179 HIS cc_start: 0.8451 (t70) cc_final: 0.8177 (t70) REVERT: H 86 GLU cc_start: 0.7469 (mm-30) cc_final: 0.6926 (mm-30) REVERT: H 163 MET cc_start: 0.3130 (mtm) cc_final: 0.2594 (ptt) outliers start: 29 outliers final: 24 residues processed: 301 average time/residue: 0.1283 time to fit residues: 52.6233 Evaluate side-chains 307 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 280 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 C residue 113 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain F residue 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 H residue 91 LEU Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain I residue 53 PHE Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 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 140 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 142 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** A 120 ASN B 64 GLN ** 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 ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.138381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.112900 restraints weight = 16703.861| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.28 r_work: 0.3176 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2697 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= 0.174 Angle : 0.518 6.365 15906 Z= 0.272 Chirality : 0.044 0.129 1806 Planarity : 0.005 0.055 2055 Dihedral : 4.038 14.901 1653 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.06 % Allowed : 14.97 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.22), residues: 1440 helix: 2.80 (0.22), residues: 498 sheet: 0.81 (0.25), residues: 402 loop : -0.28 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 94 TYR 0.011 0.001 TYR G 152 PHE 0.018 0.002 PHE D 54 TRP 0.007 0.001 TRP D 180 HIS 0.004 0.001 HIS G 27 Details of bonding type rmsd covalent geometry : bond 0.00410 (11652) covalent geometry : angle 0.51784 (15888) SS BOND : bond 0.00290 ( 9) SS BOND : angle 0.53384 ( 18) hydrogen bonds : bond 0.04114 ( 627) hydrogen bonds : angle 4.10005 ( 1773) *********************** 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 320 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 284 time to evaluate : 0.360 Fit side-chains REVERT: A 42 LYS cc_start: 0.7860 (tttt) cc_final: 0.7599 (tttt) REVERT: A 43 GLU cc_start: 0.7473 (tp30) cc_final: 0.7142 (tp30) REVERT: A 44 THR cc_start: 0.8573 (m) cc_final: 0.7606 (t) REVERT: A 68 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.7030 (mp) REVERT: A 132 GLU cc_start: 0.7436 (tt0) cc_final: 0.7014 (tm-30) REVERT: A 135 SER cc_start: 0.8081 (p) cc_final: 0.7811 (t) REVERT: A 158 SER cc_start: 0.7940 (t) cc_final: 0.7365 (p) REVERT: A 164 ASP cc_start: 0.8129 (m-30) cc_final: 0.7857 (m-30) REVERT: B 23 ARG cc_start: 0.7628 (ttt90) cc_final: 0.7164 (tpt170) REVERT: B 82 ASN cc_start: 0.8342 (m-40) cc_final: 0.7621 (m-40) REVERT: B 137 GLU cc_start: 0.6179 (tt0) cc_final: 0.5917 (tm-30) REVERT: B 149 ARG cc_start: 0.8707 (ttm-80) cc_final: 0.8374 (ttm-80) REVERT: C 53 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.7037 (t80) REVERT: C 73 GLN cc_start: 0.8514 (tp40) cc_final: 0.8241 (tp40) REVERT: C 107 MET cc_start: 0.7388 (mmm) cc_final: 0.7080 (mmt) REVERT: C 115 MET cc_start: 0.6774 (mtp) cc_final: 0.6553 (mtp) REVERT: D 26 THR cc_start: 0.8683 (p) cc_final: 0.8399 (m) REVERT: D 28 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8168 (mt-10) REVERT: D 105 ASN cc_start: 0.8554 (t0) cc_final: 0.8220 (m-40) REVERT: D 118 VAL cc_start: 0.8711 (t) cc_final: 0.8381 (m) REVERT: D 176 LEU cc_start: 0.7833 (tp) cc_final: 0.7631 (tp) REVERT: E 14 MET cc_start: 0.8601 (mtp) cc_final: 0.8319 (mtm) REVERT: E 23 ARG cc_start: 0.7459 (ttt90) cc_final: 0.7087 (tpt170) REVERT: F 77 ARG cc_start: 0.8632 (mmm-85) cc_final: 0.8288 (mtp180) REVERT: G 14 ASN cc_start: 0.8237 (m-40) cc_final: 