Starting phenix.real_space_refine on Wed Sep 25 21:41:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsp_43501/09_2024/8vsp_43501.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsp_43501/09_2024/8vsp_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsp_43501/09_2024/8vsp_43501.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsp_43501/09_2024/8vsp_43501.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsp_43501/09_2024/8vsp_43501.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsp_43501/09_2024/8vsp_43501.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 7239 2.51 5 N 1950 2.21 5 O 2157 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11388 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1609 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1625 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 195} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 2, 'ARG:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 548 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 5, 'TRANS': 64} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: E, H, F, I, D, G Time building chain proxies: 5.67, per 1000 atoms: 0.50 Number of scatterers: 11388 At special positions: 0 Unit cell: (108.231, 104.456, 139.694, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 2157 8.00 N 1950 7.00 C 7239 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 79 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 173 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.6 seconds 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2778 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 18 sheets defined 36.2% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 57 through 79 removed outlier: 3.963A pdb=" N ALA A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 221 removed outlier: 3.646A pdb=" N ARG A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 64 removed outlier: 4.198A pdb=" N TYR B 60 " --> pdb=" O PRO B 56 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B 64 " --> pdb=" O TYR B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 73 Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 78 through 89 removed outlier: 3.617A pdb=" N GLN B 84 " --> pdb=" O ARG B 80 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU B 85 " --> pdb=" O HIS B 81 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 225 removed outlier: 3.874A pdb=" N GLY B 216 " --> pdb=" O PHE B 212 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 96 removed outlier: 3.517A pdb=" N ILE C 55 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY C 76 " --> pdb=" O TYR C 72 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG C 77 " --> pdb=" O GLN C 73 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS C 96 " --> pdb=" O ASN C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 52 Processing helix chain 'D' and resid 57 through 79 removed outlier: 3.963A pdb=" N ALA D 61 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS D 77 " --> pdb=" O ASN D 73 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 221 removed outlier: 3.646A pdb=" N ARG D 220 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER D 221 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 64 removed outlier: 4.199A pdb=" N TYR E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN E 64 " --> pdb=" O TYR E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 73 Processing helix chain 'E' and resid 73 through 78 Processing helix chain 'E' and resid 78 through 89 removed outlier: 3.618A pdb=" N GLN E 84 " --> pdb=" O ARG E 80 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU E 85 " --> pdb=" O HIS E 81 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG E 88 " --> pdb=" O GLN E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 225 removed outlier: 3.874A pdb=" N GLY E 216 " --> pdb=" O PHE E 212 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU E 217 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE E 218 " --> pdb=" O GLY E 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 96 removed outlier: 3.517A pdb=" N ILE F 55 " --> pdb=" O THR F 51 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG F 77 " --> pdb=" O GLN F 73 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS F 96 " --> pdb=" O ASN F 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 52 Processing helix chain 'G' and resid 57 through 79 removed outlier: 3.964A pdb=" N ALA G 61 " --> pdb=" O ASP G 57 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS G 77 " --> pdb=" O ASN G 73 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 221 removed outlier: 3.645A pdb=" N ARG G 220 " --> pdb=" O ILE G 216 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER G 221 " --> pdb=" O ARG G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 64 removed outlier: 4.198A pdb=" N TYR H 60 " --> pdb=" O PRO H 56 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN H 64 " --> pdb=" O TYR H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 73 Processing helix chain 'H' and resid 73 through 78 Processing helix chain 'H' and resid 78 through 89 removed outlier: 3.617A pdb=" N GLN H 84 " --> pdb=" O ARG H 80 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU H 85 " --> pdb=" O HIS H 81 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG H 88 " --> pdb=" O GLN H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 225 removed outlier: 3.874A pdb=" N GLY H 216 " --> pdb=" O PHE H 212 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU H 217 " --> pdb=" O LEU H 213 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE H 218 " --> pdb=" O GLY H 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 96 removed outlier: 3.517A pdb=" N ILE I 55 " --> pdb=" O THR I 51 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY I 76 " --> pdb=" O TYR I 72 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG I 77 " --> pdb=" O GLN I 73 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS I 96 " --> pdb=" O ASN I 92 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 46 removed outlier: 6.791A pdb=" N HIS A 27 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N TYR A 36 " --> pdb=" O TYR A 25 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N TYR A 25 " --> pdb=" O TYR A 36 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ASP A 38 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N GLY A 23 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER A 22 " --> pdb=" O TYR A 16 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR A 16 " --> pdb=" O SER A 22 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN A 24 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASN A 14 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR A 26 " --> pdb=" O GLY A 12 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLY A 12 " --> pdb=" O THR A 26 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ALA B 13 " --> pdb=" O TYR A 11 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL A 13 " --> pdb=" O PHE B 11 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE B 11 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU A 15 " --> pdb=" O TYR B 9 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TYR B 9 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG B 23 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA B 38 " --> pdb=" O TYR B 30 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TYR B 32 " --> pdb=" O GLU B 36 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLU B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 95 removed outlier: 5.108A pdb=" N ILE A 106 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU A 155 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE A 108 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU A 153 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LEU A 110 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N SER A 151 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP A 112 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LYS A 149 " --> pdb=" O ASP A 112 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 95 removed outlier: 5.108A pdb=" N ILE A 106 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU A 155 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE A 108 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU A 153 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LEU A 110 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N SER A 151 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP A 112 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LYS A 149 " --> pdb=" O ASP A 112 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 130 removed outlier: 4.846A pdb=" N TRP A 123 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 98 through 102 removed outlier: 5.975A pdb=" N PHE B 155 " --> pdb=" O ASP B 121 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN B 156 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU B 147 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU B 158 " --> pdb=" O THR B 145 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 128 through 133 Processing sheet with id=AA7, first strand: chain 'D' and resid 43 through 46 removed outlier: 6.791A pdb=" N HIS D 27 " --> pdb=" O GLN D 34 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N TYR D 36 " --> pdb=" O TYR D 25 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N TYR D 25 " --> pdb=" O TYR D 36 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ASP D 38 " --> pdb=" O GLY D 23 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N GLY D 23 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER D 22 " --> pdb=" O TYR D 16 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR D 16 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN D 24 " --> pdb=" O ASN D 14 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASN D 14 " --> pdb=" O GLN D 24 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR D 26 " --> pdb=" O GLY D 12 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLY D 12 " --> pdb=" O THR D 26 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ALA E 13 " --> pdb=" O TYR D 11 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL D 13 " --> pdb=" O PHE E 11 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE E 11 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LEU D 15 " --> pdb=" O TYR E 9 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TYR E 9 " --> pdb=" O LEU D 15 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG E 23 " --> pdb=" O THR E 18 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA E 38 " --> pdb=" O TYR E 30 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR E 32 " --> pdb=" O GLU E 36 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N GLU E 36 " --> pdb=" O TYR E 32 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 90 through 95 removed outlier: 5.108A pdb=" N ILE D 106 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU D 155 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE D 108 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU D 153 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LEU D 110 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N SER D 151 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP D 112 " --> pdb=" O LYS D 149 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LYS D 149 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 90 through 95 removed outlier: 5.108A pdb=" N ILE D 106 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU D 155 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE D 108 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU D 153 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LEU D 110 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N SER D 151 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP D 112 " --> pdb=" O LYS D 149 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LYS D 149 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 128 through 130 removed outlier: 4.847A pdb=" N TRP D 123 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 98 through 102 removed outlier: 5.976A pdb=" N PHE E 155 " --> pdb=" O ASP E 121 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN E 156 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU E 147 " --> pdb=" O GLN E 156 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU E 158 " --> pdb=" O THR E 145 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 133 Processing sheet with id=AB4, first strand: chain 'G' and resid 43 through 46 removed outlier: 6.790A pdb=" N HIS G 27 " --> pdb=" O GLN G 34 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N TYR G 36 " --> pdb=" O TYR G 25 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N TYR G 25 " --> pdb=" O TYR G 36 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ASP G 38 " --> pdb=" O GLY G 23 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N GLY G 23 " --> pdb=" O ASP G 38 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER G 22 " --> pdb=" O TYR G 16 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TYR G 16 " --> pdb=" O SER G 22 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN G 24 " --> pdb=" O ASN G 14 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASN G 14 " --> pdb=" O GLN G 24 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR G 26 " --> pdb=" O GLY G 12 