0.7939 (m-40) REVERT: G 63 THR cc_start: 0.7616 (t) cc_final: 0.7385 (p) REVERT: G 144 ASP cc_start: 0.8504 (p0) cc_final: 0.8240 (p0) REVERT: G 176 LEU cc_start: 0.7710 (tt) cc_final: 0.7396 (tp) REVERT: H 86 GLU cc_start: 0.7340 (mm-30) cc_final: 0.6804 (mm-30) REVERT: H 163 MET cc_start: 0.3052 (mtm) cc_final: 0.2584 (ptt) outliers start: 36 outliers final: 29 residues processed: 296 average time/residue: 0.1256 time to fit residues: 51.3462 Evaluate side-chains 311 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 280 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 75 LEU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain 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 22 GLU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 122 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 63 optimal weight: 0.0040 chunk 108 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 56 optimal weight: 0.0870 chunk 82 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 overall best weight: 0.4370 ------------------------------------------------------------------------------- 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** A 120 ASN ** 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 = 0.3752 r_free = 0.3752 target = 0.139881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.114487 restraints weight = 16766.624| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.26 r_work: 0.3252 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2897 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= 0.119 Angle : 0.480 5.710 15906 Z= 0.252 Chirality : 0.042 0.129 1806 Planarity : 0.005 0.052 2055 Dihedral : 3.830 14.005 1653 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.32 % Allowed : 15.14 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.23), residues: 1440 helix: 3.16 (0.22), residues: 501 sheet: 1.01 (0.25), residues: 399 loop : -0.21 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 94 TYR 0.009 0.001 TYR G 152 PHE 0.019 0.001 PHE D 54 TRP 0.008 0.001 TRP B 188 HIS 0.003 0.001 HIS G 7 Details of bonding type rmsd covalent geometry : bond 0.00274 (11652) covalent geometry : angle 0.48001 (15888) SS BOND : bond 0.00195 ( 9) SS BOND : angle 0.43031 ( 18) hydrogen bonds : bond 0.03571 ( 627) hydrogen bonds : angle 3.84925 ( 1773) *********************** 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 331 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 292 time to evaluate : 0.445 Fit side-chains REVERT: A 42 LYS cc_start: 0.7901 (tttt) cc_final: 0.7672 (tttt) REVERT: A 43 GLU cc_start: 0.7425 (tp30) cc_final: 0.7215 (tp30) REVERT: A 44 THR cc_start: 0.8596 (m) cc_final: 0.7556 (t) REVERT: A 63 THR cc_start: 0.7692 (m) cc_final: 0.7486 (p) REVERT: A 68 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.7065 (mp) REVERT: A 132 GLU cc_start: 0.7466 (tt0) cc_final: 0.7062 (tm-30) REVERT: A 135 SER cc_start: 0.8162 (p) cc_final: 0.7899 (t) REVERT: A 158 SER cc_start: 0.7966 (t) cc_final: 0.7396 (p) REVERT: A 164 ASP cc_start: 0.8210 (m-30) cc_final: 0.7900 (m-30) REVERT: B 23 ARG cc_start: 0.7525 (ttt90) cc_final: 0.7078 (tpt170) REVERT: B 82 ASN cc_start: 0.8386 (m-40) cc_final: 0.7684 (m-40) REVERT: B 149 ARG cc_start: 0.8666 (ttm-80) cc_final: 0.8345 (ttm-80) REVERT: C 73 GLN cc_start: 0.8502 (tp40) cc_final: 0.8270 (tp40) REVERT: C 107 MET cc_start: 0.7408 (mmm) cc_final: 0.7073 (mmt) REVERT: C 115 MET cc_start: 0.6678 (mtp) cc_final: 0.6465 (mtp) REVERT: D 26 THR cc_start: 0.8616 (p) cc_final: 0.8395 (m) REVERT: D 28 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8226 (mt-10) REVERT: D 118 VAL cc_start: 0.8735 (t) cc_final: 0.8441 (m) REVERT: D 176 LEU cc_start: 0.7940 (tp) cc_final: 0.7739 (tp) REVERT: E 57 ASP cc_start: 0.8359 (m-30) cc_final: 0.7637 (m-30) REVERT: E 137 GLU cc_start: 0.6007 (tt0) cc_final: 0.5750 (tm-30) REVERT: E 163 