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLY G 12 " --> pdb=" O THR G 26 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ALA H 13 " --> pdb=" O TYR G 11 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL G 13 " --> pdb=" O PHE H 11 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE H 11 " --> pdb=" O VAL G 13 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU G 15 " --> pdb=" O TYR H 9 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TYR H 9 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG H 23 " --> pdb=" O THR H 18 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA H 38 " --> pdb=" O TYR H 30 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR H 32 " --> pdb=" O GLU H 36 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLU H 36 " --> pdb=" O TYR H 32 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 90 through 95 removed outlier: 5.109A pdb=" N ILE G 106 " --> pdb=" O LEU G 155 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU G 155 " --> pdb=" O ILE G 106 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE G 108 " --> pdb=" O LEU G 153 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU G 153 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LEU G 110 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N SER G 151 " --> pdb=" O LEU G 110 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ASP G 112 " --> pdb=" O LYS G 149 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LYS G 149 " --> pdb=" O ASP G 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 90 through 95 removed outlier: 5.109A pdb=" N ILE G 106 " --> pdb=" O LEU G 155 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU G 155 " --> pdb=" O ILE G 106 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE G 108 " --> pdb=" O LEU G 153 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU G 153 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LEU G 110 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N SER G 151 " --> pdb=" O LEU G 110 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ASP G 112 " --> pdb=" O LYS G 149 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LYS G 149 " --> pdb=" O ASP G 112 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 128 through 130 removed outlier: 4.846A pdb=" N TRP G 123 " --> pdb=" O VAL G 130 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 98 through 102 removed outlier: 5.976A pdb=" N PHE H 155 " --> pdb=" O ASP H 121 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN H 156 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU H 147 " --> pdb=" O GLN H 156 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU H 158 " --> pdb=" O THR H 145 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 128 through 133 651 hydrogen bonds defined for protein. 1773 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.47 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3744 1.34 - 1.46: 2599 1.46 - 1.58: 5246 1.58 - 1.69: 0 1.69 - 1.81: 63 Bond restraints: 11652 Sorted by residual: bond pdb=" N VAL B 46 " pdb=" CA VAL B 46 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.19e-02 7.06e+03 7.92e+00 bond pdb=" N VAL E 46 " pdb=" CA VAL E 46 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.19e-02 7.06e+03 7.70e+00 bond pdb=" N VAL H 46 " pdb=" CA VAL H 46 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.19e-02 7.06e+03 7.68e+00 bond pdb=" N VAL H 44 " pdb=" CA VAL H 44 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.22e+00 bond pdb=" N VAL B 44 " pdb=" CA VAL B 44 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 6.99e+00 ... (remaining 11647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 15057 1.03 - 2.06: 617 2.06 - 3.09: 174 3.09 - 4.12: 28 4.12 - 5.15: 12 Bond angle restraints: 15888 Sorted by residual: angle pdb=" CA ASP E 152 " pdb=" C ASP E 152 " pdb=" O ASP E 152 " ideal model delta sigma weight residual 122.38 117.89 4.49 1.49e+00 4.50e-01 9.07e+00 angle pdb=" CA ASP B 152 " pdb=" C ASP B 152 " pdb=" O ASP B 152 " ideal model delta sigma weight residual 122.38 117.91 4.47 1.49e+00 4.50e-01 9.00e+00 angle pdb=" CA ASP H 152 " pdb=" C ASP H 152 " pdb=" O ASP H 152 " ideal model delta sigma weight residual 122.38 117.97 4.41 1.49e+00 4.50e-01 8.76e+00 angle pdb=" C ASN E 19 " pdb=" CA ASN E 19 " pdb=" CB ASN E 19 " ideal model delta sigma weight residual 116.34 112.30 4.04 1.40e+00 5.10e-01 8.33e+00 angle pdb=" C ASN B 19 " pdb=" CA ASN B 19 " pdb=" CB ASN B 19 " ideal model delta sigma weight residual 116.34 112.31 4.03 1.40e+00 5.10e-01 8.30e+00 ... (remaining 15883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.68: 6397 11.68 - 23.36: 374 23.36 - 35.04: 123 35.04 - 46.73: 54 46.73 - 58.41: 6 Dihedral angle restraints: 6954 sinusoidal: 2655 harmonic: 4299 Sorted by residual: dihedral pdb=" CA LEU A 140 " pdb=" CB LEU A 140 " pdb=" CG LEU A 140 " pdb=" CD1 LEU A 140 " ideal model delta sinusoidal sigma weight residual 60.00 118.41 -58.41 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LEU D 140 " pdb=" CB LEU D 140 " pdb=" CG LEU D 140 " pdb=" CD1 LEU D 140 " ideal model delta sinusoidal sigma weight residual 60.00 118.36 -58.36 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA LEU G 140 " pdb=" CB LEU G 140 " pdb=" CG LEU G 140 " pdb=" CD1 LEU G 140 " ideal model delta sinusoidal sigma weight residual 60.00 118.34 -58.34 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 6951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1399 0.048 - 0.095: 286 0.095 - 0.143: 115 0.143 - 0.190: 3 0.190 - 0.238: 3 Chirality restraints: 1806 Sorted by residual: chirality pdb=" CA VAL H 44 " pdb=" N VAL H 44 " pdb=" C VAL H 44 " pdb=" CB VAL H 44 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA VAL B 44 " pdb=" N VAL B 44 " pdb=" C VAL B 44 " pdb=" CB VAL B 44 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA VAL E 44 " pdb=" N VAL E 44 " pdb=" C VAL E 44 " pdb=" CB VAL E 44 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1803 not shown) Planarity restraints: 2055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY H 54 " -0.040 5.00e-02 4.00e+02 6.01e-02 5.78e+00 pdb=" N PRO H 55 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO H 55 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 55 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 54 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO B 55 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 55 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 55 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 54 " 0.040 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO E 55 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO E 55 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 55 " 0.033 5.00e-02 4.00e+02 ... (remaining 2052 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 96 2.60 - 3.18: 9306 3.18 - 3.75: 16700 3.75 - 4.33: 23688 4.33 - 4.90: 39251 Nonbonded interactions: 89041 Sorted by model distance: nonbonded pdb=" SG CYS E 15 " pdb=" SG CYS E 79 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS H 15 " pdb=" SG CYS H 79 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS G 109 " pdb=" SG CYS G 165 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS D 109 " pdb=" SG CYS D 165 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS E 117 " pdb=" SG CYS E 173 " model vdw 2.033 3.760 ... (remaining 89036 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 27.280 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11652 Z= 0.258 Angle : 0.529 5.148 15888 Z= 0.314 Chirality : 0.045 0.238 1806 Planarity : 0.005 0.060 2055 Dihedral : 9.478 58.408 4167 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.51 % Allowed : 4.08 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.23), residues: 1440 helix: 1.17 (0.22), residues: 504 sheet: 0.70 (0.26), residues: 402 loop : -0.26 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 61 HIS 0.003 0.001 HIS H 177 PHE 0.013 0.001 PHE D 148 TYR 0.008 0.001 TYR G 25 ARG 0.002 0.000 ARG E 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 332 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.8494 (m110) cc_final: 0.8224 (m110) REVERT: A 43 GLU cc_start: 0.7263 (tp30) cc_final: 0.6944 (tp30) REVERT: A 44 THR cc_start: 0.8565 (m) cc_final: 0.7872 (t) REVERT: A 158 SER cc_start: 0.7735 (t) cc_final: 0.7181 (p) REVERT: A 164 ASP cc_start: 0.8166 (m-30) cc_final: 0.7897 (m-30) REVERT: B 14 MET cc_start: 0.8724 (mtp) cc_final: 0.8514 (mtm) REVERT: C 73 GLN cc_start: 0.8495 (tp40) cc_final: 0.8266 (tp40) REVERT: C 107 MET cc_start: 0.6894 (mmm) cc_final: 0.6427 (mmt) REVERT: C 109 MET cc_start: 0.7907 (ptm) cc_final: 0.7644 (ptm) REVERT: D 14 ASN cc_start: 0.8447 (m110) cc_final: 0.8100 (m-40) REVERT: D 28 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8213 (mt-10) REVERT: D 42 LYS cc_start: 0.8029 (tttt) cc_final: 0.7825 (tttt) REVERT: D 63 THR cc_start: 0.8263 (m) cc_final: 0.8021 (m) REVERT: D 81 SER cc_start: 0.8207 (t) cc_final: 0.7743 (p) REVERT: D 82 THR cc_start: 0.8392 (p) cc_final: 0.7898 (p) REVERT: D 87 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8208 (mm-30) REVERT: D 105 ASN cc_start: 0.8706 (t0) cc_final: 0.8312 (m-40) REVERT: D 118 VAL cc_start: 0.8567 (t) cc_final: 0.8171 (m) REVERT: D 177 LEU cc_start: 0.8152 (mt) cc_final: 0.7890 (mm) REVERT: E 14 MET cc_start: 0.8766 (mtp) cc_final: 0.8494 (mtm) REVERT: E 83 TYR cc_start: 0.8419 (t80) cc_final: 0.7969 (t80) REVERT: E 163 MET cc_start: 0.2647 (mtm) cc_final: 0.1831 (ptt) REVERT: E 176 GLU cc_start: 0.7182 (pt0) cc_final: 0.6971 (pt0) REVERT: E 185 THR cc_start: 0.8391 (m) cc_final: 0.8178 (t) REVERT: G 14 ASN cc_start: 0.8379 (m110) cc_final: 0.8100 (m-40) REVERT: G 82 THR cc_start: 0.8365 (p) cc_final: 0.8154 (p) REVERT: G 106 ILE cc_start: 0.8322 (mt) cc_final: 0.8100 (mt) REVERT: G 125 SER cc_start: 0.8025 (t) cc_final: 0.7422 (p) REVERT: G 144 ASP cc_start: 0.8433 (p0) cc_final: 0.8111 (p0) REVERT: G 176 LEU cc_start: 0.7717 (tt) cc_final: 0.7332 (tp) REVERT: G 179 HIS cc_start: 0.8252 (t70) cc_final: 0.7694 (t70) REVERT: H 6 ASP cc_start: 0.8559 (t0) cc_final: 0.8257 (t0) REVERT: H 22 GLU cc_start: 0.5616 (mt-10) cc_final: 0.5395 (mt-10) REVERT: H 30 TYR cc_start: 0.8657 (m-80) cc_final: 0.8381 (m-80) REVERT: H 93 ARG cc_start: 0.8529 (ttt180) cc_final: 0.8274 (ttt-90) REVERT: H 163 MET cc_start: 0.3111 (mtm) cc_final: 0.2582 (ptt) REVERT: I 72 TYR cc_start: 0.8638 (t80) cc_final: 0.8399 (t80) REVERT: I 73 GLN cc_start: 0.8465 (tp40) cc_final: 0.8256 (mm-40) outliers start: 6 outliers final: 1 residues processed: 338 average time/residue: 0.2502 time to fit residues: 116.9387 Evaluate side-chains 297 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 296 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 91 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 3.9990 chunk 109 optimal weight: 0.4980 chunk 60 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 103 GLN A 120 ASN B 64 GLN C 64 GLN C 75 GLN ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN D 86 ASN D 103 GLN D 120 ASN D 179 HIS ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 GLN G 14 ASN G 103 GLN G 120 ASN H 64 GLN ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 75 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11652 Z= 0.258 Angle : 0.553 6.545 15888 Z= 0.296 Chirality : 0.044 0.130 1806 Planarity : 0.005 0.057 2055 Dihedral : 4.628 47.813 1656 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.98 % Allowed : 10.12 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.22), residues: 1440 helix: 2.37 (0.22), residues: 516 sheet: 0.90 (0.25), residues: 402 loop : -0.14 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 131 HIS 0.004 0.001 HIS G 7 PHE 0.016 0.002 PHE D 54 TYR 0.017 0.001 TYR B 60 ARG 0.005 0.001 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 284 time to evaluate : 1.228 Fit side-chains REVERT: A 42 LYS cc_start: 0.7817 (tttt) cc_final: 0.7563 (tttt) REVERT: A 44 THR cc_start: 0.8587 (m) cc_final: 0.7576 (t) REVERT: A 135 SER cc_start: 0.8262 (p) cc_final: 0.8017 (t) REVERT: A 158 SER cc_start: 0.7740 (t) cc_final: 0.7207 (p) REVERT: A 164 ASP cc_start: 0.8108 (m-30) cc_final: 0.7843 (m-30) REVERT: B 23 ARG cc_start: 0.7751 (ttt90) cc_final: 0.7497 (tpt170) REVERT: C 53 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7258 (t80) REVERT: C 73 GLN cc_start: 0.8435 (tp40) cc_final: 0.8101 (tp40) REVERT: C 107 MET cc_start: 0.6935 (mmm) cc_final: 0.6441 (mmt) REVERT: C 115 MET cc_start: 0.6661 (mtp) cc_final: 0.6296 (mtp) REVERT: D 28 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8163 (mt-10) REVERT: D 42 LYS cc_start: 0.8045 (tttt) cc_final: 0.7843 (tttt) REVERT: D 118 VAL cc_start: 0.8624 (t) cc_final: 0.8398 (m) REVERT: D 177 LEU cc_start: 0.8139 (mt) cc_final: 0.7909 (mm) REVERT: E 14 MET cc_start: 0.8680 (mtp) cc_final: 0.8478 (mtm) REVERT: E 39 ARG cc_start: 0.8328 (ttp-170) cc_final: 0.8058 (ttp-110) REVERT: E 163 MET cc_start: 0.2688 (mtm) cc_final: 0.1809 (ptt) REVERT: F 91 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.7053 (mt-10) REVERT: G 43 GLU cc_start: 0.7320 (tp30) cc_final: 0.7118 (tp30) REVERT: G 82 THR cc_start: 0.8297 (p) cc_final: 0.8081 (p) REVERT: G 144 ASP cc_start: 0.8441 (p0) cc_final: 0.8184 (p0) REVERT: G 176 LEU cc_start: 0.7653 (tt) cc_final: 0.7343 (tp) REVERT: G 179 HIS cc_start: 0.8367 (t70) cc_final: 