MET cc_start: 0.2775 (mtm) cc_final: 0.2175 (ptt) REVERT: F 77 ARG cc_start: 0.8631 (mmm-85) cc_final: 0.8323 (mtp180) REVERT: G 14 ASN cc_start: 0.8208 (m-40) cc_final: 0.7960 (m-40) REVERT: G 25 TYR cc_start: 0.9007 (t80) cc_final: 0.8351 (t80) REVERT: G 113 ASN cc_start: 0.8389 (t0) cc_final: 0.7860 (t0) REVERT: G 144 ASP cc_start: 0.8525 (p0) cc_final: 0.8239 (p0) REVERT: G 176 LEU cc_start: 0.7811 (tt) cc_final: 0.7476 (tp) REVERT: H 86 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6707 (mm-30) REVERT: H 163 MET cc_start: 0.3050 (mtm) cc_final: 0.2560 (ptt) outliers start: 39 outliers final: 30 residues processed: 308 average time/residue: 0.1253 time to fit residues: 52.9145 Evaluate side-chains 318 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 287 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 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 160 MET Chi-restraints excluded: chain E residue 176 GLU 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 22 GLU 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 H residue 176 GLU 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 107 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 121 optimal weight: 0.0670 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 41 optimal weight: 0.4980 chunk 90 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 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 = 0.3741 r_free = 0.3741 target = 0.139004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.113537 restraints weight = 16693.582| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.26 r_work: 0.3216 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11661 Z= 0.141 Angle : 0.493 6.680 15906 Z= 0.258 Chirality : 0.043 0.159 1806 Planarity : 0.005 0.052 2055 Dihedral : 3.830 14.323 1653 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.57 % Allowed : 14.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.23), residues: 1440 helix: 3.17 (0.22), residues: 501 sheet: 1.01 (0.25), residues: 402 loop : -0.21 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 94 TYR 0.009 0.001 TYR G 152 PHE 0.021 0.002 PHE D 54 TRP 0.007 0.001 TRP D 180 HIS 0.003 0.001 HIS H 177 Details of bonding type rmsd covalent geometry : bond 0.00331 (11652) covalent geometry : angle 0.49357 (15888) SS BOND : bond 0.00241 ( 9) SS BOND : angle 0.38300 ( 18) hydrogen bonds : bond 0.03661 ( 627) hydrogen bonds : angle 3.84891 ( 1773) *********************** 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 326 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 284 time to evaluate : 0.502 Fit side-chains REVERT: A 42 LYS cc_start: 0.7888 (tttt) cc_final: 0.7636 (tttt) REVERT: A 43 GLU cc_start: 0.7445 (tp30) cc_final: 0.7165 (tp30) REVERT: A 44 THR cc_start: 0.8602 (m) cc_final: 0.7736 (t) REVERT: A 51 LEU cc_start: 0.8063 (mt) cc_final: 0.7861 (mp) REVERT: A 68 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.7077 (mp) REVERT: A 132 GLU cc_start: 0.7435 (tt0) cc_final: 0.7040 (tm-30) REVERT: A 135 SER cc_start: 0.8139 (p) cc_final: 0.7879 (t) REVERT: A 158 SER cc_start: 0.7974 (t) cc_final: 0.7396 (p) REVERT: B 23 ARG cc_start: 0.7532 (ttt90) cc_final: 0.7140 (tpt170) REVERT: B 82 ASN cc_start: 0.8384 (m-40) cc_final: 0.7628 (m-40) REVERT: C 73 GLN cc_start: 0.8531 (tp40) cc_final: 0.8278 (tp40) REVERT: C 107 MET cc_start: 0.7408 (mmm) cc_final: 0.7095 (mmt) REVERT: C 115 MET cc_start: 0.6676 (mtp) cc_final: 0.6445 (mtp) REVERT: D 28 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8130 (mt-10) REVERT: D 71 ASN cc_start: 0.8134 (m-40) cc_final: 0.7911 (m-40) REVERT: D 87 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8201 (mm-30) REVERT: D 118 VAL cc_start: 0.8721 (t) cc_final: 0.8423 (m) REVERT: D 176 LEU cc_start: 0.7850 (tp) cc_final: 0.7636 (tp) REVERT: E 10 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8594 (pt0) REVERT: E 23 ARG cc_start: 0.7472 (tpt170) cc_final: 0.7229 (tpt170) REVERT: E 137 GLU cc_start: 0.6083 (tt0) cc_final: 0.5853 (tm-30) REVERT: E 163 MET cc_start: 0.2600 (mtm) cc_final: 0.2182 (ptt) REVERT: F 77 ARG cc_start: 0.8640 (mmm-85) cc_final: 0.8332 (mtp180) REVERT: F 115 MET cc_start: 0.6453 (mtp) cc_final: 0.6043 (mtp) REVERT: G 14 ASN cc_start: 0.8220 (m-40) cc_final: 0.7948 (m-40) REVERT: G 25 TYR cc_start: 0.9025 (t80) cc_final: 0.8342 (t80) REVERT: G 113 ASN cc_start: 0.8401 (t0) cc_final: 0.7871 (t0) REVERT: G 144 ASP cc_start: 0.8518 (p0) cc_final: 0.8231 (p0) REVERT: G 176 LEU cc_start: 0.7837 (tt) cc_final: 0.7498 (tp) REVERT: H 86 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6749 (mm-30) REVERT: H 163 MET cc_start: 0.3104 (mtm) cc_final: 0.2590 (ptt) outliers start: 42 outliers final: 33 residues processed: 302 average time/residue: 0.1223 time to fit residues: 51.2054 Evaluate side-chains 319 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 284 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 95 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 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 81 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain H residue 176 GLU 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 107 MET Chi-restraints excluded: chain I residue 111 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 114 optimal weight: 0.6980 chunk 105 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 2 optimal weight: 0.3980 chunk 121 optimal weight: 0.4980 chunk 86 optimal weight: 5.9990 chunk 69 optimal weight: 0.3980 chunk 43 optimal weight: 0.6980 chunk 116 optimal weight: 7.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN H 64 GLN H 156 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 = 0.140287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.114933 restraints weight = 16666.936| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.24 r_work: 0.3218 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3061 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= 0.121 Angle : 0.486 7.019 15906 Z= 0.252 Chirality : 0.042 0.140 1806 Planarity : 0.005 0.051 2055 Dihedral : 3.766 14.501 1653 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.57 % Allowed : 14.88 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.23), residues: 1440 helix: 3.27 (0.22), residues: 501 sheet: 1.14 (0.25), residues: 399 loop : -0.23 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 94 TYR 0.008 0.001 TYR G 152 PHE 0.017 0.001 PHE D 54 TRP 0.007 0.001 TRP D 180 HIS 0.002 0.001 HIS D 179 Details of bonding type rmsd covalent geometry : bond 0.00280 (11652) covalent geometry : angle 0.48563 (15888) SS BOND : bond 0.00195 ( 9) SS BOND : angle 0.38700 ( 18) hydrogen bonds : bond 0.03471 ( 627) hydrogen bonds : angle 3.78490 ( 1773) *********************** 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 327 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 285 time to evaluate : 0.491 Fit side-chains REVERT: A 42 LYS cc_start: 0.7840 (tttt) cc_final: 0.7591 (tttt) REVERT: A 43 GLU cc_start: 0.7401 (tp30) cc_final: 0.7115 (tp30) REVERT: A 44 THR cc_start: 0.8570 (m) cc_final: 0.7767 (t) REVERT: A 51 LEU cc_start: 0.8047 (mt) cc_final: 0.7843 (mp) REVERT: A 63 THR cc_start: 0.7701 (m) cc_final: 0.7474 (p) REVERT: A 68 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.7087 (mp) REVERT: A 132 GLU cc_start: 0.7456 (tt0) cc_final: 0.7057 (tm-30) REVERT: A 135 SER cc_start: 0.8139 (p) cc_final: 0.7877 (t) REVERT: A 158 SER cc_start: 0.7755 (t) cc_final: 0.7154 (p) REVERT: B 23 ARG cc_start: 0.7601 (ttt90) cc_final: 0.7133 (tpt170) REVERT: B 82 ASN cc_start: 0.8391 (m-40) cc_final: 0.7671 (m-40) REVERT: C 73 GLN cc_start: 0.8515 (tp40) cc_final: 0.8253 (tp40) REVERT: C 77 ARG cc_start: 0.8721 (mmm-85) cc_final: 0.8412 (mtm180) REVERT: C 107 MET cc_start: 0.7383 (mmm) cc_final: 0.7092 (mmt) REVERT: C 115 MET cc_start: 0.6643 (mtp) cc_final: 0.6423 (mtp) REVERT: D 26 THR cc_start: 0.8671 (p) cc_final: 0.8396 (m) REVERT: D 28 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8241 (mt-10) REVERT: D 71 ASN cc_start: 0.8209 (m-40) cc_final: 0.7980 (m-40) REVERT: D 77 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.8062 (mttm) REVERT: D 87 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8208 (mm-30) REVERT: D 118 VAL cc_start: 0.8725 (t) cc_final: 0.8420 (m) REVERT: D 176 LEU cc_start: 0.7829 (tp) cc_final: 0.7613 (tp) REVERT: E 10 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8564 (pt0) REVERT: E 23 ARG cc_start: 0.7591 (tpt170) cc_final: 0.7383 (tpt170) REVERT: E 137 GLU cc_start: 0.6068 (tt0) cc_final: 0.5851 (tm-30) REVERT: E 163 MET cc_start: 0.2540 (mtm) cc_final: 0.2209 (ptt) REVERT: F 115 MET cc_start: 0.6496 (mtp) cc_final: 0.6111 (mtp) REVERT: G 14 ASN cc_start: 0.8241 (m-40) cc_final: 0.7949 (m-40) REVERT: G 25 TYR cc_start: 0.9013 (t80) cc_final: 0.8317 (t80) REVERT: G 113 ASN cc_start: 0.8396 (t0) cc_final: 0.7862 (t0) REVERT: G 144 ASP cc_start: 0.8493 (p0) cc_final: 0.8200 (p0) REVERT: G 176 LEU cc_start: 0.7883 (tt) cc_final: 0.7518 (tp) REVERT: H 86 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6740 (mm-30) REVERT: H 163 MET cc_start: 0.3148 (mtm) cc_final: 0.2632 (ptt) outliers start: 42 outliers final: 33 residues processed: 298 average time/residue: 0.1226 time to fit residues: 50.4810 Evaluate side-chains 315 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 279 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 95 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 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 F residue 81 LEU Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain H residue 176 GLU Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 53 PHE Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 111 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 99 optimal weight: 1.9990 chunk 69 optimal weight: 0.0050 chunk 40 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 11 optimal weight: 0.2980 overall best weight: 0.4594 ------------------------------------------------------------------------------- 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 = 0.140282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.114998 restraints weight = 16531.226| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.23 r_work: 0.3239 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11661 Z= 0.121 Angle : 0.486 7.044 15906 Z= 0.252 Chirality : 0.042 0.142 1806 Planarity : 0.005 0.051 2055 Dihedral : 3.741 14.093 1653 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.57 % Allowed : 14.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.23), residues: 1440 helix: 3.31 (0.22), residues: 501 sheet: 1.14 (0.25), residues: 399 loop : -0.24 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 94 TYR 0.021 0.001 TYR B 60 PHE 0.018 0.001 PHE D 54 TRP 0.007 0.001 TRP D 180 HIS 0.002 0.001 HIS H 177 Details of bonding type rmsd covalent geometry : bond 0.00281 (11652) covalent geometry : angle 0.48580 (15888) SS BOND : bond 0.00207 ( 9) SS BOND : angle 0.35183 ( 18) hydrogen bonds : bond 0.03407 ( 627) hydrogen bonds : angle 3.76573 ( 1773) *********************** 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 328 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 286 time to evaluate : 0.523 Fit side-chains REVERT: A 42 LYS cc_start: 0.7825 (tttt) cc_final: 0.7592 (tttt) REVERT: A 43 GLU cc_start: 0.7377 (tp30) cc_final: 0.7078 (tp30) REVERT: A 44 THR cc_start: 0.8575 (m) cc_final: 0.7840 (t) REVERT: A 51 LEU cc_start: 0.8060 (mt) cc_final: 0.7855 (mp) REVERT: A 63 THR cc_start: 0.7726 (m) cc_final: 0.7480 (p) REVERT: A 68 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.7100 (mp) REVERT: A 132 GLU cc_start: 0.7439 (tt0) cc_final: 0.7046 (tm-30) REVERT: A 135 SER cc_start: 0.8146 (p) cc_final: 0.7887 (t) REVERT: A 158 SER cc_start: 0.7768 (t) cc_final: 0.7176 (p) REVERT: B 23 ARG cc_start: 0.7765 (ttt90) cc_final: 0.7468 (tpt170) REVERT: B 82 ASN cc_start: 0.8390 (m-40) cc_final: 0.7662 (m-40) REVERT: C 73 GLN cc_start: 0.8514 (tp40) cc_final: 0.8268 (tp40) REVERT: C 77 ARG cc_start: 0.8735 (mmm-85) cc_final: 0.8437 (mtm180) REVERT: C 107 MET cc_start: 0.7372 (mmm) cc_final: 0.7091 (mmt) REVERT: C 115 MET cc_start: 0.6619 (mtp) cc_final: 0.6402 (mtp) REVERT: D 26 THR cc_start: 0.8672 (p) cc_final: 0.8397 (m) REVERT: D 28 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8235 (mt-10) REVERT: D 77 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.8033 (mttm) REVERT: D 87 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8219 (mm-30) REVERT: D 118 VAL cc_start: 0.8744 (t) cc_final: 0.8441 (m) REVERT: E 10 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8575 (pt0) REVERT: E 23 ARG cc_start: 0.7615 (tpt170) cc_final: 0.7401 (tpt170) REVERT: E 137 GLU cc_start: 0.6002 (tt0) cc_final: 0.5797 (tm-30) REVERT: E 163 MET cc_start: 0.2793 (mtm) cc_final: 0.2557 (ptt) REVERT: F 115 MET cc_start: 0.6484 (mtp) cc_final: 0.6267 (mtp) REVERT: G 14 ASN cc_start: 0.8233 (m-40) cc_final: 0.7944 (m-40) REVERT: G 25 TYR cc_start: 0.9028 (t80) cc_final: 0.8333 (t80) REVERT: G 87 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8463 (mm-30) REVERT: G 113 ASN cc_start: 0.8395 (t0) cc_final: 0.7867 (t0) REVERT: G 144 ASP cc_start: 0.8514 (p0) cc_final: 0.8204 (p0) REVERT: G 176 LEU cc_start: 0.7927 (tt) cc_final: 0.7527 (tp) REVERT: H 30 TYR cc_start: 0.8525 (m-80) cc_final: 0.8310 (m-80) REVERT: H 86 GLU cc_start: 0.7285 (mm-30) cc_final: 0.6749 (mm-30) REVERT: H 163 MET cc_start: 0.3112 (mtm) cc_final: 0.2632 (ptt) outliers start: 42 outliers final: 34 residues processed: 300 average time/residue: 0.1245 time to fit residues: 51.3437 Evaluate side-chains 324 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 287 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 95 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 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 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 H residue 22 GLU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain H residue 176 GLU Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 53 PHE Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 26 optimal weight: 0.0060 chunk 3 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 114 optimal weight: 0.0970 chunk 138 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 overall best weight: 0.3994 ------------------------------------------------------------------------------- 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 ** E 156 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 = 0.3762 r_free = 0.3762 target = 0.140608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.115117 restraints weight = 16747.535| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.26 r_work: 0.3242 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11661 Z= 0.113 Angle : 0.485 6.902 15906 Z= 0.251 Chirality : 0.042 0.143 1806 Planarity : 0.005 0.051 2055 Dihedral : 3.707 14.414 1653 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.32 % Allowed : 15.90 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.23), residues: 1440 helix: 3.40 (0.22), residues: 501 sheet: 1.18 (0.26), residues: 396 loop : -0.24 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 94 TYR 0.008 0.001 TYR G 152 PHE 0.017 0.001 PHE D 54 TRP 0.008 0.001 TRP D 180 HIS 0.002 0.001 HIS E 174 Details of bonding type rmsd covalent geometry : bond 0.00261 (11652) covalent geometry : angle 0.48482 (15888) SS BOND : bond 0.00199 ( 9) SS BOND : angle 0.34121 ( 