0.7993 (t70) REVERT: H 6 ASP cc_start: 0.8444 (t0) cc_final: 0.8244 (t0) REVERT: H 23 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6280 (ttt-90) REVERT: H 163 MET cc_start: 0.3135 (mtm) cc_final: 0.2538 (ptt) REVERT: I 72 TYR cc_start: 0.8622 (t80) cc_final: 0.8344 (t80) outliers start: 35 outliers final: 17 residues processed: 299 average time/residue: 0.2301 time to fit residues: 96.1895 Evaluate side-chains 287 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 267 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain F residue 53 PHE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain I residue 53 PHE Chi-restraints excluded: chain I residue 111 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 chunk 141 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 105 optimal weight: 0.0270 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 ASN D 120 ASN E 174 HIS ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN H 64 GLN H 174 HIS ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11652 Z= 0.244 Angle : 0.525 6.367 15888 Z= 0.275 Chirality : 0.044 0.136 1806 Planarity : 0.005 0.056 2055 Dihedral : 4.329 48.750 1656 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.89 % Allowed : 12.67 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.22), residues: 1440 helix: 2.61 (0.22), residues: 516 sheet: 0.95 (0.25), residues: 402 loop : -0.10 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 180 HIS 0.005 0.001 HIS G 27 PHE 0.015 0.002 PHE G 54 TYR 0.013 0.001 TYR B 60 ARG 0.005 0.001 ARG E 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 277 time to evaluate : 1.403 Fit side-chains REVERT: A 42 LYS cc_start: 0.7764 (tttt) cc_final: 0.7516 (tttt) REVERT: A 44 THR cc_start: 0.8366 (m) cc_final: 0.7940 (t) REVERT: A 51 LEU cc_start: 0.8108 (mt) cc_final: 0.7889 (mp) REVERT: A 63 THR cc_start: 0.7818 (m) cc_final: 0.7565 (p) REVERT: A 132 GLU cc_start: 0.7041 (tt0) cc_final: 0.6676 (tm-30) REVERT: A 135 SER cc_start: 0.8232 (p) cc_final: 0.7998 (t) REVERT: A 158 SER cc_start: 0.7766 (t) cc_final: 0.7226 (p) REVERT: A 164 ASP cc_start: 0.8066 (m-30) cc_final: 0.7843 (m-30) REVERT: B 23 ARG cc_start: 0.7760 (ttt90) cc_final: 0.7468 (tpt170) REVERT: B 149 ARG cc_start: 0.8660 (ttm-80) cc_final: 0.8408 (ttm-80) REVERT: B 163 MET cc_start: 0.2373 (ttm) cc_final: 0.1262 (ptt) REVERT: C 53 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.7007 (t80) REVERT: C 73 GLN cc_start: 0.8445 (tp40) cc_final: 0.8127 (tp40) REVERT: C 107 MET cc_start: 0.6947 (mmm) cc_final: 0.6530 (mmt) REVERT: D 28 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8180 (mt-10) REVERT: D 105 ASN cc_start: 0.8744 (t0) cc_final: 0.8261 (m-40) REVERT: D 118 VAL cc_start: 0.8656 (t) cc_final: 0.8404 (m) REVERT: E 39 ARG cc_start: 0.8358 (ttp-170) cc_final: 0.8151 (ttp-170) REVERT: E 70 ARG cc_start: 0.7309 (ttt180) cc_final: 0.7045 (ttt-90) REVERT: E 163 MET cc_start: 0.2706 (mtm) cc_final: 0.1764 (ptt) REVERT: F 91 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7162 (mt-10) REVERT: G 113 ASN cc_start: 0.8411 (t0) cc_final: 0.7947 (t0) REVERT: G 144 ASP cc_start: 0.8456 (p0) cc_final: 0.8146 (p0) REVERT: G 176 LEU cc_start: 0.7643 (tt) cc_final: 0.7337 (tp) REVERT: G 179 HIS cc_start: 0.8334 (t70) cc_final: 0.8035 (t70) REVERT: H 6 ASP cc_start: 0.8430 (t0) cc_final: 0.8224 (t0) REVERT: H 23 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.6330 (ttt-90) REVERT: H 163 MET cc_start: 0.3007 (mtm) cc_final: 0.2406 (ptt) outliers start: 34 outliers final: 26 residues processed: 289 average time/residue: 0.2471 time to fit residues: 99.7162 Evaluate side-chains 302 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 273 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain F residue 53 PHE Chi-restraints excluded: chain F residue 91 GLU 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 G residue 177 LEU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain I residue 53 PHE Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain I residue 113 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 139 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 120 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 ASN G 120 ASN ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11652 Z= 0.231 Angle : 0.502 5.852 15888 Z= 0.264 Chirality : 0.043 0.131 1806 Planarity : 0.005 0.053 2055 Dihedral : 4.247 45.560 1656 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.98 % Allowed : 13.95 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.22), residues: 1440 helix: 3.03 (0.22), residues: 498 sheet: 0.97 (0.25), residues: 402 loop : -0.22 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 180 HIS 0.004 0.001 HIS G 27 PHE 0.018 0.002 PHE D 54 TYR 0.009 0.001 TYR G 152 ARG 0.007 0.001 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 282 time to evaluate : 1.224 Fit side-chains REVERT: A 42 LYS cc_start: 0.7712 (tttt) cc_final: 0.7501 (tttt) REVERT: A 44 THR cc_start: 0.8419 (m) cc_final: 0.8084 (t) REVERT: A 63 THR cc_start: 0.7848 (m) cc_final: 0.7562 (p) REVERT: A 132 GLU cc_start: 0.7037 (tt0) cc_final: 0.6673 (tm-30) REVERT: A 135 SER cc_start: 0.8248 (p) cc_final: 0.8009 (t) REVERT: A 158 SER cc_start: 0.7779 (t) cc_final: 0.7237 (p) REVERT: A 164 ASP cc_start: 0.8079 (m-30) cc_final: 0.7824 (m-30) REVERT: B 23 ARG cc_start: 0.7770 (ttt90) cc_final: 0.7415 (tpt170) REVERT: B 137 GLU cc_start: 0.5713 (tt0) cc_final: 0.5465 (tm-30) REVERT: B 149 ARG cc_start: 0.8673 (ttm-80) cc_final: 0.8379 (ttm-80) REVERT: C 53 PHE cc_start: 0.7813 (OUTLIER) cc_final: 0.6896 (t80) REVERT: C 73 GLN cc_start: 0.8427 (tp40) cc_final: 0.8147 (tp40) REVERT: C 107 MET cc_start: 0.6933 (mmm) cc_final: 0.6531 (mmt) REVERT: C 115 MET cc_start: 0.6616 (mtp) cc_final: 0.6413 (mtp) REVERT: D 26 THR cc_start: 0.8635 (p) cc_final: 0.8351 (m) REVERT: D 28 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8193 (mt-10) REVERT: D 87 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8354 (mm-30) REVERT: D 105 ASN cc_start: 0.8711 (t0) cc_final: 0.8245 (m-40) REVERT: D 118 VAL cc_start: 0.8671 (t) cc_final: 0.8420 (m) REVERT: E 69 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7484 (mm-30) REVERT: E 70 ARG cc_start: 0.7234 (ttt180) cc_final: 0.6957 (ttt-90) REVERT: F 91 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7233 (mt-10) REVERT: F 115 MET cc_start: 0.6412 (mtp) cc_final: 0.6048 (mtp) REVERT: G 113 ASN cc_start: 0.8428 (t0) cc_final: 0.7933 (t0) REVERT: G 144 ASP cc_start: 0.8376 (p0) cc_final: 0.8076 (p0) REVERT: G 176 LEU cc_start: 0.7702 (tt) cc_final: 0.7396 (tp) REVERT: G 179 HIS cc_start: 0.8305 (t70) cc_final: 0.7993 (t70) REVERT: H 23 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.6323 (ttt-90) REVERT: H 86 GLU cc_start: 0.7331 (mm-30) cc_final: 0.6824 (mm-30) REVERT: H 163 MET cc_start: 0.2936 (mtm) cc_final: 0.2378 (ptt) outliers start: 35 outliers final: 24 residues processed: 293 average time/residue: 0.2522 time to fit residues: 101.4381 Evaluate side-chains 296 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 269 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain F residue 53 PHE Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain I residue 53 PHE Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 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 115 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 2 optimal weight: 0.3980 chunk 103 optimal weight: 0.9980 chunk 57 optimal weight: 0.0470 chunk 118 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 120 ASN G 120 ASN ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11652 Z= 0.213 Angle : 0.493 5.833 15888 Z= 0.259 Chirality : 0.043 0.130 1806 Planarity : 0.005 0.053 2055 Dihedral : 4.154 42.886 1656 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.23 % Allowed : 13.86 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.22), residues: 1440 helix: 3.13 (0.22), residues: 498 sheet: 1.02 (0.25), residues: 399 loop : -0.21 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 180 HIS 0.003 0.001 HIS G 7 PHE 0.018 0.002 PHE D 54 TYR 0.012 0.001 TYR B 60 ARG 0.007 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 279 time to evaluate : 1.291 Fit side-chains REVERT: A 63 THR cc_start: 0.7875 (m) cc_final: 0.7565 (p) REVERT: A 132 GLU cc_start: 0.7039 (tt0) cc_final: 0.6670 (tm-30) REVERT: A 135 SER cc_start: 0.8306 (p) cc_final: 0.8059 (t) REVERT: A 158 SER cc_start: 0.7787 (t) cc_final: 0.7244 (p) REVERT: B 23 ARG cc_start: 0.7672 (ttt90) cc_final: 0.7266 (tpt170) REVERT: B 82 ASN cc_start: 0.8457 (m-40) cc_final: 0.7852 (m-40) REVERT: B 137 GLU cc_start: 0.5823 (tt0) cc_final: 0.5590 (tm-30) REVERT: B 149 ARG cc_start: 0.8659 (ttm-80) cc_final: 0.8363 (ttm-80) REVERT: C 73 GLN cc_start: 0.8421 (tp40) cc_final: 0.8155 (tp40) REVERT: C 88 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8172 (mt) REVERT: C 107 MET cc_start: 0.6894 (mmm) cc_final: 0.6535 (mmt) REVERT: D 26 THR cc_start: 0.8619 (p) cc_final: 0.8332 (m) REVERT: D 28 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8202 (mt-10) REVERT: D 87 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8138 (mm-30) REVERT: D 105 ASN cc_start: 0.8714 (t0) cc_final: 0.8275 (m-40) REVERT: D 118 VAL cc_start: 0.8678 (t) cc_final: 0.8441 (m) REVERT: E 10 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8694 (pt0) REVERT: E 30 TYR cc_start: 0.8543 (m-80) cc_final: 0.8331 (m-80) REVERT: E 69 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7501 (mm-30) REVERT: E 163 MET cc_start: 0.2878 (mtm) cc_final: 0.1997 (ptt) REVERT: F 77 ARG cc_start: 0.8602 (mmm-85) cc_final: 0.8390 (mtp180) REVERT: F 91 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7215 (mt-10) REVERT: G 113 ASN cc_start: 0.8425 (t0) cc_final: 0.7933 (t0) REVERT: G 144 ASP cc_start: 0.8377 (p0) cc_final: 0.8079 (p0) REVERT: G 176 LEU cc_start: 0.7718 (tt) cc_final: 0.7398 (tp) REVERT: G 179 HIS cc_start: 0.8293 (t70) cc_final: 0.7993 (t70) REVERT: H 23 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6333 (ttt-90) REVERT: H 163 MET cc_start: 0.2880 (mtm) cc_final: 0.2372 (ptt) outliers start: 38 outliers final: 29 residues processed: 292 average time/residue: 0.2517 time to fit residues: 102.0166 Evaluate side-chains 307 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 274 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain F residue 53 PHE Chi-restraints excluded: chain F residue 91 GLU 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 177 LEU Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 53 PHE Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 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 46 optimal weight: 0.0980 chunk 125 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 120 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 HIS G 120 ASN ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11652 Z= 0.320 Angle : 0.539 5.842 15888 Z= 0.284 Chirality : 0.044 0.175 1806 Planarity : 0.005 0.053 2055 Dihedral : 4.269 38.741 1656 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.66 % Allowed : 14.97 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.22), residues: 1440 helix: 2.88 (0.22), residues: 501 sheet: 0.94 (0.25), residues: 402 loop : -0.24 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 123 HIS 0.004 0.001 HIS G 27 PHE 0.021 0.002 PHE D 54 TYR 0.011 0.002 TYR B 60 ARG 0.007 0.001 ARG E 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 274 time to evaluate : 1.142 Fit side-chains REVERT: A 42 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7707 (mtpt) REVERT: A 43 GLU cc_start: 0.6943 (tp30) cc_final: 0.6699 (tp30) REVERT: A 132 GLU cc_start: 0.7063 (tt0) cc_final: 0.6701 (tm-30) REVERT: A 135 SER cc_start: 0.8268 (p) cc_final: 0.8026 (t) REVERT: A 158 SER cc_start: 0.7796 (t) cc_final: 0.7244 (p) REVERT: B 23 ARG cc_start: 0.7668 (ttt90) cc_final: 0.7300 (tpt-90) REVERT: B 82 ASN cc_start: 0.8445 (m-40) cc_final: 0.7769 (m-40) REVERT: C 73 GLN cc_start: 0.8461 (tp40) cc_final: 0.8163 (tp40) REVERT: C 107 MET cc_start: 0.6918 (mmm) cc_final: 0.6601 (mmt) REVERT: D 26 THR cc_start: 0.8638 (p) cc_final: 0.8350 (m) REVERT: D 28 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8169 (mt-10) REVERT: D 87 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8179 (mm-30) REVERT: D 118 VAL cc_start: 0.8691 (t) cc_final: 0.8433 (m) REVERT: D 176 LEU cc_start: 0.7950 (tt) cc_final: 0.7573 (tp) REVERT: E 10 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8703 (pt0) REVERT: E 163 MET cc_start: 0.2759 (mtm) cc_final: 0.2205 (ptt) REVERT: F 77 ARG cc_start: 0.8642 (mmm-85) cc_final: 0.8377 (mtp180) REVERT: G 144 ASP cc_start: 0.8389 (p0) cc_final: 0.8107 (p0) REVERT: G 179 HIS cc_start: 0.8291 (t70) cc_final: 0.7987 (t70) REVERT: H 14 MET cc_start: 0.8479 (mtp) cc_final: 0.8191 (mtt) REVERT: H 23 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6373 (ttt-90) REVERT: H 86 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6802 (mm-30) REVERT: H 163 MET cc_start: 0.2932 (mtm) cc_final: 0.2477 (ptt) outliers start: 43 outliers final: 35 residues processed: 292 average time/residue: 0.2402 time to fit residues: 96.9950 Evaluate side-chains 306 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 268 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 53 PHE Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain I residue 