18) hydrogen bonds : bond 0.03304 ( 627) hydrogen bonds : angle 3.72989 ( 1773) ********************** 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 328 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 289 time to evaluate : 0.455 Fit side-chains REVERT: A 42 LYS cc_start: 0.7858 (tttt) cc_final: 0.7611 (tttt) REVERT: A 43 GLU cc_start: 0.7351 (tp30) cc_final: 0.7091 (tp30) REVERT: A 44 THR cc_start: 0.8577 (m) cc_final: 0.7857 (t) REVERT: A 63 THR cc_start: 0.7722 (m) cc_final: 0.7510 (p) REVERT: A 68 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.7077 (mp) REVERT: A 132 GLU cc_start: 0.7462 (tt0) cc_final: 0.7039 (tm-30) REVERT: A 135 SER cc_start: 0.8163 (p) cc_final: 0.7910 (t) REVERT: B 23 ARG cc_start: 0.7665 (ttt90) cc_final: 0.7309 (tpt170) REVERT: B 82 ASN cc_start: 0.8387 (m-40) cc_final: 0.7670 (m-40) REVERT: C 73 GLN cc_start: 0.8511 (tp40) cc_final: 0.8271 (tp40) REVERT: C 77 ARG cc_start: 0.8723 (mmm-85) cc_final: 0.8429 (mtm180) REVERT: C 107 MET cc_start: 0.7369 (mmm) cc_final: 0.7087 (mmt) REVERT: C 115 MET cc_start: 0.6626 (mtp) cc_final: 0.6394 (mtp) REVERT: D 3 ILE cc_start: 0.8375 (mp) cc_final: 0.8162 (mt) REVERT: D 26 THR cc_start: 0.8667 (p) cc_final: 0.8397 (m) REVERT: D 28 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8268 (mt-10) REVERT: D 87 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8239 (mm-30) REVERT: D 118 VAL cc_start: 0.8750 (t) cc_final: 0.8456 (m) REVERT: E 10 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8560 (pt0) REVERT: E 163 MET cc_start: 0.2751 (mtm) cc_final: 0.2538 (ptt) REVERT: G 14 ASN cc_start: 0.8239 (m-40) cc_final: 0.7961 (m-40) REVERT: G 25 TYR cc_start: 0.9023 (t80) cc_final: 0.8336 (t80) REVERT: G 113 ASN cc_start: 0.8390 (t0) cc_final: 0.7864 (t0) REVERT: G 144 ASP cc_start: 0.8516 (p0) cc_final: 0.8203 (p0) REVERT: G 176 LEU cc_start: 0.7932 (tt) cc_final: 0.7521 (tp) REVERT: H 30 TYR cc_start: 0.8518 (m-80) cc_final: 0.8294 (m-80) REVERT: H 86 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6788 (mm-30) REVERT: H 163 MET cc_start: 0.3106 (mtm) cc_final: 0.2625 (ptt) outliers start: 39 outliers final: 34 residues processed: 301 average time/residue: 0.1299 time to fit residues: 53.3299 Evaluate side-chains 321 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 285 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain H residue 176 GLU Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 53 PHE Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 107 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 121 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 80 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 127 optimal weight: 0.3980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.139754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.113394 restraints weight = 16612.235| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.30 r_work: 0.3229 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11661 Z= 0.129 Angle : 0.494 7.152 15906 Z= 0.256 Chirality : 0.042 0.141 1806 Planarity : 0.005 0.051 2055 Dihedral : 3.750 14.494 1653 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.32 % Allowed : 15.90 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.23), residues: 1440 helix: 3.39 (0.22), residues: 501 sheet: 1.16 (0.25), residues: 399 loop : -0.24 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 94 TYR 0.009 0.001 TYR G 152 PHE 0.014 0.001 PHE D 54 TRP 0.007 0.001 TRP H 131 HIS 0.003 0.001 HIS H 177 Details of bonding type rmsd covalent geometry : bond 0.00303 (11652) covalent geometry : angle 0.49395 (15888) SS BOND : bond 0.00237 ( 9) SS BOND : angle 0.37615 ( 18) hydrogen bonds : bond 0.03392 ( 627) hydrogen bonds : angle 3.75368 ( 1773) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3407.36 seconds wall clock time: 59 minutes 8.31 seconds (3548.31 seconds total)