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 15 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 138 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 64 GLN D 120 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN H 64 GLN ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11652 Z= 0.273 Angle : 0.524 7.091 15888 Z= 0.274 Chirality : 0.044 0.160 1806 Planarity : 0.005 0.054 2055 Dihedral : 4.020 18.626 1653 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.83 % Allowed : 15.22 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.22), residues: 1440 helix: 2.97 (0.22), residues: 498 sheet: 0.95 (0.25), residues: 402 loop : -0.25 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 180 HIS 0.003 0.001 HIS G 27 PHE 0.022 0.002 PHE D 54 TYR 0.010 0.001 TYR G 152 ARG 0.006 0.001 ARG E 94 *********************** 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 319 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 274 time to evaluate : 1.287 Fit side-chains REVERT: A 42 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7735 (mtpt) REVERT: A 43 GLU cc_start: 0.7013 (tp30) cc_final: 0.6748 (tp30) REVERT: A 132 GLU cc_start: 0.7043 (tt0) cc_final: 0.6691 (tm-30) REVERT: A 135 SER cc_start: 0.8318 (p) cc_final: 0.8065 (t) REVERT: A 158 SER cc_start: 0.7795 (t) cc_final: 0.7252 (p) REVERT: A 164 ASP cc_start: 0.8039 (m-30) cc_final: 0.7765 (m-30) REVERT: B 23 ARG cc_start: 0.7666 (ttt90) cc_final: 0.7307 (tpt-90) REVERT: B 82 ASN cc_start: 0.8456 (m-40) cc_final: 0.7771 (m-40) REVERT: C 107 MET cc_start: 0.6895 (mmm) cc_final: 0.6608 (mmt) REVERT: D 26 THR cc_start: 0.8648 (p) cc_final: 0.8371 (m) REVERT: D 28 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8134 (mt-10) REVERT: D 87 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8230 (mm-30) REVERT: D 118 VAL cc_start: 0.8688 (t) cc_final: 0.8430 (m) REVERT: E 10 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8816 (pt0) REVERT: E 163 MET cc_start: 0.2703 (mtm) cc_final: 0.2242 (ptt) REVERT: F 77 ARG cc_start: 0.8644 (mmm-85) cc_final: 0.8372 (mtp180) REVERT: G 25 TYR cc_start: 0.8986 (t80) cc_final: 0.8172 (t80) REVERT: G 144 ASP cc_start: 0.8368 (p0) cc_final: 0.8088 (p0) REVERT: G 179 HIS cc_start: 0.8275 (t70) cc_final: 0.7973 (t70) REVERT: H 23 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6323 (ttt-90) REVERT: H 86 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6791 (mm-30) REVERT: H 163 MET cc_start: 0.2992 (mtm) cc_final: 0.2545 (ptt) outliers start: 45 outliers final: 35 residues processed: 291 average time/residue: 0.2417 time to fit residues: 97.3652 Evaluate side-chains 314 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 276 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 139 THR 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 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 55 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 0.0770 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 120 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN H 64 GLN ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11652 Z= 0.256 Angle : 0.517 6.523 15888 Z= 0.271 Chirality : 0.043 0.131 1806 Planarity : 0.005 0.053 2055 Dihedral : 3.992 19.186 1653 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.74 % Allowed : 15.22 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.22), residues: 1440 helix: 3.04 (0.22), residues: 498 sheet: 1.01 (0.25), residues: 399 loop : -0.31 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 180 HIS 0.003 0.001 HIS H 177 PHE 0.019 0.002 PHE D 54 TYR 0.009 0.001 TYR G 152 ARG 0.008 0.001 ARG E 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 278 time to evaluate : 1.274 Fit side-chains REVERT: A 42 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7759 (mtpt) REVERT: A 43 GLU cc_start: 0.6908 (tp30) cc_final: 0.6590 (tp30) REVERT: A 132 GLU cc_start: 0.7044 (tt0) cc_final: 0.6673 (tm-30) REVERT: A 135 SER cc_start: 0.8316 (p) cc_final: 0.8062 (t) REVERT: A 158 SER cc_start: 0.7802 (t) cc_final: 0.7253 (p) REVERT: B 23 ARG cc_start: 0.7677 (ttt90) cc_final: 0.7426 (tpt90) REVERT: B 82 ASN cc_start: 0.8461 (m-40) cc_final: 0.7764 (m-40) REVERT: C 73 GLN cc_start: 0.8428 (tp40) cc_final: 0.8169 (tp40) REVERT: C 107 MET cc_start: 0.6905 (mmm) cc_final: 0.6622 (mmt) REVERT: D 26 THR cc_start: 0.8638 (p) cc_final: 0.8385 (m) REVERT: D 28 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8128 (mt-10) REVERT: D 87 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8255 (mm-30) REVERT: D 118 VAL cc_start: 0.8676 (t) cc_final: 0.8396 (m) REVERT: D 176 LEU cc_start: 0.7898 (tp) cc_final: 0.7688 (tp) REVERT: E 10 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8473 (pt0) REVERT: E 137 GLU cc_start: 0.6025 (tt0) cc_final: 0.5805 (tm-30) REVERT: E 163 MET cc_start: 0.2669 (mtm) cc_final: 0.2278 (ptt) REVERT: F 77 ARG cc_start: 0.8643 (mmm-85) cc_final: 0.8370 (mtp180) REVERT: G 25 TYR cc_start: 0.8987 (t80) cc_final: 0.8141 (t80) REVERT: G 75 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7894 (tt) REVERT: G 144 ASP cc_start: 0.8388 (p0) cc_final: 0.8099 (p0) REVERT: G 179 HIS cc_start: 0.8277 (t70) cc_final: 0.7988 (t70) REVERT: H 23 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6320 (ttt-90) REVERT: H 86 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6785 (mm-30) REVERT: H 163 MET cc_start: 0.2990 (mtm) cc_final: 0.2545 (ptt) outliers start: 44 outliers final: 37 residues processed: 294 average time/residue: 0.2391 time to fit residues: 97.5906 Evaluate side-chains 316 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 275 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain H residue 176 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.9980 chunk 121 optimal weight: 0.0020 chunk 129 optimal weight: 0.8980 chunk 77 optimal weight: 0.2980 chunk 56 optimal weight: 0.9990 chunk 101 optimal weight: 0.1980 chunk 39 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 122 optimal weight: 0.5980 chunk 128 optimal weight: 0.0970 chunk 84 optimal weight: 3.9990 overall best weight: 0.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11652 Z= 0.143 Angle : 0.472 5.946 15888 Z= 0.247 Chirality : 0.042 0.129 1806 Planarity : 0.005 0.053 2055 Dihedral : 3.737 15.572 1653 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.81 % Allowed : 16.50 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.23), residues: 1440 helix: 3.37 (0.22), residues: 504 sheet: 1.22 (0.25), residues: 396 loop : -0.22 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 180 HIS 0.003 0.001 HIS E 174 PHE 0.014 0.001 PHE D 54 TYR 0.007 0.001 TYR G 152 ARG 0.008 0.000 ARG E 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 285 time to evaluate : 1.283 Fit side-chains REVERT: A 43 GLU cc_start: 0.6850 (tp30) cc_final: 0.6479 (tp30) REVERT: A 95 SER cc_start: 0.8447 (t) cc_final: 0.7976 (p) REVERT: A 132 GLU cc_start: 0.7008 (tt0) cc_final: 0.6643 (tm-30) REVERT: A 135 SER cc_start: 0.8312 (p) cc_final: 0.8042 (t) REVERT: B 23 ARG cc_start: 0.7720 (ttt90) cc_final: 0.7324 (tpt170) REVERT: B 82 ASN cc_start: 0.8473 (m-40) cc_final: 0.7806 (m-40) REVERT: B 149 ARG cc_start: 0.8591 (ttm-80) cc_final: 0.8314 (ttm-80) REVERT: C 73 GLN cc_start: 0.8397 (tp40) cc_final: 0.8169 (tp40) REVERT: D 26 THR cc_start: 0.8519 (p) cc_final: 0.8311 (m) REVERT: D 28 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8170 (mt-10) REVERT: D 77 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7872 (mttm) REVERT: D 87 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8267 (mm-30) REVERT: D 113 ASN cc_start: 0.8600 (t0) cc_final: 0.8393 (t0) REVERT: D 118 VAL cc_start: 0.8691 (t) cc_final: 0.8433 (m) REVERT: D 176 LEU cc_start: 0.7794 (tp) cc_final: 0.7576 (tp) REVERT: E 10 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8430 (pt0) REVERT: E 137 GLU cc_start: 0.5974 (tt0) cc_final: 0.5752 (tm-30) REVERT: E 163 MET cc_start: 0.2567 (mtm) cc_final: 0.2299 (ptt) REVERT: G 25 TYR cc_start: 0.8836 (t80) cc_final: 0.8341 (t80) REVERT: G 75 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7895 (tt) REVERT: G 87 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8195 (mm-30) REVERT: G 113 ASN cc_start: 0.8466 (t0) cc_final: 0.7961 (t0) REVERT: G 144 ASP cc_start: 0.8335 (p0) cc_final: 0.8033 (p0) REVERT: G 179 HIS cc_start: 0.8264 (t70) cc_final: 0.7977 (t70) REVERT: H 14 MET cc_start: 0.8445 (mtp) cc_final: 0.8203 (mtm) REVERT: H 23 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6338 (ttt-90) REVERT: H 86 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6759 (mm-30) REVERT: H 163 MET cc_start: 0.2911 (mtm) cc_final: 0.2516 (ptt) outliers start: 33 outliers final: 20 residues processed: 297 average time/residue: 0.2586 time to fit residues: 105.6586 Evaluate side-chains 304 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 280 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 45 VAL 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 77 LYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain H residue 176 GLU Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 59 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.0980 chunk 83 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 95 optimal weight: 0.2980 chunk 143 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 114 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11652 Z= 0.180 Angle : 0.495 7.357 15888 Z= 0.257 Chirality : 0.043 0.177 1806 Planarity : 0.005 0.052 2055 Dihedral : 3.751 14.662 1653 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.55 % Allowed : 17.01 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.23), residues: 1440 helix: 3.36 (0.22), residues: 501 sheet: 1.22 (0.25), residues: 399 loop : -0.21 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 180 HIS 0.003 0.001 HIS E 174 PHE 0.012 0.001 PHE G 148 TYR 0.011 0.001 TYR D 152 ARG 0.009 0.001 ARG E 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 280 time to evaluate : 1.240 Fit side-chains REVERT: A 42 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7785 (mtpt) REVERT: A 43 GLU cc_start: 0.6871 (tp30) cc_final: 0.6449 (tp30) REVERT: A 132 GLU cc_start: 0.7022 (tt0) cc_final: 0.6636 (tm-30) REVERT: B 23 ARG cc_start: 0.7875 (ttt90) cc_final: 0.7572 (tpt170) REVERT: B 82 ASN cc_start: 0.8434 (m-40) cc_final: 0.7754 (m-40) REVERT: C 73 GLN cc_start: 0.8421 (tp40) cc_final: 0.8173 (tp40) REVERT: D 26 THR cc_start: 0.8636 (p) cc_final: 0.8373 (m) REVERT: D 28 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8190 (mt-10) REVERT: D 87 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8259 (mm-30) REVERT: D 118 VAL cc_start: 0.8706 (t) cc_final: 0.8441 (m) REVERT: D 176 LEU cc_start: 0.7801 (tp) cc_final: 0.7575 (tp) REVERT: E 10 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8476 (pt0) REVERT: E 137 GLU cc_start: 0.5948 (tt0) cc_final: 0.5743 (tm-30) REVERT: E 163 MET cc_start: 0.2581 (mtm) cc_final: 0.2347 (ptt) REVERT: G 25 TYR cc_start: 0.8956 (t80) cc_final: 0.8120 (t80) REVERT: G 75 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7924 (tt) REVERT: G 87 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8222 (mm-30) REVERT: G 113 ASN cc_start: 0.8473 (t0) cc_final: 0.7983 (t0) REVERT: G 144 ASP cc_start: 0.8362 (p0) cc_final: 0.8035 (p0) REVERT: G 179 HIS cc_start: 0.8280 (t70) cc_final: 0.7994 (t70) REVERT: H 14 MET cc_start: 0.8474 (mtp) cc_final: 0.8191 (mtt) REVERT: H 23 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6923 (tpt170) REVERT: H 30 TYR cc_start: 0.8614 (m-80) cc_final: 0.8384 (m-80) REVERT: H 86 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6840 (mm-30) REVERT: H 163 MET cc_start: 0.2940 (mtm) cc_final: 0.2534 (ptt) outliers start: 30 outliers final: 22 residues processed: 293 average time/residue: 0.2556 time to fit residues: 102.8361 Evaluate side-chains 304 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 278 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain F residue 49 LEU 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 75 LEU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain H residue 176 GLU Chi-restraints excluded: chain I residue 49 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.0770 chunk 34 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 114 optimal weight: 0.0020 chunk 47 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.4946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 ASN G 120 ASN H 64 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.140034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.114436 restraints weight = 16493.094| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.24 r_work: 0.3216 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11652 Z= 0.196 Angle : 0.508 8.400 15888 Z= 0.263 Chirality : 0.043 0.179 1806 Planarity : 0.005 0.052 2055 Dihedral : 3.779 14.602 1653 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.47 % Allowed : 17.52 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.23), residues: 1440 helix: 3.36 (0.22), residues: 501 sheet: 1.19 (0.25), residues: 399 loop : -0.22 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 180 HIS 0.003 0.001 HIS E 174 PHE 0.012 0.001 PHE D 54 TYR 0.011 0.001 TYR D 152 ARG 0.009 0.001 ARG E 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2948.75 seconds wall clock time: 52 minutes 54.00 seconds (3174.00 seconds total)